##The following is written by Savanna van Mesdag, going through the relevant coding and analyses for the biodiversity analyses for the six anthropogenic substrate study sites.

#setwd#

#To run the following code to carry out the analyses, the following packages must be installed#

install.packages("iNEXT", repos =   "http://chao.stat.nthu.edu.tw/wordpress/software_download/")
## Installing package into 'C:/Users/Savanna/AppData/Local/R/win-library/4.3'
## (as 'lib' is unspecified)
## Warning: unable to access index for repository http://chao.stat.nthu.edu.tw/wordpress/software_download/src/contrib:
##   cannot open URL 'http://chao.stat.nthu.edu.tw/wordpress/software_download/src/contrib/PACKAGES'
## Warning: package 'iNEXT' is not available for this version of R
## 
## A version of this package for your version of R might be available elsewhere,
## see the ideas at
## https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
## Warning: unable to access index for repository http://chao.stat.nthu.edu.tw/wordpress/software_download/bin/windows/contrib/4.3:
##   cannot open URL 'http://chao.stat.nthu.edu.tw/wordpress/software_download/bin/windows/contrib/4.3/PACKAGES'
install.packages('devtools', repos = "https://github.com/r-lib/devtools")
## Installing package into 'C:/Users/Savanna/AppData/Local/R/win-library/4.3'
## (as 'lib' is unspecified)
## Warning: unable to access index for repository https://github.com/r-lib/devtools/src/contrib:
##   cannot open URL 'https://github.com/r-lib/devtools/src/contrib/PACKAGES'
## Warning: package 'devtools' is not available for this version of R
## 
## A version of this package for your version of R might be available elsewhere,
## see the ideas at
## https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
## Warning: unable to access index for repository https://github.com/r-lib/devtools/bin/windows/contrib/4.3:
##   cannot open URL 'https://github.com/r-lib/devtools/bin/windows/contrib/4.3/PACKAGES'
install.packages('AnneChao/iNEXT', repos =  "http://chao.stat.nthu.edu.tw/wordpress/software_download/")
## Installing package into 'C:/Users/Savanna/AppData/Local/R/win-library/4.3'
## (as 'lib' is unspecified)
## Warning: unable to access index for repository http://chao.stat.nthu.edu.tw/wordpress/software_download/src/contrib:
##   cannot open URL 'http://chao.stat.nthu.edu.tw/wordpress/software_download/src/contrib/PACKAGES'
## Warning: package 'AnneChao/iNEXT' is not available for this version of R
## 
## A version of this package for your version of R might be available elsewhere,
## see the ideas at
## https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
## Warning: unable to access index for repository http://chao.stat.nthu.edu.tw/wordpress/software_download/bin/windows/contrib/4.3:
##   cannot open URL 'http://chao.stat.nthu.edu.tw/wordpress/software_download/bin/windows/contrib/4.3/PACKAGES'
install.packages("ggthemes", repos = "https://github.com/jrnold/ggthemes")
## Installing package into 'C:/Users/Savanna/AppData/Local/R/win-library/4.3'
## (as 'lib' is unspecified)
## Warning: unable to access index for repository https://github.com/jrnold/ggthemes/src/contrib:
##   cannot open URL 'https://github.com/jrnold/ggthemes/src/contrib/PACKAGES'
## Warning: package 'ggthemes' is not available for this version of R
## 
## A version of this package for your version of R might be available elsewhere,
## see the ideas at
## https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
## Warning: unable to access index for repository https://github.com/jrnold/ggthemes/bin/windows/contrib/4.3:
##   cannot open URL 'https://github.com/jrnold/ggthemes/bin/windows/contrib/4.3/PACKAGES'
install.packages("vegan", repos = " https://github.com/vegandevs/vegan")
## Installing package into 'C:/Users/Savanna/AppData/Local/R/win-library/4.3'
## (as 'lib' is unspecified)
## Warning: unable to access index for repository   https://github.com/vegandevs/vegan/src/contrib:
##   cannot open URL '  https://github.com/vegandevs/vegan/src/contrib/PACKAGES'
## Warning: package 'vegan' is not available for this version of R
## 
## A version of this package for your version of R might be available elsewhere,
## see the ideas at
## https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
## Warning: unable to access index for repository   https://github.com/vegandevs/vegan/bin/windows/contrib/4.3:
##   cannot open URL '  https://github.com/vegandevs/vegan/bin/windows/contrib/4.3/PACKAGES'

##The packages also need to be loaded prior to running the analyses and producing graphs#

library(devtools)
## Loading required package: usethis
library(iNEXT)
library(ggplot2)
library(ggthemes)
## Warning: package 'ggthemes' was built under R version 4.3.1
library(vegan)
## Loading required package: permute
## 
## Attaching package: 'permute'
## The following object is masked from 'package:devtools':
## 
##     check
## Loading required package: lattice
## This is vegan 2.6-4

#Loading Barrow data

urlfile1 <- 'https://raw.githubusercontent.com/Savannankvm/Biodiversity-analyses-for-six-study-sites/PhD-files/Barrow_Abundance_Data.csv?token=GHSAT0AAAAAACG4POBNQ6K6T4V5KYG6HMXSZHOAFWQ'

Barrow_Nos <-read.csv(urlfile1)

#To look at the Barrow data#

print(Barrow_Nos)
##    Quadrat.1 Quadrat.2 Quadrat.3 Quadrat.4 Quadrat.5 Quadrat.6 Quadrat.7
## 1          4         0       127         0        32         0         0
## 2          0         0         0         0         0         0         1
## 3          0         0         0         0         0         8         0
## 4          4         6         1         0         6         0         0
## 5          0         0         0         0         0         0         0
## 6          0        30         0         0         0         0         0
## 7          0        30         0         0         0         0         0
## 8          0         0       138         9         8         0         0
## 9          0         0         0         0         0         1         0
## 10         0        30        20       110         0         0        10
## 11         0         0         0         0         0         0       120
## 12         0         0         0         0         0         0         0
## 13         0         0         0         0         0         0         0
## 14         0         0         1         2         1         0         1
## 15         0         0         0         0         0         0        54
## 16         0         0         0         0         2         0         0
## 17         0         0         0         0         0         0         0
## 18         0         0        14         0         0         0         0
## 19        66         0         0         0         2         0         0
## 20         0        19         1        39         2        54        42
## 21         0        87        88         0         1         0         0
## 22         0         0         0         0         0         1         0
## 23         0         0         0         0         1         0         0
## 24         0        55         0        50         3       169        10
## 25         0         5         1        25         2         0         0
## 26         0         0         0         0         0         0         0
## 27         0         0         0         0         0         0         0
## 28         0         0         0         1         0         0         0
## 29         0         0         0         0         0         0        42
## 30        18         0         0         0        30         0         0
## 31         1         0         0         0         0         0         0
## 32         0        12         0         1         3         2         0
## 33         0         0         0         0         0        85         2
## 34         0        67        18        31        12       140         0
## 35         3         3         0         0         0         0         0
## 36         0         0         0         0         0         0         0
## 37         0         0         0         0         0         0         0
## 38        22         0         0         0         4         0         0
## 39         0         0         0         0         3         0         1
## 40         0         0         0         0         0         3         0
## 41         0         0         0         0         0         0        37
## 42         0         0         0         0         0         0         2
## 43         0         0         0         0       160         0         0
## 44         0         0         0         1         0         0         0
## 45         0         0         0         0         0         0         0
## 46         0        34        10         0         0         0         0
## 47         0         0         0         0         0         0         0
## 48         0         0         0         0         0         1         0
## 49         4         0         0         0         0         0         0
## 50         0         0         0         0         0         0         2
## 51         2         0         1         0         0         0         0
## 52         8        64        22         8         2         0         2
## 53         0         2         0         0         0         0         0
## 54         0         0         4        17         0         0         2
## 55         0         0         0         0         3         0         0
##    Quadrat.8 Quadrat.9 Quadrat.10 Quadrat.11
## 1          0         0          0          0
## 2          5         0          0          0
## 3          0         0          5          0
## 4          2         0          0          4
## 5          2         0          0          0
## 6          0         0          0          0
## 7          0         0          0          0
## 8          0         0          0          0
## 9          0         0          0          0
## 10         0         0          0          0
## 11        40         0          0          0
## 12         0         2          0          5
## 13        14         1          0          0
## 14         0         0          0          0
## 15        15         0          0          0
## 16         0         0          1          0
## 17         0        25          0          6
## 18         7         2          1          4
## 19         0         0          0          0
## 20        19        22         41         44
## 21         0         0          2          0
## 22         0         0          0          0
## 23         0         0          0          0
## 24        30         0         82          4
## 25         0         0          5          0
## 26         0         0         10          0
## 27         0         0          0         22
## 28         0         0          0          0
## 29         0         0          0          0
## 30         0         0          0          0
## 31         0         0          0          0
## 32         0         2          0         24
## 33         0         2          5          0
## 34        14         2         98         17
## 35         0         3          0          0
## 36       153         0          0          0
## 37         0         1          0          0
## 38         0         3          0         14
## 39         3         0          0          3
## 40         0         0          0          0
## 41         1         0          0          2
## 42         0         5          0          0
## 43         0         0          0          0
## 44         0         0          0          0
## 45         0         1          0          0
## 46         0         0          0          0
## 47         0         6          0          0
## 48         0         0          0          0
## 49         0         0          0          0
## 50         0         0          0          0
## 51         0         4          0          6
## 52         0         0          0          0
## 53         0         0          0          0
## 54         0         0          0          0
## 55       123         1          0          0

#colSums to establish sample size for each of the quadrats.

colSums(Barrow_Nos)
##  Quadrat.1  Quadrat.2  Quadrat.3  Quadrat.4  Quadrat.5  Quadrat.6  Quadrat.7 
##        132        444        446        294        277        464        328 
##  Quadrat.8  Quadrat.9 Quadrat.10 Quadrat.11 
##        428         82        250        155

#Setting m to sample size for Quadrat 1 (132 individuals.) This will give me observed #qD value that will be most representative for Quadrat and Community. Will do the same #for the other 10 communities below.

m <- c(132)

Barrow_Datam <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = m)

Barrow_Datam
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat.1 132      Observed       0 10.000000  8.518406 11.481594 0.9925382
## 2   Quadrat.2 132   Rarefaction       0 12.857628 12.160344 13.554911 0.9879180
## 3   Quadrat.2 443   Rarefaction       0 14.000000 13.313722 14.686278 1.0000000
## 4   Quadrat.2 444      Observed       0 14.000000 13.313013 14.686987 1.0000000
## 5   Quadrat.2 445 Extrapolation       0 14.000000 13.312327 14.687673 1.0000000
## 6   Quadrat.3 132   Rarefaction       0 10.197489  8.800061 11.594917 0.9843032
## 7   Quadrat.3 445   Rarefaction       0 13.988789 10.675456 17.302122 0.9887892
## 8   Quadrat.3 446      Observed       0 14.000000 10.681146 17.318854 0.9888018
## 9   Quadrat.3 447 Extrapolation       0 14.011198 10.686646 17.335751 0.9888144
## 10  Quadrat.4 132   Rarefaction       0 10.032058  8.491258 11.572857 0.9854327
## 11  Quadrat.4 293   Rarefaction       0 11.989796  9.352590 14.627002 0.9897959
## 12  Quadrat.4 294      Observed       0 12.000000  9.356754 14.643246 0.9898191
## 13  Quadrat.4 295 Extrapolation       0 12.010181  9.359742 14.660620 0.9898422
## 14  Quadrat.5 132   Rarefaction       0 15.397332 13.157679 17.636986 0.9554301
## 15  Quadrat.5 276   Rarefaction       0 18.989170 16.216759 21.761581 0.9891697
## 16  Quadrat.5 277      Observed       0 19.000000 16.222259 21.777741 0.9892989
## 17  Quadrat.5 278 Extrapolation       0 19.010701 16.227604 21.793799 0.9894266
## 18  Quadrat.6 132   Rarefaction       0  6.909497  5.649623  8.169371 0.9855357
## 19  Quadrat.6 463   Rarefaction       0  9.993534  7.181730 12.805339 0.9935345
## 20  Quadrat.6 464      Observed       0 10.000000  7.184415 12.815585 0.9935438
## 21  Quadrat.6 465 Extrapolation       0 10.006456  7.186924 12.825988 0.9935531
## 22  Quadrat.7 132   Rarefaction       0 11.415039  9.954838 12.875239 0.9721341
## 23  Quadrat.7 327   Rarefaction       0 14.990854 12.786794 17.194913 0.9908537
## 24  Quadrat.7 328      Observed       0 15.000000 12.792120 17.207880 0.9909460
## 25  Quadrat.7 329 Extrapolation       0 15.009054 12.797339 17.220769 0.9910373
## 26  Quadrat.8 132   Rarefaction       0 11.777810 10.649962 12.905657 0.9827498
## 27  Quadrat.8 427   Rarefaction       0 13.997664 12.314797 15.680530 0.9976636
## 28  Quadrat.8 428      Observed       0 14.000000 12.315836 15.684164 0.9976852
## 29  Quadrat.8 429 Extrapolation       0 14.002315 12.316440 15.688190 0.9977067
## 30  Quadrat.9  81   Rarefaction       0 15.951220 13.255822 18.646617 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 13.284194 18.715806 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 13.311155 18.783485 0.9540968
## 33  Quadrat.9 132 Extrapolation       0 17.234773 13.452179 21.017367 0.9896492
## 34 Quadrat.10 132   Rarefaction       0  8.766625  7.598694  9.934555 0.9853580
## 35 Quadrat.10 249   Rarefaction       0  9.992000  8.263039 11.720961 0.9920000
## 36 Quadrat.10 250      Observed       0 10.000000  8.266744 11.733256 0.9920320
## 37 Quadrat.10 251 Extrapolation       0 10.007968  8.269638 11.746298 0.9920639
## 38 Quadrat.11 132   Rarefaction       0 12.974684 12.189792 13.759576 0.9975639
## 39 Quadrat.11 154   Rarefaction       0 13.000000 12.239031 13.760969 1.0000000
## 40 Quadrat.11 155      Observed       0 13.000000 12.239362 13.760638 1.0000000
## 41 Quadrat.11 156 Extrapolation       0 13.000000 12.240434 13.759566 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9785954 1.0000000
## 2  0.9850432 0.9907928
## 3  0.9971503 1.0000000
## 4  0.9972073 1.0000000
## 5  0.9972192 1.0000000
## 6  0.9758222 0.9927842
## 7  0.9819760 0.9956024
## 8  0.9818231 0.9957806
## 9  0.9818341 0.9957947
## 10 0.9762198 0.9946455
## 11 0.9821047 0.9974871
## 12 0.9809729 0.9986653
## 13 0.9810113 0.9986731
## 14 0.9446201 0.9662402
## 15 0.9770771 1.0000000
## 16 0.9771980 1.0000000
## 17 0.9773176 1.0000000
## 18 0.9778394 0.9932321
## 19 0.9881480 0.9989210
## 20 0.9879961 0.9990915
## 21 0.9880047 0.9991014
## 22 0.9645701 0.9796981
## 23 0.9826658 0.9990415
## 24 0.9827573 0.9991346
## 25 0.9828480 0.9992266
## 26 0.9765755 0.9889242
## 27 0.9930479 1.0000000
## 28 0.9928490 1.0000000
## 29 0.9928806 1.0000000
## 30 0.9139897 0.9884493
## 31 0.9154642 0.9898958
## 32 0.9168903 0.9913033
## 33 0.9562033 1.0000000
## 34 0.9769310 0.9937850
## 35 0.9845709 0.9994291
## 36 0.9841022 0.9999618
## 37 0.9841566 0.9999711
## 38 0.9887989 1.0000000
## 39 0.9911910 1.0000000
## 40 0.9911673 1.0000000
## 41 0.9912704 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat.1 0.9925382 132      Observed       0 10.000000  7.347436 12.652564
## 2   Quadrat.2 0.9879180 132   Rarefaction       0 12.857628 12.055632 13.659623
## 3   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.869181 15.130819
## 4   Quadrat.3 0.9843032 132   Rarefaction       0 10.197489  7.015284 13.379695
## 5   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  8.403858 19.551793
## 6   Quadrat.3 0.9888018 446      Observed       0 14.000000  8.410555 19.589445
## 7   Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  8.412770 19.609627
## 8   Quadrat.4 0.9854327 132   Rarefaction       0 10.032058  6.210412 13.853703
## 9   Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  6.847937 17.117316
## 10  Quadrat.4 0.9898191 294      Observed       0 12.000000  6.859366 17.140634
## 11  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  6.861080 17.159282
## 12  Quadrat.5 0.9554301 132   Rarefaction       0 15.397332 12.406239 18.388426
## 13  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 13.022859 24.943287
## 14  Quadrat.5 0.9892989 277      Observed       0 19.000000 13.008596 24.991404
## 15  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 12.988624 25.032778
## 16  Quadrat.6 0.9855357 132   Rarefaction       0  6.909497  3.973087  9.845907
## 17  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  3.539118 16.441371
## 18  Quadrat.6 0.9935438 464      Observed       0 10.000000  3.545411 16.454589
## 19  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  3.548724 16.464188
## 20  Quadrat.7 0.9721341 132   Rarefaction       0 11.415039  9.178356 13.651722
## 21  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227 10.917039 19.059416
## 22  Quadrat.7 0.9909460 328      Observed       0 15.000000 10.906595 19.093405
## 23  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054 10.893280 19.124828
## 24  Quadrat.8 0.9827498 132   Rarefaction       0 11.777809 10.178981 13.376638
## 25  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 11.219786 16.773417
## 26  Quadrat.8 0.9976852 428      Observed       0 14.000000 11.218165 16.781835
## 27  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 11.215168 16.789461
## 28  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 10.968489 20.860080
## 29  Quadrat.9 0.9526800  82      Observed       0 16.000000 10.961243 21.038757
## 30  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320 10.907210 21.187430
## 31  Quadrat.9 0.9896492 132 Extrapolation       0 17.234773  9.255157 25.214388
## 32 Quadrat.10 0.9853580 132   Rarefaction       0  8.766625  6.801708 10.731542
## 33 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  7.123719 12.844322
## 34 Quadrat.10 0.9920320 250      Observed       0 10.000000  7.134638 12.865362
## 35 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  7.138566 12.877370
## 36 Quadrat.11 0.9975639 132   Rarefaction       0 12.974684 12.016039 13.933329
## 37 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.898619 14.101381
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.2489362 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4177643  4.283388
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3270716  2.711414
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.6187886 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2991860  3.892149
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2028301  3.072360
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.8386797 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.6158096  7.827779
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6679935  5.542077
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.6315204 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3271711  9.330790
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3664956  7.770762
## 13  Quadrat.3  Species richness 14.000000 23.977578 7.3853787 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2919257  5.408001
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2004466  4.118224
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.3827914 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3428775  5.836257
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3219499  4.193791
## 19  Quadrat.5  Species richness 19.000000 19.896751 5.9204262 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4391813  4.408462
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2242257  2.333942
## 22  Quadrat.6  Species richness 10.000000 14.490302 4.5786611 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1804382  4.003416
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1257561  3.462767
## 25  Quadrat.7  Species richness 15.000000 15.897256 2.9614210 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3335538  5.923623
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3015956  4.260340
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.1438733 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3209901  5.717488
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2318099  3.930402
## 31  Quadrat.9  Species richness 16.000000 17.580488 4.9083930 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.2229819  7.072144
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.9270947  3.978739
##          UCL
## 1  14.904046
## 2   5.920994
## 3   3.993511
## 4  17.124731
## 5   5.064936
## 6   3.867439
## 7  14.643782
## 8  10.241708
## 9   8.160564
## 10 15.237757
## 11 10.613277
## 12  9.207399
## 13 38.452655
## 14  6.552329
## 15  4.903960
## 16 25.074807
## 17  7.180312
## 18  5.455811
## 19 31.500573
## 20  6.130021
## 21  3.212891
## 22 23.464313
## 23  4.710721
## 24  3.955722
## 25 21.701535
## 26  7.231130
## 27  5.442573
## 28 18.451330
## 29  6.975747
## 30  4.839080
## 31 27.200761
## 32 11.866145
## 33  7.612884
Barrow_Datam_1 <- iNEXT(Barrow_Nos, q=c(0,1,2), datatype= "abundance", size = m)

Barrow_Datam_1
## Compare 11 assemblages with Hill number order q = 0, 1, 2.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1    Quadrat.1 132      Observed       0 10.000000  8.355403 11.644597
## 2    Quadrat.1 132      Observed       1  4.909318  4.061803  5.756833
## 3    Quadrat.1 132      Observed       2  3.293762  2.601903  3.985621
## 4    Quadrat.2 132   Rarefaction       0 12.857628 12.212677 13.502578
## 5    Quadrat.2 443   Rarefaction       0 14.000000 13.357001 14.642999
## 6    Quadrat.2 444      Observed       0 14.000000 13.356621 14.643379
## 7    Quadrat.2 445 Extrapolation       0 14.000000 13.356323 14.643677
## 8    Quadrat.2 132   Rarefaction       1  9.459158  8.918912  9.999404
## 9    Quadrat.2 443   Rarefaction       1  9.823991  9.259369 10.388612
## 10   Quadrat.2 444      Observed       1  9.824330  9.259696 10.388965
## 11   Quadrat.2 445 Extrapolation       1  9.824669  9.260021 10.389318
## 12   Quadrat.2 132   Rarefaction       2  8.033307  7.434171  8.632443
## 13   Quadrat.2 443   Rarefaction       2  8.347955  7.698722  8.997189
## 14   Quadrat.2 444      Observed       2  8.348268  7.698984  8.997552
## 15   Quadrat.2 445 Extrapolation       2  8.348579  7.699244  8.997914
## 16   Quadrat.3 132   Rarefaction       0 10.197489  8.720555 11.674424
## 17   Quadrat.3 445   Rarefaction       0 13.988789 10.716439 17.261139
## 18   Quadrat.3 446      Observed       0 14.000000 10.722983 17.277017
## 19   Quadrat.3 447 Extrapolation       0 14.011198 10.729032 17.293364
## 20   Quadrat.3 132   Rarefaction       1  5.617833  5.032103  6.203564
## 21   Quadrat.3 445   Rarefaction       1  5.827069  5.185672  6.468465
## 22   Quadrat.3 446      Observed       1  5.827336  5.185867  6.468805
## 23   Quadrat.3 447 Extrapolation       1  5.827603  5.186062  6.469144
## 24   Quadrat.3 132   Rarefaction       2  4.394210  3.975877  4.812542
## 25   Quadrat.3 445   Rarefaction       2  4.475778  4.039580  4.911975
## 26   Quadrat.3 446      Observed       2  4.475856  4.039641  4.912071
## 27   Quadrat.3 447 Extrapolation       2  4.475934  4.039702  4.912167
## 28   Quadrat.4 132   Rarefaction       0 10.032058  8.628026 11.436089
## 29   Quadrat.4 293   Rarefaction       0 11.989796  9.257614 14.721978
## 30   Quadrat.4 294      Observed       0 12.000000  9.259767 14.740233
## 31   Quadrat.4 295 Extrapolation       0 12.010181  9.261421 14.758941
## 32   Quadrat.4 132   Rarefaction       1  6.166823  5.600832  6.732814
## 33   Quadrat.4 293   Rarefaction       1  6.330211  5.730430  6.929991
## 34   Quadrat.4 294      Observed       1  6.330739  5.730835  6.930643
## 35   Quadrat.4 295 Extrapolation       1  6.331265  5.731239  6.931292
## 36   Quadrat.4 132   Rarefaction       2  4.688936  4.047979  5.329893
## 37   Quadrat.4 293   Rarefaction       2  4.762630  4.099127  5.426133
## 38   Quadrat.4 294      Observed       2  4.762839  4.099271  5.426407
## 39   Quadrat.4 295 Extrapolation       2  4.763046  4.099415  5.426678
## 40   Quadrat.5 132   Rarefaction       0 15.397332 13.361775 17.432890
## 41   Quadrat.5 276   Rarefaction       0 18.989170 15.956328 22.022011
## 42   Quadrat.5 277      Observed       0 19.000000 15.961314 22.038686
## 43   Quadrat.5 278 Extrapolation       0 19.010701 15.966183 22.055219
## 44   Quadrat.5 132   Rarefaction       1  4.853180  4.099044  5.607315
## 45   Quadrat.5 276   Rarefaction       1  5.075744  4.279060  5.872429
## 46   Quadrat.5 277      Observed       1  5.076505  4.279680  5.873331
## 47   Quadrat.5 278 Extrapolation       1  5.077264  4.280297  5.874230
## 48   Quadrat.5 132   Rarefaction       2  2.736650  2.329072  3.144227
## 49   Quadrat.5 276   Rarefaction       2  2.755710  2.341086  3.170334
## 50   Quadrat.5 277      Observed       2  2.755773  2.341126  3.170421
## 51   Quadrat.5 278 Extrapolation       2  2.755837  2.341165  3.170508
## 52   Quadrat.6 132   Rarefaction       0  6.909497  6.097496  7.721498
## 53   Quadrat.6 463   Rarefaction       0  9.993534  7.680759 12.306310
## 54   Quadrat.6 464      Observed       0 10.000000  7.682969 12.317031
## 55   Quadrat.6 465 Extrapolation       0 10.006456  7.685058 12.327854
## 56   Quadrat.6 132   Rarefaction       1  4.179489  3.972510  4.386467
## 57   Quadrat.6 463   Rarefaction       1  4.290416  4.067512  4.513320
## 58   Quadrat.6 464      Observed       1  4.290540  4.067620  4.513460
## 59   Quadrat.6 465 Extrapolation       1  4.290664  4.067727  4.513600
## 60   Quadrat.6 132   Rarefaction       2  3.634645  3.454400  3.814889
## 61   Quadrat.6 463   Rarefaction       2  3.687666  3.501116  3.874216
## 62   Quadrat.6 464      Observed       2  3.687712  3.501156  3.874267
## 63   Quadrat.6 465 Extrapolation       2  3.687758  3.501197  3.874319
## 64   Quadrat.7 132   Rarefaction       0 11.415039  9.910243 12.919835
## 65   Quadrat.7 327   Rarefaction       0 14.990854 12.452636 17.529071
## 66   Quadrat.7 328      Observed       0 15.000000 12.456820 17.543180
## 67   Quadrat.7 329 Extrapolation       0 15.009054 12.460907 17.557201
## 68   Quadrat.7 132   Rarefaction       1  6.178858  5.661132  6.696585
## 69   Quadrat.7 327   Rarefaction       1  6.414833  5.861249  6.968416
## 70   Quadrat.7 328      Observed       1  6.415378  5.861716  6.969041
## 71   Quadrat.7 329 Extrapolation       1  6.415922  5.862181  6.969663
## 72   Quadrat.7 132   Rarefaction       2  4.713915  4.182304  5.245526
## 73   Quadrat.7 327   Rarefaction       2  4.794980  4.242164  5.347797
## 74   Quadrat.7 328      Observed       2  4.795151  4.242289  5.348012
## 75   Quadrat.7 329 Extrapolation       2  4.795320  4.242414  5.348226
## 76   Quadrat.8 132   Rarefaction       0 11.777810 10.790845 12.764774
## 77   Quadrat.8 427   Rarefaction       0 13.997664 12.381995 15.613332
## 78   Quadrat.8 428      Observed       0 14.000000 12.382318 15.617682
## 79   Quadrat.8 429 Extrapolation       0 14.002315 12.382111 15.622519
## 80   Quadrat.8 132   Rarefaction       1  6.011288  5.416407  6.606170
## 81   Quadrat.8 427   Rarefaction       1  6.244162  5.617995  6.870329
## 82   Quadrat.8 428      Observed       1  6.244415  5.618223  6.870608
## 83   Quadrat.8 429 Extrapolation       1  6.244668  5.618450  6.870886
## 84   Quadrat.8 132   Rarefaction       2  4.275118  3.794242  4.755995
## 85   Quadrat.8 427   Rarefaction       2  4.350257  3.849672  4.850842
## 86   Quadrat.8 428      Observed       2  4.350337  3.849731  4.850943
## 87   Quadrat.8 429 Extrapolation       2  4.350417  3.849790  4.851044
## 88   Quadrat.9  81   Rarefaction       0 15.951220 12.882478 19.019961
## 89   Quadrat.9  82      Observed       0 16.000000 12.913446 19.086554
## 90   Quadrat.9  83 Extrapolation       0 16.047320 12.942115 19.152525
## 91   Quadrat.9 132 Extrapolation       0 17.234773 13.296078 21.173467
## 92   Quadrat.9  81   Rarefaction       1  8.437735  6.558472 10.316997
## 93   Quadrat.9  82      Observed       1  8.450869  6.567350 10.334388
## 94   Quadrat.9  83 Extrapolation       1  8.463836  6.576109 10.351562
## 95   Quadrat.9 132 Extrapolation       1  8.932639  6.888316 10.976962
## 96   Quadrat.9  81   Rarefaction       2  5.471837  4.201971  6.741703
## 97   Quadrat.9  82      Observed       2  5.475570  4.203874  6.747266
## 98   Quadrat.9  83 Extrapolation       2  5.479218  4.205731  6.752704
## 99   Quadrat.9 132 Extrapolation       2  5.592621  4.262889  6.922353
## 100 Quadrat.10 132   Rarefaction       0  8.766625  7.323990 10.209260
## 101 Quadrat.10 249   Rarefaction       0  9.992000  7.833468 12.150532
## 102 Quadrat.10 250      Observed       0 10.000000  7.835149 12.164851
## 103 Quadrat.10 251 Extrapolation       0 10.007968  7.835912 12.180024
## 104 Quadrat.10 132   Rarefaction       1  4.289710  3.797624  4.781796
## 105 Quadrat.10 249   Rarefaction       1  4.372858  3.861287  4.884428
## 106 Quadrat.10 250      Observed       1  4.373262  3.861593  4.884930
## 107 Quadrat.10 251 Extrapolation       1  4.373664  3.861898  4.885430
## 108 Quadrat.10 132   Rarefaction       2  3.406166  3.042529  3.769803
## 109 Quadrat.10 249   Rarefaction       2  3.435819  3.064508  3.807129
## 110 Quadrat.10 250      Observed       2  3.435954  3.064608  3.807300
## 111 Quadrat.10 251 Extrapolation       2  3.436088  3.064707  3.807468
## 112 Quadrat.11 132   Rarefaction       0 12.974684 12.184609 13.764759
## 113 Quadrat.11 154   Rarefaction       0 13.000000 12.182098 13.817902
## 114 Quadrat.11 155      Observed       0 13.000000 12.179849 13.820151
## 115 Quadrat.11 156 Extrapolation       0 13.000000 12.177943 13.822057
## 116 Quadrat.11 132   Rarefaction       1  8.616984  7.482074  9.751895
## 117 Quadrat.11 154   Rarefaction       1  8.678467  7.537488  9.819447
## 118 Quadrat.11 155      Observed       1  8.680817  7.539611  9.822024
## 119 Quadrat.11 156 Extrapolation       1  8.683151  7.541720  9.824583
## 120 Quadrat.11 132   Rarefaction       2  6.560505  5.263673  7.857338
## 121 Quadrat.11 154   Rarefaction       2  6.600529  5.285981  7.915077
## 122 Quadrat.11 155      Observed       2  6.602088  5.286848  7.917329
## 123 Quadrat.11 156 Extrapolation       2  6.603628  5.287703  7.919554
##            SC    SC.LCL    SC.UCL
## 1   0.9925382 0.9777687 1.0000000
## 2   0.9925382 0.9777687 1.0000000
## 3   0.9925382 0.9777687 1.0000000
## 4   0.9879180 0.9844999 0.9913361
## 5   1.0000000 0.9976404 1.0000000
## 6   1.0000000 0.9980788 1.0000000
## 7   1.0000000 0.9980889 1.0000000
## 8   0.9879180 0.9844999 0.9913361
## 9   1.0000000 0.9976404 1.0000000
## 10  1.0000000 0.9980788 1.0000000
## 11  1.0000000 0.9980889 1.0000000
## 12  0.9879180 0.9844999 0.9913361
## 13  1.0000000 0.9976404 1.0000000
## 14  1.0000000 0.9980788 1.0000000
## 15  1.0000000 0.9980889 1.0000000
## 16  0.9843032 0.9759600 0.9926463
## 17  0.9887892 0.9821804 0.9953981
## 18  0.9888018 0.9817769 0.9958268
## 19  0.9888144 0.9817913 0.9958375
## 20  0.9843032 0.9759600 0.9926463
## 21  0.9887892 0.9821804 0.9953981
## 22  0.9888018 0.9817769 0.9958268
## 23  0.9888144 0.9817913 0.9958375
## 24  0.9843032 0.9759600 0.9926463
## 25  0.9887892 0.9821804 0.9953981
## 26  0.9888018 0.9817769 0.9958268
## 27  0.9888144 0.9817913 0.9958375
## 28  0.9854327 0.9757612 0.9951042
## 29  0.9897959 0.9801879 0.9994039
## 30  0.9898191 0.9796442 0.9999940
## 31  0.9898422 0.9796751 1.0000000
## 32  0.9854327 0.9757612 0.9951042
## 33  0.9897959 0.9801879 0.9994039
## 34  0.9898191 0.9796442 0.9999940
## 35  0.9898422 0.9796751 1.0000000
## 36  0.9854327 0.9757612 0.9951042
## 37  0.9897959 0.9801879 0.9994039
## 38  0.9898191 0.9796442 0.9999940
## 39  0.9898422 0.9796751 1.0000000
## 40  0.9554301 0.9423949 0.9684654
## 41  0.9891697 0.9787392 0.9996002
## 42  0.9892989 0.9788745 0.9997233
## 43  0.9894266 0.9790080 0.9998453
## 44  0.9554301 0.9423949 0.9684654
## 45  0.9891697 0.9787392 0.9996002
## 46  0.9892989 0.9788745 0.9997233
## 47  0.9894266 0.9790080 0.9998453
## 48  0.9554301 0.9423949 0.9684654
## 49  0.9891697 0.9787392 0.9996002
## 50  0.9892989 0.9788745 0.9997233
## 51  0.9894266 0.9790080 0.9998453
## 52  0.9855357 0.9794654 0.9916061
## 53  0.9935345 0.9881203 0.9989486
## 54  0.9935438 0.9879729 0.9991147
## 55  0.9935531 0.9879838 0.9991223
## 56  0.9855357 0.9794654 0.9916061
## 57  0.9935345 0.9881203 0.9989486
## 58  0.9935438 0.9879729 0.9991147
## 59  0.9935531 0.9879838 0.9991223
## 60  0.9855357 0.9794654 0.9916061
## 61  0.9935345 0.9881203 0.9989486
## 62  0.9935438 0.9879729 0.9991147
## 63  0.9935531 0.9879838 0.9991223
## 64  0.9721341 0.9629581 0.9813101
## 65  0.9908537 0.9822146 0.9994928
## 66  0.9909460 0.9823081 0.9995839
## 67  0.9910373 0.9824008 0.9996738
## 68  0.9721341 0.9629581 0.9813101
## 69  0.9908537 0.9822146 0.9994928
## 70  0.9909460 0.9823081 0.9995839
## 71  0.9910373 0.9824008 0.9996738
## 72  0.9721341 0.9629581 0.9813101
## 73  0.9908537 0.9822146 0.9994928
## 74  0.9909460 0.9823081 0.9995839
## 75  0.9910373 0.9824008 0.9996738
## 76  0.9827498 0.9769708 0.9885288
## 77  0.9976636 0.9926335 1.0000000
## 78  0.9976852 0.9923560 1.0000000
## 79  0.9977067 0.9923830 1.0000000
## 80  0.9827498 0.9769708 0.9885288
## 81  0.9976636 0.9926335 1.0000000
## 82  0.9976852 0.9923560 1.0000000
## 83  0.9977067 0.9923830 1.0000000
## 84  0.9827498 0.9769708 0.9885288
## 85  0.9976636 0.9926335 1.0000000
## 86  0.9976852 0.9923560 1.0000000
## 87  0.9977067 0.9923830 1.0000000
## 88  0.9512195 0.9179699 0.9844691
## 89  0.9526800 0.9182420 0.9871180
## 90  0.9540968 0.9196883 0.9885053
## 91  0.9896492 0.9594669 1.0000000
## 92  0.9512195 0.9179699 0.9844691
## 93  0.9526800 0.9182420 0.9871180
## 94  0.9540968 0.9196883 0.9885053
## 95  0.9896492 0.9594669 1.0000000
## 96  0.9512195 0.9179699 0.9844691
## 97  0.9526800 0.9182420 0.9871180
## 98  0.9540968 0.9196883 0.9885053
## 99  0.9896492 0.9594669 1.0000000
## 100 0.9853580 0.9764441 0.9942720
## 101 0.9920000 0.9831756 1.0000000
## 102 0.9920320 0.9824315 1.0000000
## 103 0.9920639 0.9824829 1.0000000
## 104 0.9853580 0.9764441 0.9942720
## 105 0.9920000 0.9831756 1.0000000
## 106 0.9920320 0.9824315 1.0000000
## 107 0.9920639 0.9824829 1.0000000
## 108 0.9853580 0.9764441 0.9942720
## 109 0.9920000 0.9831756 1.0000000
## 110 0.9920320 0.9824315 1.0000000
## 111 0.9920639 0.9824829 1.0000000
## 112 0.9975639 0.9891425 1.0000000
## 113 1.0000000 0.9910623 1.0000000
## 114 1.0000000 0.9911759 1.0000000
## 115 1.0000000 0.9912767 1.0000000
## 116 0.9975639 0.9891425 1.0000000
## 117 1.0000000 0.9910623 1.0000000
## 118 1.0000000 0.9911759 1.0000000
## 119 1.0000000 0.9912767 1.0000000
## 120 0.9975639 0.9891425 1.0000000
## 121 1.0000000 0.9910623 1.0000000
## 122 1.0000000 0.9911759 1.0000000
## 123 1.0000000 0.9912767 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage        SC   m        Method Order.q        qD    qD.LCL
## 1    Quadrat.1 0.9925382 132      Observed       0 10.000000  7.107900
## 2    Quadrat.1 0.9925382 132      Observed       1  4.909318  4.066632
## 3    Quadrat.1 0.9925382 132      Observed       2  3.293762  2.600425
## 4    Quadrat.2 0.9879180 132   Rarefaction       0 12.857628 12.138231
## 5    Quadrat.2 1.0000000 444      Observed       0 14.000000 13.194140
## 6    Quadrat.2 0.9879180 132   Rarefaction       1  9.459158  8.929841
## 7    Quadrat.2 1.0000000 444      Observed       1  9.824330  9.280446
## 8    Quadrat.2 0.9879180 132   Rarefaction       2  8.033307  7.437373
## 9    Quadrat.2 1.0000000 444      Observed       2  8.348268  7.713364
## 10   Quadrat.3 0.9843032 132   Rarefaction       0 10.197489  7.501929
## 11   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  9.382453
## 12   Quadrat.3 0.9888018 446      Observed       0 14.000000  9.398247
## 13   Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  9.401465
## 14   Quadrat.3 0.9843032 132   Rarefaction       1  5.617833  4.950871
## 15   Quadrat.3 0.9887892 444   Rarefaction       1  5.826806  5.117659
## 16   Quadrat.3 0.9888018 446      Observed       1  5.827336  5.118150
## 17   Quadrat.3 0.9888144 447 Extrapolation       1  5.827603  5.118348
## 18   Quadrat.3 0.9843032 132   Rarefaction       2  4.394210  3.954231
## 19   Quadrat.3 0.9887892 444   Rarefaction       2  4.475700  4.019407
## 20   Quadrat.3 0.9888018 446      Observed       2  4.475856  4.019554
## 21   Quadrat.3 0.9888144 447 Extrapolation       2  4.475934  4.019626
## 22   Quadrat.4 0.9854327 132   Rarefaction       0 10.032058  5.354773
## 23   Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  5.648717
## 24   Quadrat.4 0.9898191 294      Observed       0 12.000000  5.657561
## 25   Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  5.659851
## 26   Quadrat.4 0.9854327 132   Rarefaction       1  6.166823  5.461281
## 27   Quadrat.4 0.9897959 292   Rarefaction       1  6.329838  5.622428
## 28   Quadrat.4 0.9898191 294      Observed       1  6.330739  5.623301
## 29   Quadrat.4 0.9898422 295 Extrapolation       1  6.331265  5.623764
## 30   Quadrat.4 0.9854327 132   Rarefaction       2  4.688936  4.041978
## 31   Quadrat.4 0.9897959 292   Rarefaction       2  4.762483  4.113475
## 32   Quadrat.4 0.9898191 294      Observed       2  4.762839  4.113759
## 33   Quadrat.4 0.9898422 295 Extrapolation       2  4.763046  4.113889
## 34   Quadrat.5 0.9554301 132   Rarefaction       0 15.397332 12.462965
## 35   Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 13.253318
## 36   Quadrat.5 0.9892989 277      Observed       0 19.000000 13.242137
## 37   Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 13.222972
## 38   Quadrat.5 0.9554301 132   Rarefaction       1  4.853180  4.100650
## 39   Quadrat.5 0.9891697 275   Rarefaction       1  5.075318  4.269101
## 40   Quadrat.5 0.9892989 277      Observed       1  5.076505  4.269691
## 41   Quadrat.5 0.9894266 278 Extrapolation       1  5.077264  4.269996
## 42   Quadrat.5 0.9554301 132   Rarefaction       2  2.736650  2.332519
## 43   Quadrat.5 0.9891697 275   Rarefaction       2  2.755674  2.341858
## 44   Quadrat.5 0.9892989 277      Observed       2  2.755773  2.341877
## 45   Quadrat.5 0.9894266 278 Extrapolation       2  2.755837  2.341885
## 46   Quadrat.6 0.9855357 132   Rarefaction       0  6.909497  4.531212
## 47   Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  4.677705
## 48   Quadrat.6 0.9935438 464      Observed       0 10.000000  4.683524
## 49   Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  4.687949
## 50   Quadrat.6 0.9855357 132   Rarefaction       1  4.179489  3.921961
## 51   Quadrat.6 0.9935345 462   Rarefaction       1  4.290353  4.059760
## 52   Quadrat.6 0.9935438 464      Observed       1  4.290540  4.059974
## 53   Quadrat.6 0.9935531 465 Extrapolation       1  4.290664  4.060116
## 54   Quadrat.6 0.9855357 132   Rarefaction       2  3.634645  3.438005
## 55   Quadrat.6 0.9935345 462   Rarefaction       2  3.687642  3.504795
## 56   Quadrat.6 0.9935438 464      Observed       2  3.687712  3.504865
## 57   Quadrat.6 0.9935531 465 Extrapolation       2  3.687758  3.504902
## 58   Quadrat.7 0.9721341 132   Rarefaction       0 11.415039  9.017320
## 59   Quadrat.7 0.9908537 327   Rarefaction       0 14.988227 10.466491
## 60   Quadrat.7 0.9909460 328      Observed       0 15.000000 10.459623
## 61   Quadrat.7 0.9910373 329 Extrapolation       0 15.009054 10.449961
## 62   Quadrat.7 0.9721341 132   Rarefaction       1  6.178858  5.607271
## 63   Quadrat.7 0.9908537 327   Rarefaction       1  6.414677  5.846489
## 64   Quadrat.7 0.9909460 328      Observed       1  6.415378  5.847081
## 65   Quadrat.7 0.9910373 329 Extrapolation       1  6.415922  5.847543
## 66   Quadrat.7 0.9721341 132   Rarefaction       2  4.713915  4.191975
## 67   Quadrat.7 0.9908537 327   Rarefaction       2  4.794932  4.234885
## 68   Quadrat.7 0.9909460 328      Observed       2  4.795151  4.234995
## 69   Quadrat.7 0.9910373 329 Extrapolation       2  4.795320  4.235077
## 70   Quadrat.8 0.9827498 132   Rarefaction       0 11.777809 10.323816
## 71   Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 10.254646
## 72   Quadrat.8 0.9976852 428      Observed       0 14.000000 10.250651
## 73   Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 10.245186
## 74   Quadrat.8 0.9827498 132   Rarefaction       1  6.011288  5.405026
## 75   Quadrat.8 0.9976636 427   Rarefaction       1  6.244048  5.634044
## 76   Quadrat.8 0.9976852 428      Observed       1  6.244415  5.634349
## 77   Quadrat.8 0.9977067 429 Extrapolation       1  6.244668  5.634524
## 78   Quadrat.8 0.9827498 132   Rarefaction       2  4.275118  3.793524
## 79   Quadrat.8 0.9976636 427   Rarefaction       2  4.350221  3.851243
## 80   Quadrat.8 0.9976852 428      Observed       2  4.350337  3.851327
## 81   Quadrat.8 0.9977067 429 Extrapolation       2  4.350417  3.851374
## 82   Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 11.081951
## 83   Quadrat.9 0.9526800  82      Observed       0 16.000000 11.115915
## 84   Quadrat.9 0.9540968  83 Extrapolation       0 16.047320 11.100682
## 85   Quadrat.9 0.9896492 132 Extrapolation       0 17.234773 10.000772
## 86   Quadrat.9 0.9512195  80   Rarefaction       1  8.427859  6.426819
## 87   Quadrat.9 0.9526800  82      Observed       1  8.450869  6.442178
## 88   Quadrat.9 0.9540968  83 Extrapolation       1  8.463836  6.447247
## 89   Quadrat.9 0.9896492 132 Extrapolation       1  8.932639  6.752595
## 90   Quadrat.9 0.9512195  80   Rarefaction       2  5.469031  4.181805
## 91   Quadrat.9 0.9526800  82      Observed       2  5.475570  4.185014
## 92   Quadrat.9 0.9540968  83 Extrapolation       2  5.479218  4.185809
## 93   Quadrat.9 0.9896492 132 Extrapolation       2  5.592621  4.240765
## 94  Quadrat.10 0.9853580 132   Rarefaction       0  8.766625  5.697879
## 95  Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  5.659791
## 96  Quadrat.10 0.9920320 250      Observed       0 10.000000  5.669107
## 97  Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  5.671969
## 98  Quadrat.10 0.9853580 132   Rarefaction       1  4.289710  3.773066
## 99  Quadrat.10 0.9920000 248   Rarefaction       1  4.372453  3.836010
## 100 Quadrat.10 0.9920320 250      Observed       1  4.373262  3.836770
## 101 Quadrat.10 0.9920639 251 Extrapolation       1  4.373664  3.836920
## 102 Quadrat.10 0.9853580 132   Rarefaction       2  3.406166  3.043027
## 103 Quadrat.10 0.9920000 248   Rarefaction       2  3.435684  3.061583
## 104 Quadrat.10 0.9920320 250      Observed       2  3.435954  3.061824
## 105 Quadrat.10 0.9920639 251 Extrapolation       2  3.436088  3.061834
## 106 Quadrat.11 0.9975639 132   Rarefaction       0 12.974684 11.714090
## 107 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.581174
## 108 Quadrat.11 0.9975639 132   Rarefaction       1  8.616984  7.565287
## 109 Quadrat.11 1.0000000 155      Observed       1  8.680817  7.616043
## 110 Quadrat.11 0.9975639 132   Rarefaction       2  6.560505  5.295133
## 111 Quadrat.11 1.0000000 155      Observed       2  6.602088  5.314757
##        qD.UCL
## 1   12.892100
## 2    5.752004
## 3    3.987098
## 4   13.577024
## 5   14.805860
## 6    9.988475
## 7   10.368215
## 8    8.629241
## 9    8.983172
## 10  12.893049
## 11  18.573199
## 12  18.601753
## 13  18.620932
## 14   6.284796
## 15   6.535954
## 16   6.536522
## 17   6.536858
## 18   4.834188
## 19   4.931994
## 20   4.932159
## 21   4.932242
## 22  14.709342
## 23  18.316537
## 24  18.342439
## 25  18.360510
## 26   6.872364
## 27   7.037249
## 28   7.038176
## 29   7.038767
## 30   5.335893
## 31   5.411491
## 32   5.411918
## 33   5.412203
## 34  18.331699
## 35  24.712828
## 36  24.757863
## 37  24.798430
## 38   5.605709
## 39   5.881535
## 40   5.883320
## 41   5.884531
## 42   3.140780
## 43   3.169491
## 44   3.169670
## 45   3.169788
## 46   9.287782
## 47  15.302784
## 48  15.316476
## 49  15.324963
## 50   4.437017
## 51   4.520946
## 52   4.521107
## 53   4.521212
## 54   3.831284
## 55   3.870490
## 56   3.870559
## 57   3.870614
## 58  13.812757
## 59  19.509964
## 60  19.540377
## 61  19.568147
## 62   6.750445
## 63   6.982864
## 64   6.983676
## 65   6.984301
## 66   5.235856
## 67   5.354979
## 68   5.355306
## 69   5.355562
## 70  13.231803
## 71  17.738558
## 72  17.749349
## 73  17.759444
## 74   6.617551
## 75   6.854051
## 76   6.854482
## 77   6.854812
## 78   4.756713
## 79   4.849199
## 80   4.849347
## 81   4.849459
## 82  20.746618
## 83  20.884085
## 84  20.993958
## 85  24.468773
## 86  10.428898
## 87  10.459559
## 88  10.480424
## 89  11.112684
## 90   6.756258
## 91   6.766126
## 92   6.772627
## 93   6.944476
## 94  11.835370
## 95  14.308250
## 96  14.330893
## 97  14.343967
## 98   4.806354
## 99   4.908896
## 100  4.909753
## 101  4.910408
## 102  3.769304
## 103  3.809784
## 104  3.810084
## 105  3.810342
## 106 14.235278
## 107 14.418826
## 108  9.668681
## 109  9.745591
## 110  7.825877
## 111  7.889420
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.1343104 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4710447  4.178960
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3665161  2.634104
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.3761036 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.3060506  3.878695
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2067327  3.064711
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.7514014 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.6065318  7.845963
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6709804  5.536223
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.5734038 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3622389  9.262058
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.4112541  7.683038
## 13  Quadrat.3  Species richness 14.000000 23.977578 6.8614339 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.3320932  5.329274
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2139511  4.091755
## 16  Quadrat.4  Species richness 12.000000 16.484694 3.6596892 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3309526  5.859629
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3394287  4.159533
## 19  Quadrat.5  Species richness 19.000000 19.896751 3.9775981 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4359880  4.414721
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2226355  2.337059
## 22  Quadrat.6  Species richness 10.000000 14.490302 5.6076286 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1830397  3.998317
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1370932  3.440546
## 25  Quadrat.7  Species richness 15.000000 15.897256 4.5107172 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3319608  5.926745
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3340657  4.196700
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.0093768 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3289641  5.701860
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2520909  3.890652
## 31  Quadrat.9  Species richness 16.000000 17.580488 5.1752361 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.2589636  7.001621
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.8908027  4.049870
##          UCL
## 1  14.679384
## 2   6.025422
## 3   4.070820
## 4  16.649077
## 5   5.078391
## 6   3.875088
## 7  14.472720
## 8  10.223524
## 9   8.166418
## 10 15.123851
## 11 10.682009
## 12  9.295124
## 13 37.425742
## 14  6.631055
## 15  4.930428
## 16 23.657553
## 17  7.156940
## 18  5.490069
## 19 27.692700
## 20  6.123762
## 21  3.209774
## 22 25.481052
## 23  4.715819
## 24  3.977942
## 25 24.738099
## 26  7.228007
## 27  5.506213
## 28 18.187722
## 29  6.991375
## 30  4.878830
## 31 27.723764
## 32 11.936668
## 33  7.541753
n <- c(444)

Barrow_Datan <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = n)

Barrow_Datan
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.316164 11.66868 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.319564 11.68044 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.321349 11.69357 0.9926504
## 4   Quadrat.1 444 Extrapolation       0 10.491821  7.676266 13.30738 0.9999340
## 5   Quadrat.2 444      Observed       0 14.000000 13.239362 14.76064 1.0000000
## 6   Quadrat.3 444   Rarefaction       0 13.977578 10.787678 17.16748 0.9887892
## 7   Quadrat.3 445   Rarefaction       0 13.988789 10.792597 17.18498 0.9887892
## 8   Quadrat.3 446      Observed       0 14.000000 10.797515 17.20249 0.9888018
## 9   Quadrat.3 447 Extrapolation       0 14.011198 10.802418 17.21998 0.9888144
## 10  Quadrat.4 293   Rarefaction       0 11.989796  9.282094 14.69750 0.9897959
## 11  Quadrat.4 294      Observed       0 12.000000  9.285349 14.71465 0.9898191
## 12  Quadrat.4 295 Extrapolation       0 12.010181  9.288012 14.73235 0.9898422
## 13  Quadrat.4 444 Extrapolation       0 13.295523  9.486234 17.10481 0.9927601
## 14  Quadrat.5 276   Rarefaction       0 18.989170 16.960279 21.01806 0.9891697
## 15  Quadrat.5 277      Observed       0 19.000000 16.966998 21.03300 0.9892989
## 16  Quadrat.5 278 Extrapolation       0 19.010701 16.973544 21.04786 0.9894266
## 17  Quadrat.5 444 Extrapolation       0 19.775973 16.635024 22.91692 0.9985587
## 18  Quadrat.6 444   Rarefaction       0  9.868852  7.131837 12.60587 0.9933473
## 19  Quadrat.6 463   Rarefaction       0  9.993534  7.176607 12.81046 0.9935345
## 20  Quadrat.6 464      Observed       0 10.000000  7.178852 12.82115 0.9935438
## 21  Quadrat.6 465 Extrapolation       0 10.006456  7.181083 12.83183 0.9935531
## 22  Quadrat.7 327   Rarefaction       0 14.990854 12.732565 17.24914 0.9908537
## 23  Quadrat.7 328      Observed       0 15.000000 12.738792 17.26121 0.9909460
## 24  Quadrat.7 329 Extrapolation       0 15.009054 12.744909 17.27320 0.9910373
## 25  Quadrat.7 444 Extrapolation       0 15.620576 12.883930 18.35722 0.9972081
## 26  Quadrat.8 427   Rarefaction       0 13.997664 12.064107 15.93122 0.9976636
## 27  Quadrat.8 428      Observed       0 14.000000 12.064589 15.93541 0.9976852
## 28  Quadrat.8 429 Extrapolation       0 14.002315 12.065021 15.93961 0.9977067
## 29  Quadrat.8 444 Extrapolation       0 14.034567 12.068267 16.00087 0.9980060
## 30  Quadrat.9  81   Rarefaction       0 15.951220 13.201819 18.70062 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 13.231305 18.76869 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 13.259195 18.83544 0.9540968
## 33  Quadrat.9 444 Extrapolation       0 17.580462 10.095900 25.06502 0.9999992
## 34 Quadrat.10 249   Rarefaction       0  9.992000  7.855036 12.12896 0.9920000
## 35 Quadrat.10 250      Observed       0 10.000000  7.858817 12.14118 0.9920320
## 36 Quadrat.10 251 Extrapolation       0 10.007968  7.861459 12.15448 0.9920639
## 37 Quadrat.10 444 Extrapolation       0 11.076621  8.061419 14.09182 0.9963385
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.091901 13.90810 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.089263 13.91074 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.086757 13.91324 1.0000000
## 41 Quadrat.11 444 Extrapolation       0 13.000000 11.535205 14.46479 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9786644 1.0000000
## 2  0.9775804 1.0000000
## 3  0.9778381 1.0000000
## 4  0.9979412 1.0000000
## 5  0.9976016 1.0000000
## 6  0.9816257 0.9959528
## 7  0.9816225 0.9959560
## 8  0.9816334 0.9959703
## 9  0.9816443 0.9959845
## 10 0.9808457 0.9987461
## 11 0.9803172 0.9993210
## 12 0.9803514 0.9993330
## 13 0.9847618 1.0000000
## 14 0.9779492 1.0000000
## 15 0.9780577 1.0000000
## 16 0.9781655 1.0000000
## 17 0.9880464 1.0000000
## 18 0.9876976 0.9989969
## 19 0.9877616 0.9993073
## 20 0.9877704 0.9993172
## 21 0.9877792 0.9993270
## 22 0.9831842 0.9985232
## 23 0.9832532 0.9986387
## 24 0.9833217 0.9987529
## 25 0.9888976 1.0000000
## 26 0.9929316 1.0000000
## 27 0.9927786 1.0000000
## 28 0.9928098 1.0000000
## 29 0.9932508 1.0000000
## 30 0.9111539 0.9912851
## 31 0.9125552 0.9928049
## 32 0.9139357 0.9942579
## 33 0.9942113 1.0000000
## 34 0.9840980 0.9999020
## 35 0.9833525 1.0000000
## 36 0.9834146 1.0000000
## 37 0.9917753 1.0000000
## 38 0.9911910 1.0000000
## 39 0.9911654 1.0000000
## 40 0.9912693 1.0000000
## 41 0.9989471 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  7.507014 12.46505
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  7.513499 12.48650
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  7.513314 12.50161
## 4   Quadrat.1 0.9999340 444 Extrapolation       0 10.491821  7.437647 13.54599
## 5   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.876843 15.12316
## 6   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  7.121305 20.83435
## 7   Quadrat.3 0.9888018 446      Observed       0 14.000000  7.132685 20.86731
## 8   Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  7.134304 20.88809
## 9   Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  6.544234 17.42102
## 10  Quadrat.4 0.9898191 294      Observed       0 12.000000  6.553891 17.44611
## 11  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  6.557907 17.46245
## 12  Quadrat.4 0.9927601 444 Extrapolation       0 13.295523  6.940415 19.65063
## 13  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 13.433397 24.53275
## 14  Quadrat.5 0.9892989 277      Observed       0 19.000000 13.414640 24.58536
## 15  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 13.388066 24.63334
## 16  Quadrat.5 0.9985587 444 Extrapolation       0 19.775973 11.100283 28.45166
## 17  Quadrat.6 0.9933473 444   Rarefaction       0  9.868852  2.999875 16.73783
## 18  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  3.090282 16.89021
## 19  Quadrat.6 0.9935438 464      Observed       0 10.000000  3.095386 16.90461
## 20  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  3.098179 16.91473
## 21  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227  9.554886 20.42157
## 22  Quadrat.7 0.9909460 328      Observed       0 15.000000  9.536958 20.46304
## 23  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054  9.514461 20.50365
## 24  Quadrat.7 0.9972081 444 Extrapolation       0 15.620576  7.757115 23.48404
## 25  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 10.603248 17.38996
## 26  Quadrat.8 0.9976852 428      Observed       0 14.000000 10.600702 17.39930
## 27  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 10.597153 17.40748
## 28  Quadrat.8 0.9980060 444 Extrapolation       0 14.034567 10.545694 17.52344
## 29  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 10.912594 20.91598
## 30  Quadrat.9 0.9526800  82      Observed       0 16.000000 10.936823 21.06318
## 31  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320 10.916670 21.17797
## 32  Quadrat.9 0.9999992 444 Extrapolation       0 17.580462  9.289816 25.87111
## 33 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  6.911854 13.05619
## 34 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.923777 13.07622
## 35 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  6.929297 13.08664
## 36 Quadrat.10 0.9963385 444 Extrapolation       0 11.076621  7.520649 14.63259
## 37 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.419275 14.58073
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 1.6921984 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4810236  4.159402
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3873711  2.593229
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.1935912 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2335388  4.020815
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.1535406  3.168966
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.9005751 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.5737754  7.910165
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6637443  5.550405
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.5899817 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3145627  9.355502
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3930068  7.718802
## 13  Quadrat.3  Species richness 14.000000 23.977578 5.5160687 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2735121  5.444091
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2049160  4.109464
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.4322005 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3768903  5.769593
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3955468  4.049544
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.4149544 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4564988  4.374521
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2268975  2.328706
## 22  Quadrat.6  Species richness 10.000000 14.490302 4.5634613 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1608487  4.041811
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1241476  3.465919
## 25  Quadrat.7  Species richness 15.000000 15.897256 3.6699711 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3050604  5.979469
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3145513  4.234947
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.0513091 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.2998250  5.758971
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2283570  3.937169
## 31  Quadrat.9  Species richness 16.000000 17.580488 7.1021201 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.1470829  7.220903
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.8726923  4.085366
##          UCL
## 1  13.812860
## 2   6.044980
## 3   4.111696
## 4  16.291360
## 5   4.936270
## 6   3.770834
## 7  14.765095
## 8  10.159323
## 9   8.152235
## 10 15.156343
## 11 10.588565
## 12  9.259360
## 13 34.788874
## 14  6.516239
## 15  4.912720
## 16 25.171647
## 17  7.246976
## 18  5.600059
## 19 28.549902
## 20  6.163963
## 21  3.218127
## 22 23.434522
## 23  4.672326
## 24  3.952569
## 25 23.090267
## 26  7.175284
## 27  5.467966
## 28 18.269908
## 29  6.934264
## 30  4.832312
## 31 31.500387
## 32 11.717386
## 33  7.506257
o <- c(446)

Barrow_Datao <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = o)

Barrow_Datao
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.134448 11.85040 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.133881 11.86612 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.132965 11.88196 0.9926504
## 4   Quadrat.1 446 Extrapolation       0 10.491952  6.847584 14.13632 0.9999359
## 5   Quadrat.2 443   Rarefaction       0 14.000000 13.240087 14.75991 1.0000000
## 6   Quadrat.2 444      Observed       0 14.000000 13.239362 14.76064 1.0000000
## 7   Quadrat.2 445 Extrapolation       0 14.000000 13.238859 14.76114 1.0000000
## 8   Quadrat.2 446 Extrapolation       0 14.000000 13.238353 14.76165 1.0000000
## 9   Quadrat.3 446      Observed       0 14.000000 11.056723 16.94328 0.9888018
## 10  Quadrat.4 293   Rarefaction       0 11.989796  9.083292 14.89630 0.9897959
## 11  Quadrat.4 294      Observed       0 12.000000  9.085900 14.91410 0.9898191
## 12  Quadrat.4 295 Extrapolation       0 12.010181  9.087996 14.93237 0.9898422
## 13  Quadrat.4 446 Extrapolation       0 13.309986  9.179293 17.44068 0.9927929
## 14  Quadrat.5 276   Rarefaction       0 18.989170 16.450429 21.52791 0.9891697
## 15  Quadrat.5 277      Observed       0 19.000000 16.458054 21.54195 0.9892989
## 16  Quadrat.5 278 Extrapolation       0 19.010701 16.465383 21.55602 0.9894266
## 17  Quadrat.5 446 Extrapolation       0 19.778838 16.522739 23.03494 0.9985929
## 18  Quadrat.6 446   Rarefaction       0  9.882147  7.115340 12.64895 0.9933680
## 19  Quadrat.6 463   Rarefaction       0  9.993534  7.164917 12.82215 0.9935345
## 20  Quadrat.6 464      Observed       0 10.000000  7.167758 12.83224 0.9935438
## 21  Quadrat.6 465 Extrapolation       0 10.006456  7.170435 12.84248 0.9935531
## 22  Quadrat.7 327   Rarefaction       0 14.990854 12.598634 17.38307 0.9908537
## 23  Quadrat.7 328      Observed       0 15.000000 12.603139 17.39686 0.9909460
## 24  Quadrat.7 329 Extrapolation       0 15.009054 12.607529 17.41058 0.9910373
## 25  Quadrat.7 446 Extrapolation       0 15.626132 12.598269 18.65399 0.9972641
## 26  Quadrat.8 427   Rarefaction       0 13.997664 12.176558 15.81877 0.9976636
## 27  Quadrat.8 428      Observed       0 14.000000 12.176376 15.82362 0.9976852
## 28  Quadrat.8 429 Extrapolation       0 14.002315 12.175292 15.82934 0.9977067
## 29  Quadrat.8 446 Extrapolation       0 14.038536 12.154038 15.92303 0.9980429
## 30  Quadrat.9  81   Rarefaction       0 15.951220 13.528041 18.37440 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 13.551045 18.44895 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 13.572208 18.52243 0.9540968
## 33  Quadrat.9 446 Extrapolation       0 17.580463  9.087537 26.07339 0.9999993
## 34 Quadrat.10 249   Rarefaction       0  9.992000  7.658223 12.32578 0.9920000
## 35 Quadrat.10 250      Observed       0 10.000000  7.661079 12.33892 0.9920320
## 36 Quadrat.10 251 Extrapolation       0 10.007968  7.663303 12.35263 0.9920639
## 37 Quadrat.10 446 Extrapolation       0 11.083929  7.724077 14.44378 0.9963677
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.212069 13.78793 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.208055 13.79195 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.204701 13.79530 1.0000000
## 41 Quadrat.11 446 Extrapolation       0 13.000000 11.210389 14.78961 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9765820 1.0000000
## 2  0.9756735 1.0000000
## 3  0.9758985 1.0000000
## 4  0.9969374 1.0000000
## 5  0.9974446 1.0000000
## 6  0.9977261 1.0000000
## 7  0.9977363 1.0000000
## 8  0.9977465 1.0000000
## 9  0.9816764 0.9959272
## 10 0.9800130 0.9995789
## 11 0.9795480 1.0000000
## 12 0.9795794 1.0000000
## 13 0.9840861 1.0000000
## 14 0.9788376 0.9995017
## 15 0.9786808 0.9999171
## 16 0.9788120 1.0000000
## 17 0.9899345 1.0000000
## 18 0.9882178 0.9985182
## 19 0.9883260 0.9987430
## 20 0.9881707 0.9989169
## 21 0.9881798 0.9989263
## 22 0.9823892 0.9993181
## 23 0.9822999 0.9995920
## 24 0.9823845 0.9996902
## 25 0.9887379 1.0000000
## 26 0.9928420 1.0000000
## 27 0.9923609 1.0000000
## 28 0.9923927 1.0000000
## 29 0.9928963 1.0000000
## 30 0.9070434 0.9953957
## 31 0.9083326 0.9970274
## 32 0.9096116 0.9985820
## 33 0.9932707 1.0000000
## 34 0.9833885 1.0000000
## 35 0.9827617 1.0000000
## 36 0.9828182 1.0000000
## 37 0.9907897 1.0000000
## 38 0.9884728 1.0000000
## 39 0.9881254 1.0000000
## 40 0.9882415 1.0000000
## 41 0.9980334 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  6.544446 13.42762
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  6.549537 13.45046
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  6.547937 13.46699
## 4   Quadrat.1 0.9999359 446 Extrapolation       0 10.491952  6.379864 14.60404
## 5   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.998245 15.00175
## 6   Quadrat.3 0.9888018 446      Observed       0 14.000000  8.930527 19.06947
## 7   Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  5.320115 18.64514
## 8   Quadrat.4 0.9898191 294      Observed       0 12.000000  5.329954 18.67005
## 9   Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  5.336184 18.68418
## 10  Quadrat.4 0.9927929 446 Extrapolation       0 13.309986  5.742479 20.87749
## 11  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 14.587188 23.37896
## 12  Quadrat.5 0.9892989 277      Observed       0 19.000000 14.582918 23.41708
## 13  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 14.571261 23.45014
## 14  Quadrat.5 0.9985929 446 Extrapolation       0 19.778838 13.457145 26.10053
## 15  Quadrat.6 0.9933680 446   Rarefaction       0  9.882147  4.013165 15.75113
## 16  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  4.174713 15.80578
## 17  Quadrat.6 0.9935438 464      Observed       0 10.000000  4.181006 15.81899
## 18  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  4.186693 15.82622
## 19  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227  9.685474 20.29098
## 20  Quadrat.7 0.9909460 328      Observed       0 15.000000  9.665775 20.33423
## 21  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054  9.642579 20.37553
## 22  Quadrat.7 0.9972641 446 Extrapolation       0 15.626132  7.844562 23.40770
## 23  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 10.513020 17.48018
## 24  Quadrat.8 0.9976852 428      Observed       0 14.000000 10.509863 17.49014
## 25  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 10.505741 17.49889
## 26  Quadrat.8 0.9980429 446 Extrapolation       0 14.038536 10.438214 17.63886
## 27  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 10.106288 21.72228
## 28  Quadrat.9 0.9526800  82      Observed       0 16.000000 10.102781 21.89722
## 29  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320 10.057436 22.03720
## 30  Quadrat.9 0.9999993 446 Extrapolation       0 17.580463  7.989876 27.17105
## 31 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  6.309618 13.65842
## 32 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.320233 13.67977
## 33 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  6.323026 13.69291
## 34 Quadrat.10 0.9963677 446 Extrapolation       0 11.083929  6.735001 15.43286
## 35 Quadrat.11 1.0000000 155      Observed       0 13.000000 10.892692 15.10731
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.0996582 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4680093  4.184910
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3736642  2.620094
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.5201281 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2888436  3.912420
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2016084  3.074754
## 7  Quadrat.11  Species richness 13.000000 13.000000 1.0701914 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.6071456  7.844760
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6633684  5.551142
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.6102566 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.2946743  9.394482
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3324311  7.837528
## 13  Quadrat.3  Species richness 14.000000 23.977578 5.7727434 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2782176  5.434868
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.1805670  4.157187
## 16  Quadrat.4  Species richness 12.000000 16.484694 3.6312606 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3564431  5.809669
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3491657  4.140449
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.8917000 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4250226  4.436213
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2086171  2.364534
## 22  Quadrat.6  Species richness 10.000000 14.490302 4.5922117 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1676823  4.028417
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1231621  3.467851
## 25  Quadrat.7  Species richness 15.000000 15.897256 5.6169600 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3561000  5.879433
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3253894  4.213705
## 28  Quadrat.8  Species richness 14.000000 14.249416 1.9503406 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3437962  5.672789
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2637552  3.867790
## 31  Quadrat.9  Species richness 16.000000 17.580488 5.3282757 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.1548646  7.205651
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.8396552  4.150118
##          UCL
## 1  14.611466
## 2   6.019472
## 3   4.084831
## 4  16.931360
## 5   5.044666
## 6   3.865045
## 7  15.097537
## 8  10.224727
## 9   8.151498
## 10 15.196081
## 11 10.549585
## 12  9.140634
## 13 35.291948
## 14  6.525461
## 15  4.864997
## 16 23.601834
## 17  7.206900
## 18  5.509153
## 19 29.484307
## 20  6.102271
## 21  3.182299
## 22 23.490871
## 23  4.685720
## 24  3.950637
## 25 26.906295
## 26  7.275319
## 27  5.489208
## 28 18.072013
## 29  7.020446
## 30  4.901692
## 31 28.023716
## 32 11.732637
## 33  7.441505
p <- c(294)

Barrow_Datap <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = p)

Barrow_Datap
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.157559 11.82729 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.155856 11.84414 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.152710 11.86221 0.9926504
## 4   Quadrat.1 294 Extrapolation       0 10.453588  7.416620 13.49056 0.9993590
## 5   Quadrat.2 294   Rarefaction       0 13.842723 13.081651 14.60379 0.9975280
## 6   Quadrat.2 443   Rarefaction       0 14.000000 13.274651 14.72535 1.0000000
## 7   Quadrat.2 444      Observed       0 14.000000 13.274170 14.72583 1.0000000
## 8   Quadrat.2 445 Extrapolation       0 14.000000 13.273913 14.72609 1.0000000
## 9   Quadrat.3 294   Rarefaction       0 12.282806  9.519577 15.04603 0.9884423
## 10  Quadrat.3 445   Rarefaction       0 13.988789 10.126464 17.85111 0.9887892
## 11  Quadrat.3 446      Observed       0 14.000000 10.130597 17.86940 0.9888018
## 12  Quadrat.3 447 Extrapolation       0 14.011198 10.134351 17.88804 0.9888144
## 13  Quadrat.4 294      Observed       0 12.000000  9.867623 14.13238 0.9898191
## 14  Quadrat.5 276   Rarefaction       0 18.989170 16.270616 21.70772 0.9891697
## 15  Quadrat.5 277      Observed       0 19.000000 16.278139 21.72186 0.9892989
## 16  Quadrat.5 278 Extrapolation       0 19.010701 16.285524 21.73588 0.9894266
## 17  Quadrat.5 294 Extrapolation       0 19.165546 16.385718 21.94537 0.9912744
## 18  Quadrat.6 294   Rarefaction       0  8.718208  6.454883 10.98153 0.9910892
## 19  Quadrat.6 463   Rarefaction       0  9.993534  6.859460 13.12761 0.9935345
## 20  Quadrat.6 464      Observed       0 10.000000  6.861059 13.13894 0.9935438
## 21  Quadrat.6 465 Extrapolation       0 10.006456  6.862648 13.15026 0.9935531
## 22  Quadrat.7 294   Rarefaction       0 14.636720 11.951554 17.32188 0.9877769
## 23  Quadrat.7 327   Rarefaction       0 14.990854 12.186427 17.79528 0.9908537
## 24  Quadrat.7 328      Observed       0 15.000000 12.191943 17.80806 0.9909460
## 25  Quadrat.7 329 Extrapolation       0 15.009054 12.197363 17.82074 0.9910373
## 26  Quadrat.8 294   Rarefaction       0 13.458543 12.096667 14.82042 0.9939557
## 27  Quadrat.8 427   Rarefaction       0 13.997664 12.211493 15.78383 0.9976636
## 28  Quadrat.8 428      Observed       0 14.000000 12.209784 15.79022 0.9976852
## 29  Quadrat.8 429 Extrapolation       0 14.002315 12.208081 15.79655 0.9977067
## 30  Quadrat.9  81   Rarefaction       0 15.951220 13.315089 18.58735 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 13.343736 18.65626 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 13.370939 18.72370 0.9540968
## 33  Quadrat.9 294 Extrapolation       0 17.577975 11.086676 24.06928 0.9999248
## 34 Quadrat.10 249   Rarefaction       0  9.992000  8.007359 11.97664 0.9920000
## 35 Quadrat.10 250      Observed       0 10.000000  8.010657 11.98934 0.9920320
## 36 Quadrat.10 251 Extrapolation       0 10.007968  8.012396 12.00354 0.9920639
## 37 Quadrat.10 294 Extrapolation       0 10.322062  8.055383 12.58874 0.9933202
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.090530 13.90947 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.089263 13.91074 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.087868 13.91213 1.0000000
## 41 Quadrat.11 294 Extrapolation       0 13.000000 11.778218 14.22178 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9762254 1.0000000
## 2  0.9755019 1.0000000
## 3  0.9757452 1.0000000
## 4  0.9922308 1.0000000
## 5  0.9948124 1.0000000
## 6  0.9971448 1.0000000
## 7  0.9972077 1.0000000
## 8  0.9972200 1.0000000
## 9  0.9802245 0.9966601
## 10 0.9809301 0.9966484
## 11 0.9805585 0.9970452
## 12 0.9805730 0.9970557
## 13 0.9819410 0.9976972
## 14 0.9781894 1.0000000
## 15 0.9782970 1.0000000
## 16 0.9784035 1.0000000
## 17 0.9799773 1.0000000
## 18 0.9847713 0.9974072
## 19 0.9876214 0.9994476
## 20 0.9876316 0.9994560
## 21 0.9876417 0.9994644
## 22 0.9808553 0.9946985
## 23 0.9833523 0.9983550
## 24 0.9834353 0.9984566
## 25 0.9835176 0.9985570
## 26 0.9882560 0.9996554
## 27 0.9913887 1.0000000
## 28 0.9913461 1.0000000
## 29 0.9913770 1.0000000
## 30 0.9153551 0.9870839
## 31 0.9167746 0.9885854
## 32 0.9181581 0.9900355
## 33 0.9848191 1.0000000
## 34 0.9831685 1.0000000
## 35 0.9822769 1.0000000
## 36 0.9823377 1.0000000
## 37 0.9846568 1.0000000
## 38 0.9909463 1.0000000
## 39 0.9907457 1.0000000
## 40 0.9908541 1.0000000
## 41 0.9969242 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  6.506469 13.46560
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  6.510792 13.48921
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  6.508157 13.50677
## 4   Quadrat.1 0.9993590 294 Extrapolation       0 10.453588  6.297210 14.60997
## 5   Quadrat.2 0.9975280 294   Rarefaction       0 13.842723 12.970594 14.71485
## 6   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.906258 15.09374
## 7   Quadrat.3 0.9884423 294   Rarefaction       0 12.282806  2.394112 22.17150
## 8   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  3.818162 24.13749
## 9   Quadrat.3 0.9888018 446      Observed       0 14.000000  3.830567 24.16943
## 10  Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  3.832297 24.19010
## 11  Quadrat.4 0.9898191 294      Observed       0 12.000000  7.922449 16.07755
## 12  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 11.111579 26.85457
## 13  Quadrat.5 0.9892989 277      Observed       0 19.000000 11.081495 26.91851
## 14  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 11.044196 26.97721
## 15  Quadrat.5 0.9912744 294 Extrapolation       0 19.165546 10.485328 27.84576
## 16  Quadrat.6 0.9910892 294   Rarefaction       0  8.718208  2.850119 14.58630
## 17  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  3.147664 16.83283
## 18  Quadrat.6 0.9935438 464      Observed       0 10.000000  3.154073 16.84593
## 19  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  3.157264 16.85565
## 20  Quadrat.7 0.9877769 294   Rarefaction       0 14.636719 10.046184 19.22725
## 21  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227  9.773091 20.20336
## 22  Quadrat.7 0.9909460 328      Observed       0 15.000000  9.766305 20.23370
## 23  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054  9.752886 20.26522
## 24  Quadrat.8 0.9939557 294   Rarefaction       0 13.458543  9.638701 17.27839
## 25  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602  8.759113 19.23409
## 26  Quadrat.8 0.9976852 428      Observed       0 14.000000  8.753931 19.24607
## 27  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315  8.747404 19.25723
## 28  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 10.496868 21.33170
## 29  Quadrat.9 0.9526800  82      Observed       0 16.000000 10.489852 21.51015
## 30  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320 10.444373 21.65027
## 31  Quadrat.9 0.9999248 294 Extrapolation       0 17.577975  8.255400 26.90055
## 32 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  6.045501 13.92254
## 33 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.055553 13.94445
## 34 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  6.059342 13.95659
## 35 Quadrat.10 0.9933202 294 Extrapolation       0 10.322062  6.143308 14.50082
## 36 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.464236 14.53576
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.0964413 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.5463289  4.031406
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.4216014  2.526139
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.4487745 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2444932  3.999345
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.1739642  3.128936
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.7857358 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.5803328  7.897312
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6294534  5.617614
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.4897086 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3149963  9.354652
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3662227  7.771297
## 13  Quadrat.3  Species richness 14.000000 23.977578 5.6214835 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2841170  5.423306
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.1811819  4.155982
## 16  Quadrat.4  Species richness 12.000000 16.484694 3.8545667 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3409869  5.839962
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3577253  4.123673
## 19  Quadrat.5  Species richness 19.000000 19.896751 5.1491645 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4609259  4.365844
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2573307  2.269058
## 22  Quadrat.6  Species richness 10.000000 14.490302 5.0307848 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1671472  4.029466
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1205636  3.472944
## 25  Quadrat.7  Species richness 15.000000 15.897256 4.7846527 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3628081  5.866285
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3372495  4.190460
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.3250444 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3252672  5.709106
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2470928  3.900448
## 31  Quadrat.9  Species richness 16.000000 17.580488 5.2581287 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.0521817  7.406906
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.7489320  4.327932
##          UCL
## 1  14.605162
## 2   6.172976
## 3   4.178786
## 4  16.791510
## 5   4.957740
## 6   3.810863
## 7  14.540014
## 8  10.172175
## 9   8.085026
## 10 14.959811
## 11 10.589415
## 12  9.206864
## 13 34.995484
## 14  6.537024
## 15  4.866202
## 16 24.039506
## 17  7.176607
## 18  5.525930
## 19 29.988928
## 20  6.172640
## 21  3.277775
## 22 24.350459
## 23  4.684671
## 24  3.945544
## 25 25.275003
## 26  7.288467
## 27  5.512453
## 28 18.806419
## 29  6.984130
## 30  4.869034
## 31 27.886231
## 32 11.531383
## 33  7.263691
q <- c(277)

Barrow_Dataq <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = q)

Barrow_Dataq
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.353522 11.63133 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.353497 11.64650 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.351709 11.66321 0.9926504
## 4   Quadrat.1 277 Extrapolation       0 10.441066  7.728853 13.15328 0.9991707
## 5   Quadrat.2 277   Rarefaction       0 13.796516 12.930595 14.66244 0.9970534
## 6   Quadrat.2 443   Rarefaction       0 14.000000 13.046379 14.95362 1.0000000
## 7   Quadrat.2 444      Observed       0 14.000000 13.045550 14.95445 1.0000000
## 8   Quadrat.2 445 Extrapolation       0 14.000000 13.044876 14.95512 1.0000000
## 9   Quadrat.3 277   Rarefaction       0 12.085167  9.583924 14.58641 0.9883089
## 10  Quadrat.3 445   Rarefaction       0 13.988789 10.364079 17.61350 0.9887892
## 11  Quadrat.3 446      Observed       0 14.000000 10.368908 17.63109 0.9888018
## 12  Quadrat.3 447 Extrapolation       0 14.011198 10.373379 17.64902 0.9888144
## 13  Quadrat.4 277   Rarefaction       0 11.823373  9.011989 14.63476 0.9894244
## 14  Quadrat.4 293   Rarefaction       0 11.989796  9.081642 14.89795 0.9897959
## 15  Quadrat.4 294      Observed       0 12.000000  9.085900 14.91410 0.9898191
## 16  Quadrat.4 295 Extrapolation       0 12.010181  9.089031 14.93133 0.9898422
## 17  Quadrat.5 277      Observed       0 19.000000 16.517976 21.48202 0.9892989
## 18  Quadrat.6 277   Rarefaction       0  8.563578  6.711582 10.41557 0.9907356
## 19  Quadrat.6 463   Rarefaction       0  9.993534  7.153443 12.83363 0.9935345
## 20  Quadrat.6 464      Observed       0 10.000000  7.154503 12.84550 0.9935438
## 21  Quadrat.6 465 Extrapolation       0 10.006456  7.155424 12.85749 0.9935531
## 22  Quadrat.7 277   Rarefaction       0 14.414662 12.520022 16.30930 0.9861919
## 23  Quadrat.7 327   Rarefaction       0 14.990854 12.968510 17.01320 0.9908537
## 24  Quadrat.7 328      Observed       0 15.000000 12.974725 17.02527 0.9909460
## 25  Quadrat.7 329 Extrapolation       0 15.009054 12.980831 17.03728 0.9910373
## 26  Quadrat.8 277   Rarefaction       0 13.350121 11.976519 14.72372 0.9933171
## 27  Quadrat.8 427   Rarefaction       0 13.997664 12.274243 15.72108 0.9976636
## 28  Quadrat.8 428      Observed       0 14.000000 12.273996 15.72600 0.9976852
## 29  Quadrat.8 429 Extrapolation       0 14.002315 12.273110 15.73152 0.9977067
## 30  Quadrat.9  81   Rarefaction       0 15.951220 13.333697 18.56874 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 13.360315 18.63968 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 13.385034 18.70961 0.9540968
## 33  Quadrat.9 277 Extrapolation       0 17.576276 10.300009 24.85254 0.9998739
## 34 Quadrat.10 249   Rarefaction       0  9.992000  7.930171 12.05383 0.9920000
## 35 Quadrat.10 250      Observed       0 10.000000  7.932963 12.06704 0.9920320
## 36 Quadrat.10 251 Extrapolation       0 10.007968  7.935141 12.08079 0.9920639
## 37 Quadrat.10 277 Extrapolation       0 10.204313  7.984842 12.42378 0.9928493
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.275713 13.72429 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.274170 13.72583 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.272866 13.72713 1.0000000
## 41 Quadrat.11 277 Extrapolation       0 13.000000 12.046567 13.95343 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9787135 1.0000000
## 2  0.9773957 1.0000000
## 3  0.9776031 1.0000000
## 4  0.9922044 1.0000000
## 5  0.9942867 0.9998201
## 6  0.9971448 1.0000000
## 7  0.9973283 1.0000000
## 8  0.9973381 1.0000000
## 9  0.9807007 0.9959171
## 10 0.9814890 0.9960895
## 11 0.9811704 0.9964333
## 12 0.9811832 0.9964455
## 13 0.9812229 0.9976260
## 14 0.9815273 0.9980645
## 15 0.9807177 0.9989205
## 16 0.9807582 0.9989262
## 17 0.9772980 1.0000000
## 18 0.9843745 0.9970968
## 19 0.9871233 0.9999457
## 20 0.9869741 1.0000000
## 21 0.9869826 1.0000000
## 22 0.9789867 0.9933971
## 23 0.9826267 0.9990806
## 24 0.9827033 0.9991887
## 25 0.9827792 0.9992955
## 26 0.9883494 0.9982848
## 27 0.9923416 1.0000000
## 28 0.9918590 1.0000000
## 29 0.9918916 1.0000000
## 30 0.9086564 0.9937827
## 31 0.9098671 0.9954929
## 32 0.9110722 0.9971213
## 33 0.9817175 1.0000000
## 34 0.9835949 1.0000000
## 35 0.9832624 1.0000000
## 36 0.9833273 1.0000000
## 37 0.9848738 1.0000000
## 38 0.9916787 1.0000000
## 39 0.9915570 1.0000000
## 40 0.9916759 1.0000000
## 41 0.9978290 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD     qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  6.9675723 13.00450
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  6.9711496 13.02885
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  6.9676317 13.04729
## 4   Quadrat.1 0.9991707 277 Extrapolation       0 10.441066  6.7145541 14.16758
## 5   Quadrat.2 0.9970534 277   Rarefaction       0 13.796516 12.6683513 14.92468
## 6   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.5688728 15.43113
## 7   Quadrat.3 0.9883089 277   Rarefaction       0 12.085167  4.7357960 19.43454
## 8   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  6.2652690 21.69038
## 9   Quadrat.3 0.9888018 446      Observed       0 14.000000  6.2767793 21.72322
## 10  Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  6.2787286 21.74367
## 11  Quadrat.4 0.9894244 277   Rarefaction       0 11.823373  7.0801886 16.56656
## 12  Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  7.1561913 16.80906
## 13  Quadrat.4 0.9898191 294      Observed       0 12.000000  7.1681229 16.83188
## 14  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  7.1711536 16.84921
## 15  Quadrat.5 0.9892989 277      Observed       0 19.000000 11.7768084 26.22319
## 16  Quadrat.6 0.9907356 277   Rarefaction       0  8.563578  1.2600757 15.86708
## 17  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  0.8355919 19.14490
## 18  Quadrat.6 0.9935438 464      Observed       0 10.000000  0.8393818 19.16062
## 19  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  0.8407154 19.17220
## 20  Quadrat.7 0.9861919 277   Rarefaction       0 14.414662 11.0695765 17.75975
## 21  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227 10.3924189 19.58404
## 22  Quadrat.7 0.9909460 328      Observed       0 15.000000 10.3745036 19.62550
## 23  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054 10.3533612 19.66475
## 24  Quadrat.8 0.9933171 277   Rarefaction       0 13.350121 10.8292255 15.87102
## 25  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 10.2991051 17.69410
## 26  Quadrat.8 0.9976852 428      Observed       0 14.000000 10.2948523 17.70515
## 27  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 10.2893799 17.71525
## 28  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 10.0517617 21.77681
## 29  Quadrat.9 0.9526800  82      Observed       0 16.000000 10.0170783 21.98292
## 30  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320  9.9431467 22.15149
## 31  Quadrat.9 0.9998739 277 Extrapolation       0 17.576276  6.7862513 28.36630
## 32 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  6.8833667 13.08467
## 33 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.8943651 13.10563
## 34 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  6.8976021 13.11833
## 35 Quadrat.10 0.9928493 277 Extrapolation       0 10.204313  6.9669717 13.44165
## 36 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.8809543 14.11905
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.0463668 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4697712  4.181456
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3684790  2.630257
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.7652267 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2901191  3.909920
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.1957475  3.086242
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.9789003 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.6012390  7.856337
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6974509  5.484342
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.4853153 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3212572  9.342381
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3677173  7.768368
## 13  Quadrat.3  Species richness 14.000000 23.977578 4.4956402 15.166286
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2668176  5.457212
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.1865839  4.145394
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.6427440 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3430251  5.835968
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3384883  4.161376
## 19  Quadrat.5  Species richness 19.000000 19.896751 5.6784016 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4583070  4.370977
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2356932  2.311466
## 22  Quadrat.6  Species richness 10.000000 14.490302 4.8576131 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1865752  3.991388
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1413383  3.432226
## 25  Quadrat.7  Species richness 15.000000 15.897256 3.7615742 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3800273  5.832536
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3333724  4.198059
## 28  Quadrat.8  Species richness 14.000000 14.249416 1.9026721 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3659628  5.629344
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2753819  3.845002
## 31  Quadrat.9  Species richness 16.000000 17.580488 4.2507509 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.2688968  6.982152
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.8970409  4.037644
##          UCL
## 1  14.507017
## 2   6.022926
## 3   4.074668
## 4  17.411745
## 5   5.047166
## 6   3.853558
## 7  14.918609
## 8  10.213151
## 9   8.218299
## 10 14.951200
## 11 10.601686
## 12  9.209793
## 13 32.788871
## 14  6.503117
## 15  4.876790
## 16 25.584305
## 17  7.180601
## 18  5.488226
## 19 31.026214
## 20  6.167507
## 21  3.235367
## 22 24.011048
## 23  4.722749
## 24  3.986262
## 25 23.269806
## 26  7.322216
## 27  5.504854
## 28 17.978585
## 29  7.063891
## 30  4.924480
## 31 25.911806
## 32 11.956136
## 33  7.553979
r <- c(464)

Barrow_Datar <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = r)

Barrow_Datar
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.225359 11.75949 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.229157 11.77084 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.231344 11.78358 0.9926504
## 4   Quadrat.1 464 Extrapolation       0 10.492969  7.619585 13.36635 0.9999512
## 5   Quadrat.2 443   Rarefaction       0 14.000000 13.010975 14.98903 1.0000000
## 6   Quadrat.2 444      Observed       0 14.000000 13.010069 14.98993 1.0000000
## 7   Quadrat.2 445 Extrapolation       0 14.000000 13.009373 14.99063 1.0000000
## 8   Quadrat.2 464 Extrapolation       0 14.000000 12.995602 15.00440 1.0000000
## 9   Quadrat.3 445   Rarefaction       0 13.988789 10.823647 17.15393 0.9887892
## 10  Quadrat.3 446      Observed       0 14.000000 10.828263 17.17174 0.9888018
## 11  Quadrat.3 447 Extrapolation       0 14.011198 10.832861 17.18954 0.9888144
## 12  Quadrat.3 464 Extrapolation       0 14.199656 10.908412 17.49090 0.9890259
## 13  Quadrat.4 293   Rarefaction       0 11.989796  8.951456 15.02814 0.9897959
## 14  Quadrat.4 294      Observed       0 12.000000  8.954356 15.04564 0.9898191
## 15  Quadrat.4 295 Extrapolation       0 12.010181  8.956245 15.06412 0.9898422
## 16  Quadrat.4 464 Extrapolation       0 13.437240  9.091074 17.78341 0.9930818
## 17  Quadrat.5 276   Rarefaction       0 18.989170 16.352948 21.62539 0.9891697
## 18  Quadrat.5 277      Observed       0 19.000000 16.356754 21.64325 0.9892989
## 19  Quadrat.5 278 Extrapolation       0 19.010701 16.360393 21.66101 0.9894266
## 20  Quadrat.5 464 Extrapolation       0 19.801753 15.666975 23.93653 0.9988664
## 21  Quadrat.6 464      Observed       0 10.000000  7.503174 12.49683 0.9935438
## 22  Quadrat.7 327   Rarefaction       0 14.990854 12.965211 17.01650 0.9908537
## 23  Quadrat.7 328      Observed       0 15.000000 12.971631 17.02837 0.9909460
## 24  Quadrat.7 329 Extrapolation       0 15.009054 12.977951 17.04016 0.9910373
## 25  Quadrat.7 464 Extrapolation       0 15.671373 13.171372 18.17137 0.9977207
## 26  Quadrat.8 427   Rarefaction       0 13.997664 12.377669 15.61766 0.9976636
## 27  Quadrat.8 428      Observed       0 14.000000 12.376513 15.62349 0.9976852
## 28  Quadrat.8 429 Extrapolation       0 14.002315 12.374918 15.62971 0.9977067
## 29  Quadrat.8 464 Extrapolation       0 14.071118 12.304382 15.83785 0.9983453
## 30  Quadrat.9  81   Rarefaction       0 15.951220 12.554472 19.34797 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 12.576269 19.42373 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 12.596714 19.49793 0.9540968
## 33  Quadrat.9 464 Extrapolation       0 17.580473  7.527080 27.63387 0.9999996
## 34 Quadrat.10 249   Rarefaction       0  9.992000  8.013077 11.97092 0.9920000
## 35 Quadrat.10 250      Observed       0 10.000000  8.013812 11.98619 0.9920320
## 36 Quadrat.10 251 Extrapolation       0 10.007968  8.014181 12.00175 0.9920639
## 37 Quadrat.10 464 Extrapolation       0 11.147134  7.745663 14.54861 0.9966205
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.176428 13.82357 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.173185 13.82681 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.170139 13.82986 1.0000000
## 41 Quadrat.11 464 Extrapolation       0 13.000000 11.302873 14.69713 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9791572 1.0000000
## 2  0.9777387 1.0000000
## 3  0.9779986 1.0000000
## 4  0.9981829 1.0000000
## 5  0.9971503 1.0000000
## 6  0.9973641 1.0000000
## 7  0.9973753 1.0000000
## 8  0.9975768 1.0000000
## 9  0.9813246 0.9962539
## 10 0.9813353 0.9962683
## 11 0.9813461 0.9962827
## 12 0.9815317 0.9965201
## 13 0.9808002 0.9987916
## 14 0.9798173 0.9998209
## 15 0.9798533 0.9998310
## 16 0.9851709 1.0000000
## 17 0.9775352 1.0000000
## 18 0.9776328 1.0000000
## 19 0.9777306 1.0000000
## 20 0.9889149 1.0000000
## 21 0.9877168 0.9993708
## 22 0.9832366 0.9984707
## 23 0.9833234 0.9985685
## 24 0.9834095 0.9986651
## 25 0.9905293 1.0000000
## 26 0.9918703 1.0000000
## 27 0.9913017 1.0000000
## 28 0.9913333 1.0000000
## 29 0.9923023 1.0000000
## 30 0.9104272 0.9920119
## 31 0.9119365 0.9934236
## 32 0.9134015 0.9947921
## 33 0.9894505 1.0000000
## 34 0.9822671 1.0000000
## 35 0.9820446 1.0000000
## 36 0.9821063 1.0000000
## 37 0.9905239 1.0000000
## 38 0.9894669 1.0000000
## 39 0.9893284 1.0000000
## 40 0.9894356 1.0000000
## 41 0.9983654 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  7.414080 12.55799
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  7.420755 12.57924
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  7.421504 12.59342
## 4   Quadrat.1 0.9999512 464 Extrapolation       0 10.492969  7.382085 13.60385
## 5   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.633467 15.36653
## 6   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  6.312107 21.64354
## 7   Quadrat.3 0.9888018 446      Observed       0 14.000000  6.324498 21.67550
## 8   Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  6.326764 21.69563
## 9   Quadrat.3 0.9890259 464 Extrapolation       0 14.199656  6.365334 22.03398
## 10  Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  6.410802 17.55445
## 11  Quadrat.4 0.9898191 294      Observed       0 12.000000  6.420467 17.57953
## 12  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  6.422896 17.59747
## 13  Quadrat.4 0.9930818 464 Extrapolation       0 13.437240  6.804716 20.06976
## 14  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 12.157480 25.80867
## 15  Quadrat.5 0.9892989 277      Observed       0 19.000000 12.135759 25.86424
## 16  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 12.106959 25.91444
## 17  Quadrat.5 0.9988664 464 Extrapolation       0 19.801753  9.804161 29.79935
## 18  Quadrat.6 0.9935438 464      Observed       0 10.000000  4.000258 15.99974
## 19  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227 10.944354 19.03210
## 20  Quadrat.7 0.9909460 328      Observed       0 15.000000 10.934647 19.06535
## 21  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054 10.921019 19.09709
## 22  Quadrat.7 0.9977207 464 Extrapolation       0 15.671373  9.602213 21.74053
## 23  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602  9.396474 18.59673
## 24  Quadrat.8 0.9976852 428      Observed       0 14.000000  9.391606 18.60839
## 25  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315  9.385678 18.61895
## 26  Quadrat.8 0.9983453 464 Extrapolation       0 14.071118  9.205871 18.93637
## 27  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285  8.386695 23.44187
## 28  Quadrat.9 0.9526800  82      Observed       0 16.000000  8.346568 23.65343
## 29  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320  8.266604 23.82804
## 30  Quadrat.9 0.9999996 464 Extrapolation       0 17.580473  5.053646 30.10730
## 31 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  5.768594 14.19945
## 32 Quadrat.10 0.9920320 250      Observed       0 10.000000  5.778068 14.22193
## 33 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  5.780482 14.23545
## 34 Quadrat.10 0.9966205 464 Extrapolation       0 11.147134  5.958450 16.33582
## 35 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.045005 14.95499
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 1.9581705 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4564643  4.207537
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3474511  2.671470
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.8229111 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2612646  3.966474
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.1739407  3.128982
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.6609116 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.5823364  7.893385
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6547118  5.568109
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.4858151 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3137861  9.357024
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3764305  7.751290
## 13  Quadrat.3  Species richness 14.000000 23.977578 7.1254845 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2937192  5.404486
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.1964396  4.126077
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.3610026 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3881610  5.747503
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3835088  4.073138
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.3709739 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.5148244  4.260205
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2586492  2.266473
## 22  Quadrat.6  Species richness 10.000000 14.490302 5.2888962 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1729777  4.018038
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1226920  3.468772
## 25  Quadrat.7  Species richness 15.000000 15.897256 3.0206805 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3686130  5.854908
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3485279  4.168354
## 28  Quadrat.8  Species richness 14.000000 14.249416 1.9688600 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3637466  5.633687
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2655044  3.864362
## 31  Quadrat.9  Species richness 16.000000 17.580488 5.3337752 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.3506327  6.821953
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.9834523  3.868280
##          UCL
## 1  14.334156
## 2   5.996845
## 3   4.033454
## 4  17.524804
## 5   4.990612
## 6   3.810817
## 7  14.295363
## 8  10.176102
## 9   8.134532
## 10 14.952180
## 11 10.587043
## 12  9.226871
## 13 37.943271
## 14  6.555844
## 15  4.896106
## 16 25.032102
## 17  7.269066
## 18  5.576465
## 19 28.463702
## 20  6.278279
## 21  3.280360
## 22 24.856348
## 23  4.696098
## 24  3.949716
## 25 21.817681
## 26  7.299844
## 27  5.534559
## 28 18.108311
## 29  7.059548
## 30  4.905120
## 31 28.034495
## 32 12.116336
## 33  7.723343
s <- c(328)

Barrow_Datas <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = s)

Barrow_Datas
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.372169 11.61268 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.369285 11.63071 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.365247 11.64968 0.9926504
## 4   Quadrat.1 328 Extrapolation       0 10.470749  7.224757 13.71674 0.9996171
## 5   Quadrat.2 328   Rarefaction       0 13.913256 13.099813 14.72670 0.9983142
## 6   Quadrat.2 443   Rarefaction       0 14.000000 13.132265 14.86774 1.0000000
## 7   Quadrat.2 444      Observed       0 14.000000 13.131564 14.86844 1.0000000
## 8   Quadrat.2 445 Extrapolation       0 14.000000 13.130931 14.86907 1.0000000
## 9   Quadrat.3 328   Rarefaction       0 12.672411 10.208083 15.13674 0.9886292
## 10  Quadrat.3 445   Rarefaction       0 13.988789 10.965150 17.01243 0.9887892
## 11  Quadrat.3 446      Observed       0 14.000000 10.971651 17.02835 0.9888018
## 12  Quadrat.3 447 Extrapolation       0 14.011198 10.977962 17.04443 0.9888144
## 13  Quadrat.4 293   Rarefaction       0 11.989796  9.087239 14.89235 0.9897959
## 14  Quadrat.4 294      Observed       0 12.000000  9.090208 14.90979 0.9898191
## 15  Quadrat.4 295 Extrapolation       0 12.010181  9.092550 14.92781 0.9898422
## 16  Quadrat.4 328 Extrapolation       0 12.333494  9.158382 15.50861 0.9905762
## 17  Quadrat.5 276   Rarefaction       0 18.989170 16.684642 21.29370 0.9891697
## 18  Quadrat.5 277      Observed       0 19.000000 16.692462 21.30754 0.9892989
## 19  Quadrat.5 278 Extrapolation       0 19.010701 16.700134 21.32127 0.9894266
## 20  Quadrat.5 328 Extrapolation       0 19.410597 16.927832 21.89336 0.9941986
## 21  Quadrat.6 328   Rarefaction       0  9.010393  6.986923 11.03386 0.9917281
## 22  Quadrat.6 463   Rarefaction       0  9.993534  7.516269 12.47080 0.9935345
## 23  Quadrat.6 464      Observed       0 10.000000  7.519555 12.48044 0.9935438
## 24  Quadrat.6 465 Extrapolation       0 10.006456  7.522590 12.49032 0.9935531
## 25  Quadrat.7 328      Observed       0 15.000000 12.337545 17.66246 0.9909460
## 26  Quadrat.8 328   Rarefaction       0 13.644876 12.170236 15.11952 0.9950884
## 27  Quadrat.8 427   Rarefaction       0 13.997664 12.319783 15.67554 0.9976636
## 28  Quadrat.8 428      Observed       0 14.000000 12.320031 15.67997 0.9976852
## 29  Quadrat.8 429 Extrapolation       0 14.002315 12.319689 15.68494 0.9977067
## 30  Quadrat.9  81   Rarefaction       0 15.951220 13.484923 18.41752 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 13.519239 18.48076 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 13.551910 18.54273 0.9540968
## 33  Quadrat.9 328 Extrapolation       0 17.579594 10.778431 24.38076 0.9999732
## 34 Quadrat.10 249   Rarefaction       0  9.992000  8.215777 11.76822 0.9920000
## 35 Quadrat.10 250      Observed       0 10.000000  8.218564 11.78144 0.9920320
## 36 Quadrat.10 251 Extrapolation       0 10.007968  8.220878 11.79506 0.9920639
## 37 Quadrat.10 328 Extrapolation       0 10.534805  8.348388 12.72122 0.9941712
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.275518 13.72448 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.274170 13.72583 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.272885 13.72712 1.0000000
## 41 Quadrat.11 328 Extrapolation       0 13.000000 11.674338 14.32566 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9765253 1.0000000
## 2  0.9760040 1.0000000
## 3  0.9762177 1.0000000
## 4  0.9932847 1.0000000
## 5  0.9959869 1.0000000
## 6  0.9976253 1.0000000
## 7  0.9979072 1.0000000
## 8  0.9979172 1.0000000
## 9  0.9827801 0.9944783
## 10 0.9827880 0.9947905
## 11 0.9826251 0.9949786
## 12 0.9826351 0.9949937
## 13 0.9809641 0.9986278
## 14 0.9804404 0.9991977
## 15 0.9804752 0.9992092
## 16 0.9815915 0.9995608
## 17 0.9799763 0.9983631
## 18 0.9800979 0.9985000
## 19 0.9802185 0.9986348
## 20 0.9852341 1.0000000
## 21 0.9869827 0.9964736
## 22 0.9884649 0.9986041
## 23 0.9883112 0.9987763
## 24 0.9883181 0.9987881
## 25 0.9826840 0.9992079
## 26 0.9905507 0.9996261
## 27 0.9930156 1.0000000
## 28 0.9926981 1.0000000
## 29 0.9927282 1.0000000
## 30 0.9152091 0.9872299
## 31 0.9164324 0.9889276
## 32 0.9176298 0.9905637
## 33 0.9866159 1.0000000
## 34 0.9838557 1.0000000
## 35 0.9835682 1.0000000
## 36 0.9836374 1.0000000
## 37 0.9878438 1.0000000
## 38 0.9895790 1.0000000
## 39 0.9889572 1.0000000
## 40 0.9890594 1.0000000
## 41 0.9967933 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  6.350156 13.62191
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  6.353431 13.64657
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  6.350019 13.66490
## 4   Quadrat.1 0.9996171 328 Extrapolation       0 10.470749  6.064690 14.87681
## 5   Quadrat.2 0.9983142 328   Rarefaction       0 13.913256 12.940456 14.88606
## 6   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.906851 15.09315
## 7   Quadrat.3 0.9886292 328   Rarefaction       0 12.672411  8.088191 17.25663
## 8   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  9.211835 18.74382
## 9   Quadrat.3 0.9888018 446      Observed       0 14.000000  9.223365 18.77664
## 10  Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  9.226325 18.79607
## 11  Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  6.581249 17.38400
## 12  Quadrat.4 0.9898191 294      Observed       0 12.000000  6.590727 17.40927
## 13  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  6.592013 17.42835
## 14  Quadrat.4 0.9905762 328 Extrapolation       0 12.333494  6.679850 17.98714
## 15  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 15.781222 22.18492
## 16  Quadrat.5 0.9892989 277      Observed       0 19.000000 15.785149 22.21485
## 17  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 15.782287 22.23912
## 18  Quadrat.5 0.9941986 328 Extrapolation       0 19.410597 15.530480 23.29071
## 19  Quadrat.6 0.9917281 328   Rarefaction       0  9.010393  4.273471 13.74731
## 20  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  4.610228 15.37026
## 21  Quadrat.6 0.9935438 464      Observed       0 10.000000  4.616221 15.38378
## 22  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  4.619308 15.39360
## 23  Quadrat.7 0.9909460 328      Observed       0 15.000000  9.889373 20.11063
## 24  Quadrat.8 0.9950884 328   Rarefaction       0 13.644876 10.926474 16.36328
## 25  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 10.637019 17.35618
## 26  Quadrat.8 0.9976852 428      Observed       0 14.000000 10.632764 17.36724
## 27  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 10.627684 17.37695
## 28  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 11.213881 20.61469
## 29  Quadrat.9 0.9526800  82      Observed       0 16.000000 11.193484 20.80652
## 30  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320 11.130334 20.96431
## 31  Quadrat.9 0.9999732 328 Extrapolation       0 17.579594  8.320654 26.83853
## 32 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  7.245531 12.72251
## 33 Quadrat.10 0.9920320 250      Observed       0 10.000000  7.257415 12.74258
## 34 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  7.261610 12.75433
## 35 Quadrat.10 0.9941712 328 Extrapolation       0 10.534805  7.519126 13.55048
## 36 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.262071 14.73793
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 1.4808701 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4835002  4.154548
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3818604  2.604030
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.3458743 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2592166  3.970488
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.1749467  3.127010
## 7  Quadrat.11  Species richness 13.000000 13.000000 1.0808019 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.6403990  7.779585
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.7350170  5.410713
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.6504519 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3315444  9.322218
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3955002  7.713914
## 13  Quadrat.3  Species richness 14.000000 23.977578 5.8655951 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2995540  5.393050
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2038516  4.111550
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.0977844 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.4072547  5.710080
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.4052129  4.030598
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.8537105 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4723125  4.343526
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2452865  2.292664
## 22  Quadrat.6  Species richness 10.000000 14.490302 3.9778180 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1766655  4.010810
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1251311  3.463992
## 25  Quadrat.7  Species richness 15.000000 15.897256 4.1267435 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3453356  5.900531
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3494425  4.166562
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.3572812 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3250415  5.709548
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2291453  3.935624
## 31  Quadrat.9  Species richness 16.000000 17.580488 6.6242772 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.3294079  6.863553
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.9222336  3.988267
##          UCL
## 1  13.398664
## 2   6.049834
## 3   4.100895
## 4  16.589829
## 5   4.986598
## 6   3.812789
## 7  15.118333
## 8  10.289903
## 9   8.291927
## 10 15.274862
## 11 10.621849
## 12  9.264247
## 13 35.473934
## 14  6.567280
## 15  4.910634
## 16 24.516204
## 17  7.306489
## 18  5.619004
## 19 29.409849
## 20  6.194957
## 21  3.254169
## 22 22.286682
## 23  4.703326
## 24  3.954496
## 25 23.985525
## 26  7.254222
## 27  5.536351
## 28 18.869602
## 29  6.983687
## 30  4.833857
## 31 30.563833
## 32 12.074736
## 33  7.603356
t <- c(428)

Barrow_Datat <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = t)

Barrow_Datat
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.150675 11.83417 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.150762 11.84924 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.150337 11.86459 0.9926504
## 4   Quadrat.1 428 Extrapolation       0 10.490616  7.093026 13.88821 0.9999158
## 5   Quadrat.2 428   Rarefaction       0 13.998741 13.189568 14.80791 0.9998402
## 6   Quadrat.2 443   Rarefaction       0 14.000000 13.180578 14.81942 1.0000000
## 7   Quadrat.2 444      Observed       0 14.000000 13.179849 14.82015 1.0000000
## 8   Quadrat.2 445 Extrapolation       0 14.000000 13.179590 14.82041 1.0000000
## 9   Quadrat.3 428   Rarefaction       0 13.798204 10.990522 16.60589 0.9887888
## 10  Quadrat.3 445   Rarefaction       0 13.988789 11.085706 16.89187 0.9887892
## 11  Quadrat.3 446      Observed       0 14.000000 11.091286 16.90871 0.9888018
## 12  Quadrat.3 447 Extrapolation       0 14.011198 11.096852 16.92554 0.9888144
## 13  Quadrat.4 293   Rarefaction       0 11.989796  9.734338 14.24525 0.9897959
## 14  Quadrat.4 294      Observed       0 12.000000  9.738792 14.26121 0.9898191
## 15  Quadrat.4 295 Extrapolation       0 12.010181  9.743009 14.27735 0.9898422
## 16  Quadrat.4 428 Extrapolation       0 13.177419 10.028401 16.32644 0.9924920
## 17  Quadrat.5 276   Rarefaction       0 18.989170 16.302499 21.67584 0.9891697
## 18  Quadrat.5 277      Observed       0 19.000000 16.307387 21.69261 0.9892989
## 19  Quadrat.5 278 Extrapolation       0 19.010701 16.312126 21.70928 0.9894266
## 20  Quadrat.5 428 Extrapolation       0 19.750396 15.984046 23.51675 0.9982535
## 21  Quadrat.6 428   Rarefaction       0  9.760945  7.200462 12.32143 0.9931727
## 22  Quadrat.6 463   Rarefaction       0  9.993534  7.275104 12.71196 0.9935345
## 23  Quadrat.6 464      Observed       0 10.000000  7.276987 12.72301 0.9935438
## 24  Quadrat.6 465 Extrapolation       0 10.006456  7.278574 12.73434 0.9935531
## 25  Quadrat.7 327   Rarefaction       0 14.990854 12.517304 17.46440 0.9908537
## 26  Quadrat.7 328      Observed       0 15.000000 12.522085 17.47791 0.9909460
## 27  Quadrat.7 329 Extrapolation       0 15.009054 12.526764 17.49134 0.9910373
## 28  Quadrat.7 428 Extrapolation       0 15.571831 12.597111 18.54655 0.9967162
## 29  Quadrat.8 428      Observed       0 14.000000 12.416110 15.58389 0.9976852
## 30  Quadrat.9  81   Rarefaction       0 15.951220 13.406069 18.49637 0.9512195
## 31  Quadrat.9  82      Observed       0 16.000000 13.435027 18.56497 0.9526800
## 32  Quadrat.9  83 Extrapolation       0 16.047320 13.462405 18.63223 0.9540968
## 33  Quadrat.9 428 Extrapolation       0 17.580445  6.990704 28.17019 0.9999987
## 34 Quadrat.10 249   Rarefaction       0  9.992000  7.965281 12.01872 0.9920000
## 35 Quadrat.10 250      Observed       0 10.000000  7.969699 12.03030 0.9920320
## 36 Quadrat.10 251 Extrapolation       0 10.007968  7.973576 12.04236 0.9920639
## 37 Quadrat.10 428 Extrapolation       0 11.015996  8.299931 13.73206 0.9960960
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.067056 13.93294 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.066311 13.93369 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.065862 13.93414 1.0000000
## 41 Quadrat.11 428 Extrapolation       0 13.000000 11.805532 14.19447 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9773983 1.0000000
## 2  0.9768375 1.0000000
## 3  0.9770519 1.0000000
## 4  0.9968388 1.0000000
## 5  0.9975221 1.0000000
## 6  0.9976404 1.0000000
## 7  0.9980155 1.0000000
## 8  0.9980251 1.0000000
## 9  0.9823575 0.9952202
## 10 0.9823105 0.9952680
## 11 0.9823252 0.9952785
## 12 0.9823398 0.9952889
## 13 0.9810425 0.9985494
## 14 0.9808600 0.9987782
## 15 0.9808834 0.9988010
## 16 0.9844551 1.0000000
## 17 0.9783356 1.0000000
## 18 0.9784357 1.0000000
## 19 0.9785349 1.0000000
## 20 0.9870606 1.0000000
## 21 0.9869838 0.9993616
## 22 0.9870893 0.9999797
## 23 0.9868546 1.0000000
## 24 0.9868639 1.0000000
## 25 0.9815807 1.0000000
## 26 0.9816697 1.0000000
## 27 0.9817579 1.0000000
## 28 0.9877761 1.0000000
## 29 0.9932647 1.0000000
## 30 0.9096346 0.9928045
## 31 0.9109715 0.9943885
## 32 0.9122692 0.9959243
## 33 0.9840312 1.0000000
## 34 0.9843039 0.9996961
## 35 0.9838208 1.0000000
## 36 0.9838714 1.0000000
## 37 0.9909968 1.0000000
## 38 0.9919660 1.0000000
## 39 0.9919452 1.0000000
## 40 0.9920628 1.0000000
## 41 0.9993720 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  6.821859 13.15021
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  6.826863 13.17314
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  6.824758 13.19017
## 4   Quadrat.1 0.9999158 428 Extrapolation       0 10.490616  6.640439 14.34079
## 5   Quadrat.2 0.9998402 428   Rarefaction       0 13.998741 13.040674 14.95681
## 6   Quadrat.2 1.0000000 444      Observed       0 14.000000 13.029335 14.97066
## 7   Quadrat.3 0.9887888 428   Rarefaction       0 13.798204  9.234420 18.36199
## 8   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  9.389321 18.56633
## 9   Quadrat.3 0.9888018 446      Observed       0 14.000000  9.400716 18.59928
## 10  Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  9.403202 18.61919
## 11  Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  7.119110 16.84614
## 12  Quadrat.4 0.9898191 294      Observed       0 12.000000  7.129064 16.87094
## 13  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  7.133788 16.88657
## 14  Quadrat.4 0.9924920 428 Extrapolation       0 13.177419  7.580733 18.77410
## 15  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 12.079392 25.88675
## 16  Quadrat.5 0.9892989 277      Observed       0 19.000000 12.050788 25.94921
## 17  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 12.015236 26.00617
## 18  Quadrat.5 0.9982535 428 Extrapolation       0 19.750396  9.287970 30.21282
## 19  Quadrat.6 0.9931727 428   Rarefaction       0  9.760945  3.590409 15.93148
## 20  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  3.748607 16.23188
## 21  Quadrat.6 0.9935438 464      Observed       0 10.000000  3.753276 16.24672
## 22  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  3.760261 16.25265
## 23  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227  9.262501 20.71395
## 24  Quadrat.7 0.9909460 328      Observed       0 15.000000  9.240582 20.75942
## 25  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054  9.214600 20.80351
## 26  Quadrat.7 0.9967162 428 Extrapolation       0 15.571831  7.471680 23.67198
## 27  Quadrat.8 0.9976852 428      Observed       0 14.000000 10.823728 17.17627
## 28  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285  6.668987 25.15958
## 29  Quadrat.9 0.9526800  82      Observed       0 16.000000  6.588218 25.41178
## 30  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320  6.468038 25.62660
## 31  Quadrat.9 0.9999987 428 Extrapolation       0 17.580445  2.233744 32.92715
## 32 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  7.003610 12.96443
## 33 Quadrat.10 0.9920320 250      Observed       0 10.000000  7.015918 12.98408
## 34 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  7.020238 12.99570
## 35 Quadrat.10 0.9960960 428 Extrapolation       0 11.015996  7.513184 14.51881
## 36 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.757867 14.24213
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.1466037 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.5421276  4.039641
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.4317057  2.506335
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.7853945 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.3035166  3.883661
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2101454  3.058022
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.8359788 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.6249780  7.809809
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6616427  5.554524
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.6000247 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3223145  9.340309
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3587838  7.785877
## 13  Quadrat.3  Species richness 14.000000 23.977578 7.0772531 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2864539  5.418725
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.1993733  4.120327
## 16  Quadrat.4  Species richness 12.000000 16.484694 3.6809820 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3310258  5.859486
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3259169  4.186016
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.8096428 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4437428  4.399522
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2397825  2.303451
## 22  Quadrat.6  Species richness 10.000000 14.490302 5.5091242 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1562083  4.050906
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1215810  3.470950
## 25  Quadrat.7  Species richness 15.000000 15.897256 4.6892455 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3484281  5.894470
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3188282  4.226565
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.0126841 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3542168  5.652365
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2486453  3.897405
## 31  Quadrat.9  Species richness 16.000000 17.580488 6.1031587 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.2995824  6.922010
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.9715625  3.891584
##          UCL
## 1  14.703478
## 2   6.164741
## 3   4.198590
## 4  17.451273
## 5   5.073424
## 6   3.881777
## 7  14.638488
## 8  10.259678
## 9   8.148116
## 10 15.176027
## 11 10.603758
## 12  9.192284
## 13 37.848740
## 14  6.541604
## 15  4.901856
## 16 23.699286
## 17  7.157083
## 18  5.463587
## 19 29.323478
## 20  6.138962
## 21  3.243382
## 22 25.287987
## 23  4.663231
## 24  3.947538
## 25 25.088008
## 26  7.260283
## 27  5.476348
## 28 18.194204
## 29  7.040870
## 30  4.872077
## 31 29.542459
## 32 12.016279
## 33  7.700039
u <- c(82)

Barrow_Datau <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = u)

Barrow_Datau
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat.1  82   Rarefaction       0  9.369742  8.372033 10.367451 0.9789969
## 2   Quadrat.1 131   Rarefaction       0  9.992424  8.615770 11.369079 0.9924242
## 3   Quadrat.1 132      Observed       0 10.000000  8.614096 11.385904 0.9925382
## 4   Quadrat.1 133 Extrapolation       0 10.007462  8.611068 11.403856 0.9926504
## 5   Quadrat.2  82   Rarefaction       0 12.036400 11.174665 12.898136 0.9778099
## 6   Quadrat.2 443   Rarefaction       0 14.000000 13.114614 14.885386 1.0000000
## 7   Quadrat.2 444      Observed       0 14.000000 13.114579 14.885421 1.0000000
## 8   Quadrat.2 445 Extrapolation       0 14.000000 13.114297 14.885703 1.0000000
## 9   Quadrat.3  82   Rarefaction       0  9.243779  8.294161 10.193397 0.9756266
## 10  Quadrat.3 445   Rarefaction       0 13.988789 10.533131 17.444447 0.9887892
## 11  Quadrat.3 446      Observed       0 14.000000 10.538013 17.461987 0.9888018
## 12  Quadrat.3 447 Extrapolation       0 14.011198 10.542545 17.479851 0.9888144
## 13  Quadrat.4  82   Rarefaction       0  9.193435  8.189549 10.197322 0.9798275
## 14  Quadrat.4 293   Rarefaction       0 11.989796  9.311165 14.668427 0.9897959
## 15  Quadrat.4 294      Observed       0 12.000000  9.314384 14.685616 0.9898191
## 16  Quadrat.4 295 Extrapolation       0 12.010181  9.317161 14.703201 0.9898422
## 17  Quadrat.5  82   Rarefaction       0 12.591493 11.055619 14.127367 0.9305785
## 18  Quadrat.5 276   Rarefaction       0 18.989170 16.476746 21.501594 0.9891697
## 19  Quadrat.5 277      Observed       0 19.000000 16.482848 21.517152 0.9892989
## 20  Quadrat.5 278 Extrapolation       0 19.010701 16.488796 21.532606 0.9894266
## 21  Quadrat.6  82   Rarefaction       0  6.087174  5.224966  6.949383 0.9812474
## 22  Quadrat.6 463   Rarefaction       0  9.993534  6.936414 13.050655 0.9935345
## 23  Quadrat.6 464      Observed       0 10.000000  6.937670 13.062330 0.9935438
## 24  Quadrat.6 465 Extrapolation       0 10.006456  6.938918 13.073994 0.9935531
## 25  Quadrat.7  82   Rarefaction       0  9.832873  8.840568 10.825177 0.9636396
## 26  Quadrat.7 327   Rarefaction       0 14.990854 12.973185 17.008522 0.9908537
## 27  Quadrat.7 328      Observed       0 15.000000 12.980540 17.019460 0.9909460
## 28  Quadrat.7 329 Extrapolation       0 15.009054 12.987799 17.030309 0.9910373
## 29  Quadrat.8  82   Rarefaction       0 10.638591  9.905958 11.371224 0.9694677
## 30  Quadrat.8 427   Rarefaction       0 13.997664 12.577512 15.417815 0.9976636
## 31  Quadrat.8 428      Observed       0 14.000000 12.578354 15.421646 0.9976852
## 32  Quadrat.8 429 Extrapolation       0 14.002315 12.578898 15.425732 0.9977067
## 33  Quadrat.9  82      Observed       0 16.000000 13.125720 18.874280 0.9526800
## 34 Quadrat.10  82   Rarefaction       0  7.785099  6.567201  9.002998 0.9736181
## 35 Quadrat.10 249   Rarefaction       0  9.992000  7.908601 12.075399 0.9920000
## 36 Quadrat.10 250      Observed       0 10.000000  7.911831 12.088169 0.9920320
## 37 Quadrat.10 251 Extrapolation       0 10.007968  7.914587 12.101349 0.9920639
## 38 Quadrat.11  82   Rarefaction       0 12.495443 11.546883 13.444003 0.9789548
## 39 Quadrat.11 154   Rarefaction       0 13.000000 12.011720 13.988280 1.0000000
## 40 Quadrat.11 155      Observed       0 13.000000 12.010069 13.989931 1.0000000
## 41 Quadrat.11 156 Extrapolation       0 13.000000 12.007614 13.992386 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9654625 0.9925314
## 2  0.9774583 1.0000000
## 3  0.9761011 1.0000000
## 4  0.9763565 1.0000000
## 5  0.9726329 0.9829869
## 6  0.9972891 1.0000000
## 7  0.9975582 1.0000000
## 8  0.9975684 1.0000000
## 9  0.9654898 0.9857633
## 10 0.9814551 0.9961234
## 11 0.9811523 0.9964513
## 12 0.9811652 0.9964636
## 13 0.9688220 0.9908330
## 14 0.9812522 0.9983396
## 15 0.9808697 0.9987685
## 16 0.9809017 0.9987827
## 17 0.9176199 0.9435372
## 18 0.9768262 1.0000000
## 19 0.9769241 1.0000000
## 20 0.9770221 1.0000000
## 21 0.9730535 0.9894413
## 22 0.9874019 0.9996670
## 23 0.9874139 0.9996737
## 24 0.9874258 0.9996803
## 25 0.9527795 0.9744997
## 26 0.9843290 0.9973783
## 27 0.9844034 0.9974885
## 28 0.9844775 0.9975971
## 29 0.9618515 0.9770839
## 30 0.9935096 1.0000000
## 31 0.9930490 1.0000000
## 32 0.9930794 1.0000000
## 33 0.9220018 0.9833582
## 34 0.9626013 0.9846349
## 35 0.9834060 1.0000000
## 36 0.9828295 1.0000000
## 37 0.9828941 1.0000000
## 38 0.9677251 0.9901846
## 39 0.9915696 1.0000000
## 40 0.9915368 1.0000000
## 41 0.9916362 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat.1 0.9789970  82   Rarefaction       0  9.369742  7.605502 11.133982
## 2   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  7.418653 12.553415
## 3   Quadrat.1 0.9925382 132      Observed       0 10.000000  7.423962 12.576038
## 4   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  7.422546 12.592377
## 5   Quadrat.2 0.9778099  82   Rarefaction       0 12.036400 11.023793 13.049007
## 6   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.809820 15.190180
## 7   Quadrat.3 0.9756266  82   Rarefaction       0  9.243779  7.494770 10.992789
## 8   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  7.104981 20.850670
## 9   Quadrat.3 0.9888018 446      Observed       0 14.000000  7.115227 20.884773
## 10  Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  7.117189 20.905208
## 11  Quadrat.4 0.9798275  82   Rarefaction       0  9.193435  6.516967 11.869903
## 12  Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  6.606749 17.358505
## 13  Quadrat.4 0.9898191 294      Observed       0 12.000000  6.617222 17.382778
## 14  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  6.622603 17.397759
## 15  Quadrat.5 0.9305786  82   Rarefaction       0 12.591494 10.276025 14.906963
## 16  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 12.192666 25.773479
## 17  Quadrat.5 0.9892989 277      Observed       0 19.000000 12.172887 25.827113
## 18  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 12.146440 25.874962
## 19  Quadrat.6 0.9812474  82   Rarefaction       0  6.087174  4.037724  8.136624
## 20  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  3.927639 16.052850
## 21  Quadrat.6 0.9935438 464      Observed       0 10.000000  3.932555 16.067445
## 22  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  3.935631 16.077282
## 23  Quadrat.7 0.9636396  82   Rarefaction       0  9.832873  8.052113 11.613634
## 24  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227 12.305920 17.670535
## 25  Quadrat.7 0.9909460 328      Observed       0 15.000000 12.307568 17.692432
## 26  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054 12.306645 17.711463
## 27  Quadrat.8 0.9694677  82   Rarefaction       0 10.638590  9.578877 11.698304
## 28  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 11.454806 16.538397
## 29  Quadrat.8 0.9976852 428      Observed       0 14.000000 11.452807 16.547193
## 30  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 11.449453 16.555177
## 31  Quadrat.9 0.9526800  82      Observed       0 16.000000 11.397534 20.602466
## 32 Quadrat.10 0.9736181  82   Rarefaction       0  7.785099  5.930088  9.640111
## 33 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  6.793951 13.174090
## 34 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.806186 13.193814
## 35 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  6.811258 13.204678
## 36 Quadrat.11 0.9789548  82   Rarefaction       0 12.495442 11.468799 13.522086
## 37 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.432998 14.567002
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.0948322 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4751740  4.170867
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.4046256  2.559411
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.3101542 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2882326  3.913617
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2007838  3.076371
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.7191506 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.6102839  7.838609
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6750930  5.528162
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.7064862 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3138902  9.356820
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3561738  7.790993
## 13  Quadrat.3  Species richness 14.000000 23.977578 6.5853223 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.3069445  5.378564
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2216660  4.076634
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.5542727 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3586237  5.805395
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3706839  4.098274
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.5841548 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4493587  4.388515
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2285722  2.325423
## 22  Quadrat.6  Species richness 10.000000 14.490302 4.3337488 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1842178  3.996008
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1463227  3.422457
## 25  Quadrat.7  Species richness 15.000000 15.897256 4.4419834 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3347627  5.921254
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3258281  4.212845
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.1471903 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3358796  5.688306
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2520206  3.890790
## 31  Quadrat.9  Species richness 16.000000 17.580488 4.4825554 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.2304081  7.057589
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.9557967  3.922484
##          UCL
## 1  14.602008
## 2   6.033515
## 3   4.145514
## 4  16.519819
## 5   5.043468
## 6   3.863429
## 7  14.409509
## 8  10.230878
## 9   8.174478
## 10 15.384688
## 11 10.587247
## 12  9.187169
## 13 36.884573
## 14  6.581765
## 15  4.945549
## 16 25.410904
## 17  7.211174
## 18  5.551328
## 19 28.881529
## 20  6.149969
## 21  3.221410
## 22 22.984293
## 23  4.718129
## 24  3.996031
## 25 24.603384
## 26  7.233499
## 27  5.490068
## 28 18.457831
## 29  7.004929
## 30  4.878692
## 31 26.366135
## 32 11.880700
## 33  7.669139
v <- c(250)

Barrow_Datav <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = v)

Barrow_Datav
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.176209 11.80864 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.176376 11.82362 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.175475 11.83945 0.9926504
## 4   Quadrat.1 250 Extrapolation       0 10.413191  7.640724 13.18566 0.9987516
## 5   Quadrat.2 250   Rarefaction       0 13.704789 12.717929 14.69165 0.9961519
## 6   Quadrat.2 443   Rarefaction       0 14.000000 13.045598 14.95440 1.0000000
## 7   Quadrat.2 444      Observed       0 14.000000 13.045550 14.95445 1.0000000
## 8   Quadrat.2 445 Extrapolation       0 14.000000 13.045005 14.95499 1.0000000
## 9   Quadrat.3 250   Rarefaction       0 11.765789  9.841516 13.69006 0.9880285
## 10  Quadrat.3 445   Rarefaction       0 13.988789 11.035003 16.94258 0.9887892
## 11  Quadrat.3 446      Observed       0 14.000000 11.041049 16.95895 0.9888018
## 12  Quadrat.3 447 Extrapolation       0 14.011198 11.046793 16.97560 0.9888144
## 13  Quadrat.4 250   Rarefaction       0 11.529057  8.838548 14.21957 0.9887975
## 14  Quadrat.4 293   Rarefaction       0 11.989796  8.947024 15.03257 0.9897959
## 15  Quadrat.4 294      Observed       0 12.000000  8.949212 15.05079 0.9898191
## 16  Quadrat.4 295 Extrapolation       0 12.010181  8.950984 15.06938 0.9898422
## 17  Quadrat.5 250   Rarefaction       0 18.658257 16.448275 20.86824 0.9853869
## 18  Quadrat.5 276   Rarefaction       0 18.989170 16.638893 21.33945 0.9891697
## 19  Quadrat.5 277      Observed       0 19.000000 16.643714 21.35629 0.9892989
## 20  Quadrat.5 278 Extrapolation       0 19.010701 16.648364 21.37304 0.9894266
## 21  Quadrat.6 250   Rarefaction       0  8.304937  6.595163 10.01471 0.9901154
## 22  Quadrat.6 463   Rarefaction       0  9.993534  7.503516 12.48355 0.9935345
## 23  Quadrat.6 464      Observed       0 10.000000  7.506945 12.49306 0.9935438
## 24  Quadrat.6 465 Extrapolation       0 10.006456  7.510169 12.50274 0.9935531
## 25  Quadrat.7 250   Rarefaction       0 14.006600 11.812466 16.20073 0.9836745
## 26  Quadrat.7 327   Rarefaction       0 14.990854 12.406670 17.57504 0.9908537
## 27  Quadrat.7 328      Observed       0 15.000000 12.410691 17.58931 0.9909460
## 28  Quadrat.7 329 Extrapolation       0 15.009054 12.414619 17.60349 0.9910373
## 29  Quadrat.8 250   Rarefaction       0 13.154051 11.683922 14.62418 0.9921715
## 30  Quadrat.8 427   Rarefaction       0 13.997664 12.208921 15.78641 0.9976636
## 31  Quadrat.8 428      Observed       0 14.000000 12.209784 15.79022 0.9976852
## 32  Quadrat.8 429 Extrapolation       0 14.002315 12.210006 15.79462 0.9977067
## 33  Quadrat.9  81   Rarefaction       0 15.951220 12.742779 19.15966 0.9512195
## 34  Quadrat.9  82      Observed       0 16.000000 12.773128 19.22687 0.9526800
## 35  Quadrat.9  83 Extrapolation       0 16.047320 12.801873 19.29277 0.9540968
## 36  Quadrat.9 250 Extrapolation       0 17.570917 10.985552 24.15628 0.9997135
## 37 Quadrat.10 250      Observed       0 10.000000  8.184994 11.81501 0.9920320
## 38 Quadrat.11 154   Rarefaction       0 13.000000 12.210185 13.78982 1.0000000
## 39 Quadrat.11 155      Observed       0 13.000000 12.208055 13.79195 1.0000000
## 40 Quadrat.11 156 Extrapolation       0 13.000000 12.205756 13.79424 1.0000000
## 41 Quadrat.11 250 Extrapolation       0 13.000000 11.976383 14.02362 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9779878 1.0000000
## 2  0.9770971 1.0000000
## 3  0.9772848 1.0000000
## 4  0.9903472 1.0000000
## 5  0.9935029 0.9988008
## 6  0.9971573 1.0000000
## 7  0.9972059 1.0000000
## 8  0.9972164 1.0000000
## 9  0.9818862 0.9941708
## 10 0.9827311 0.9948473
## 11 0.9824005 0.9952031
## 12 0.9824141 0.9952147
## 13 0.9791925 0.9984026
## 14 0.9802685 0.9993234
## 15 0.9796923 0.9999459
## 16 0.9797222 0.9999622
## 17 0.9730692 0.9977046
## 18 0.9762970 1.0000000
## 19 0.9764110 1.0000000
## 20 0.9765239 1.0000000
## 21 0.9850142 0.9952167
## 22 0.9890382 0.9980308
## 23 0.9888772 0.9982103
## 24 0.9888856 0.9982205
## 25 0.9761898 0.9911591
## 26 0.9829143 0.9987930
## 27 0.9830040 0.9988879
## 28 0.9830930 0.9989817
## 29 0.9880204 0.9963226
## 30 0.9937811 1.0000000
## 31 0.9933283 1.0000000
## 32 0.9933606 1.0000000
## 33 0.9086783 0.9937607
## 34 0.9099446 0.9954154
## 35 0.9111985 0.9969950
## 36 0.9808000 1.0000000
## 37 0.9833439 1.0000000
## 38 0.9916201 1.0000000
## 39 0.9915815 1.0000000
## 40 0.9916942 1.0000000
## 41 0.9967949 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  6.575078 13.39699
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  6.578120 13.42188
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  6.575502 13.43942
## 4   Quadrat.1 0.9987516 250 Extrapolation       0 10.413191  6.356522 14.46986
## 5   Quadrat.2 0.9961519 250   Rarefaction       0 13.704789 12.652275 14.75730
## 6   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.638204 15.36180
## 7   Quadrat.3 0.9880285 250   Rarefaction       0 11.765789  7.032712 16.49887
## 8   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  8.740290 19.21536
## 9   Quadrat.3 0.9888018 446      Observed       0 14.000000  8.754096 19.24590
## 10  Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  8.756566 19.26583
## 11  Quadrat.4 0.9887975 250   Rarefaction       0 11.529057  5.372341 17.68577
## 12  Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  5.509529 18.45572
## 13  Quadrat.4 0.9898191 294      Observed       0 12.000000  5.518546 18.48145
## 14  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  5.521800 18.49856
## 15  Quadrat.5 0.9853869 250   Rarefaction       0 18.658258 11.055331 26.26118
## 16  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073  9.933082 28.03306
## 17  Quadrat.5 0.9892989 277      Observed       0 19.000000  9.900010 28.09999
## 18  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701  9.860693 28.16071
## 19  Quadrat.6 0.9901154 250   Rarefaction       0  8.304937  4.413161 12.19671
## 20  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  4.967735 15.01275
## 21  Quadrat.6 0.9935438 464      Observed       0 10.000000  4.974385 15.02561
## 22  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  4.977841 15.03507
## 23  Quadrat.7 0.9836745 250   Rarefaction       0 14.006601 10.750578 17.26262
## 24  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227 10.646124 19.33033
## 25  Quadrat.7 0.9909460 328      Observed       0 15.000000 10.639966 19.36003
## 26  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054 10.630795 19.38731
## 27  Quadrat.8 0.9921715 250   Rarefaction       0 13.154051 11.270230 15.03787
## 28  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 11.425184 16.56802
## 29  Quadrat.8 0.9976852 428      Observed       0 14.000000 11.423923 16.57608
## 30  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 11.421263 16.58337
## 31  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285 10.044336 21.78423
## 32  Quadrat.9 0.9526800  82      Observed       0 16.000000 10.036285 21.96371
## 33  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320  9.987439 22.10720
## 34  Quadrat.9 0.9997135 250 Extrapolation       0 17.570917  7.626757 27.51508
## 35 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.449104 13.55090
## 36 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.698419 14.30158
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.1625385 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4289952  4.261376
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3570763  2.652606
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.6398377 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2950965  3.900164
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2016699  3.074634
## 7  Quadrat.11  Species richness 13.000000 13.000000 1.1025409 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.5700803  7.917407
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6431139  5.590840
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.6030844 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3072883  9.369760
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3513734  7.800401
## 13  Quadrat.3  Species richness 14.000000 23.977578 5.7617000 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2870810  5.417496
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2221880  4.075611
## 16  Quadrat.4  Species richness 12.000000 16.484694 3.5548090 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3426849  5.836634
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3625224  4.114270
## 19  Quadrat.5  Species richness 19.000000 19.896751 5.0310282 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4038897  4.477632
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2266202  2.329249
## 22  Quadrat.6  Species richness 10.000000 14.490302 4.7309019 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1560610  4.051194
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1077215  3.498114
## 25  Quadrat.7  Species richness 15.000000 15.897256 3.8417911 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3533476  5.884828
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3043231  4.254994
## 28  Quadrat.8  Species richness 14.000000 14.249416 2.1905441 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3468298  5.666844
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2624180  3.870411
## 31  Quadrat.9  Species richness 16.000000 17.580488 4.2662770 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.3977491  6.729606
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 1.0293562  3.778310
##          UCL
## 1  14.734710
## 2   5.943006
## 3   4.052319
## 4  17.165987
## 5   5.056921
## 6   3.865165
## 7  15.160940
## 8  10.152081
## 9   8.111800
## 10 15.182024
## 11 10.574308
## 12  9.177760
## 13 35.270303
## 14  6.542833
## 15  4.946572
## 16 23.451991
## 17  7.179935
## 18  5.535332
## 19 29.757385
## 20  6.060851
## 21  3.217584
## 22 23.762699
## 23  4.662942
## 24  3.920374
## 25 23.427028
## 26  7.269925
## 27  5.447919
## 28 18.542803
## 29  7.026391
## 30  4.899071
## 31 25.942237
## 32 12.208682
## 33  7.813313
w <- c(155)

Barrow_Dataw <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance", size = w)

Barrow_Dataw
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat.1 131   Rarefaction       0  9.992424  8.472332 11.512517 0.9924242
## 2   Quadrat.1 132      Observed       0 10.000000  8.474606 11.525394 0.9925382
## 3   Quadrat.1 133 Extrapolation       0 10.007462  8.475735 11.539189 0.9926504
## 4   Quadrat.1 155 Extrapolation       0 10.146009  8.474784 11.817235 0.9947338
## 5   Quadrat.2 155   Rarefaction       0 13.106420 12.382329 13.830510 0.9904352
## 6   Quadrat.2 443   Rarefaction       0 14.000000 13.180578 14.819422 1.0000000
## 7   Quadrat.2 444      Observed       0 14.000000 13.179849 14.820151 1.0000000
## 8   Quadrat.2 445 Extrapolation       0 14.000000 13.179140 14.820860 1.0000000
## 9   Quadrat.3 155   Rarefaction       0 10.541638  8.943204 12.140073 0.9857132
## 10  Quadrat.3 445   Rarefaction       0 13.988789 10.689756 17.287822 0.9887892
## 11  Quadrat.3 446      Observed       0 14.000000 10.696298 17.303702 0.9888018
## 12  Quadrat.3 447 Extrapolation       0 14.011198 10.702596 17.319801 0.9888144
## 13  Quadrat.4 155   Rarefaction       0 10.355688  8.722049 11.989327 0.9863965
## 14  Quadrat.4 293   Rarefaction       0 11.989796  9.280091 14.699501 0.9897959
## 15  Quadrat.4 294      Observed       0 12.000000  9.282751 14.717249 0.9898191
## 16  Quadrat.4 295 Extrapolation       0 12.010181  9.284268 14.736094 0.9898422
## 17  Quadrat.5 155   Rarefaction       0 16.331555 14.570183 18.092927 0.9634357
## 18  Quadrat.5 276   Rarefaction       0 18.989170 16.825794 21.152545 0.9891697
## 19  Quadrat.5 277      Observed       0 19.000000 16.831169 21.168831 0.9892989
## 20  Quadrat.5 278 Extrapolation       0 19.010701 16.836366 21.185036 0.9894266
## 21  Quadrat.6 155   Rarefaction       0  7.227255  6.084267  8.370243 0.9868378
## 22  Quadrat.6 463   Rarefaction       0  9.993534  7.490801 12.496268 0.9935345
## 23  Quadrat.6 464      Observed       0 10.000000  7.492834 12.507166 0.9935438
## 24  Quadrat.6 465 Extrapolation       0 10.006456  7.494692 12.518220 0.9935531
## 25  Quadrat.7 155   Rarefaction       0 12.027598 10.340229 13.714967 0.9746475
## 26  Quadrat.7 327   Rarefaction       0 14.990854 12.663657 17.318050 0.9908537
## 27  Quadrat.7 328      Observed       0 15.000000 12.669474 17.330526 0.9909460
## 28  Quadrat.7 329 Extrapolation       0 15.009054 12.675189 17.342919 0.9910373
## 29  Quadrat.8 155   Rarefaction       0 12.140675 11.157105 13.124244 0.9856570
## 30  Quadrat.8 427   Rarefaction       0 13.997664 12.495767 15.499560 0.9976636
## 31  Quadrat.8 428      Observed       0 14.000000 12.495304 15.504696 0.9976852
## 32  Quadrat.8 429 Extrapolation       0 14.002315 12.494810 15.509820 0.9977067
## 33  Quadrat.9  81   Rarefaction       0 15.951220 13.335624 18.566815 0.9512195
## 34  Quadrat.9  82      Observed       0 16.000000 13.368644 18.631356 0.9526800
## 35  Quadrat.9  83 Extrapolation       0 16.047320 13.399879 18.694761 0.9540968
## 36  Quadrat.9 155 Extrapolation       0 17.408663 12.821285 21.996042 0.9948556
## 37 Quadrat.10 155   Rarefaction       0  9.074264  7.413476 10.735052 0.9878047
## 38 Quadrat.10 249   Rarefaction       0  9.992000  7.893164 12.090836 0.9920000
## 39 Quadrat.10 250      Observed       0 10.000000  7.896868 12.103132 0.9920320
## 40 Quadrat.10 251 Extrapolation       0 10.007968  7.899688 12.116248 0.9920639
## 41 Quadrat.11 155      Observed       0 13.000000 12.154434 13.845566 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9783029 1.0000000
## 2  0.9774163 1.0000000
## 3  0.9776294 1.0000000
## 4  0.9816178 1.0000000
## 5  0.9869781 0.9938923
## 6  0.9976404 1.0000000
## 7  0.9977807 1.0000000
## 8  0.9977910 1.0000000
## 9  0.9770797 0.9943467
## 10 0.9827026 0.9948759
## 11 0.9825195 0.9950841
## 12 0.9825334 0.9950954
## 13 0.9774183 0.9953747
## 14 0.9806374 0.9989545
## 15 0.9795775 1.0000000
## 16 0.9796163 1.0000000
## 17 0.9531774 0.9736940
## 18 0.9773817 1.0000000
## 19 0.9774887 1.0000000
## 20 0.9775954 1.0000000
## 21 0.9807809 0.9928948
## 22 0.9877409 0.9993281
## 23 0.9876209 0.9994667
## 24 0.9876296 0.9994765
## 25 0.9666717 0.9826233
## 26 0.9833329 0.9983744
## 27 0.9834233 0.9984686
## 28 0.9835129 0.9985617
## 29 0.9812191 0.9900950
## 30 0.9925827 1.0000000
## 31 0.9923919 1.0000000
## 32 0.9924258 1.0000000
## 33 0.9085032 0.9939358
## 34 0.9096361 0.9957239
## 35 0.9107531 0.9974405
## 36 0.9550277 1.0000000
## 37 0.9792461 0.9963634
## 38 0.9842147 0.9997853
## 39 0.9834705 1.0000000
## 40 0.9835344 1.0000000
## 41 0.9889934 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9924242 130   Rarefaction       0  9.986034  7.409951 12.56212
## 2   Quadrat.1 0.9925382 132      Observed       0 10.000000  7.418019 12.58198
## 3   Quadrat.1 0.9926504 133 Extrapolation       0 10.007462  7.419136 12.59579
## 4   Quadrat.1 0.9947338 155 Extrapolation       0 10.146009  7.428549 12.86347
## 5   Quadrat.2 0.9904352 155   Rarefaction       0 13.106420 12.311768 13.90107
## 6   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.830577 15.16942
## 7   Quadrat.3 0.9857132 155   Rarefaction       0 10.541638  6.810449 14.27283
## 8   Quadrat.3 0.9887892 444   Rarefaction       0 13.977826  8.332011 19.62364
## 9   Quadrat.3 0.9888018 446      Observed       0 14.000000  8.338788 19.66121
## 10  Quadrat.3 0.9888144 447 Extrapolation       0 14.011198  8.342526 19.67987
## 11  Quadrat.4 0.9863965 155   Rarefaction       0 10.355688  5.721083 14.99029
## 12  Quadrat.4 0.9897959 292   Rarefaction       0 11.982627  6.296231 17.66902
## 13  Quadrat.4 0.9898191 294      Observed       0 12.000000  6.306039 17.69396
## 14  Quadrat.4 0.9898422 295 Extrapolation       0 12.010181  6.308852 17.71151
## 15  Quadrat.5 0.9634357 155   Rarefaction       0 16.331556 13.933947 18.72916
## 16  Quadrat.5 0.9891697 275   Rarefaction       0 18.983073 11.590621 26.37552
## 17  Quadrat.5 0.9892989 277      Observed       0 19.000000 11.562137 26.43786
## 18  Quadrat.5 0.9894266 278 Extrapolation       0 19.010701 11.526988 26.49441
## 19  Quadrat.6 0.9868378 155   Rarefaction       0  7.227255  4.446078 10.00843
## 20  Quadrat.6 0.9935345 462   Rarefaction       0  9.990245  3.376183 16.60431
## 21  Quadrat.6 0.9935438 464      Observed       0 10.000000  3.381099 16.61890
## 22  Quadrat.6 0.9935531 465 Extrapolation       0 10.006456  3.383119 16.62979
## 23  Quadrat.7 0.9746475 155   Rarefaction       0 12.027598  9.783226 14.27197
## 24  Quadrat.7 0.9908537 327   Rarefaction       0 14.988227 10.596194 19.38026
## 25  Quadrat.7 0.9909460 328      Observed       0 15.000000 10.579796 19.42020
## 26  Quadrat.7 0.9910373 329 Extrapolation       0 15.009054 10.560867 19.45724
## 27  Quadrat.8 0.9856570 155   Rarefaction       0 12.140675 10.804334 13.47702
## 28  Quadrat.8 0.9976636 427   Rarefaction       0 13.996602 11.034594 16.95861
## 29  Quadrat.8 0.9976852 428      Observed       0 14.000000 11.032278 16.96772
## 30  Quadrat.8 0.9977067 429 Extrapolation       0 14.002315 11.028504 16.97613
## 31  Quadrat.9 0.9512195  80   Rarefaction       0 15.914285  7.840092 23.98848
## 32  Quadrat.9 0.9526800  82      Observed       0 16.000000  7.753850 24.24615
## 33  Quadrat.9 0.9540968  83 Extrapolation       0 16.047320  7.627811 24.46683
## 34  Quadrat.9 0.9948556 155 Extrapolation       0 17.408663  3.598220 31.21911
## 35 Quadrat.10 0.9878047 155   Rarefaction       0  9.074264  6.515172 11.63336
## 36 Quadrat.10 0.9920000 248   Rarefaction       0  9.984021  6.899754 13.06829
## 37 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.911284 13.08872
## 38 Quadrat.10 0.9920639 251 Extrapolation       0 10.007968  6.915549 13.10039
## 39 Quadrat.11 1.0000000 155      Observed       0 13.000000 10.995293 15.00471
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 1.6647053 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4946814  4.132633
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.3779525  2.611689
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.7259876 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2972052  3.896031
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2137455  3.050966
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.7701882 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.5107747  8.033644
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.5875749  5.699695
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.5914301 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3365902  9.312329
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.4115809  7.682397
## 13  Quadrat.3  Species richness 14.000000 23.977578 5.7948816 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2980075  5.396081
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2041684  4.110929
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.0380590 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3107510  5.899224
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3099997  4.217213
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.3467184 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4545205  4.378398
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2420023  2.299101
## 22  Quadrat.6  Species richness 10.000000 14.490302 4.7916955 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1664974  4.030739
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1263421  3.461618
## 25  Quadrat.7  Species richness 15.000000 15.897256 4.0916338 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3252257  5.939946
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3072112  4.249334
## 28  Quadrat.8  Species richness 14.000000 14.249416 1.6685024 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3304967  5.698856
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2343654  3.925393
## 31  Quadrat.9  Species richness 16.000000 17.580488 4.9779188 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.0863392  7.339959
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.8907089  4.050054
##          UCL
## 1  13.758975
## 2   6.071749
## 3   4.093235
## 4  17.334837
## 5   5.061054
## 6   3.888833
## 7  14.509541
## 8  10.035844
## 9   8.002946
## 10 15.159182
## 11 10.631738
## 12  9.295764
## 13 35.335338
## 14  6.564249
## 15  4.911255
## 16 24.399144
## 17  7.117345
## 18  5.432390
## 19 28.416162
## 20  6.160085
## 21  3.247732
## 22 23.881852
## 23  4.683397
## 24  3.956870
## 25 23.916711
## 26  7.214807
## 27  5.453579
## 28 17.519621
## 29  6.994379
## 30  4.844089
## 31 27.337029
## 32 11.598330
## 33  7.541569

#Now to run the analysis again without specificying the size, can do this for #looking at the other diversity indices#

Barrow_Data <- iNEXT(Barrow_Nos, q=c(0), datatype= "abundance")

Barrow_Data
## Compare 11 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1    Quadrat.1   1   Rarefaction       0  1.000000  1.000000  1.000000
## 10   Quadrat.1  66   Rarefaction       0  8.947705  7.692405 10.203006
## 20   Quadrat.1 132      Observed       0 10.000000  8.466405 11.533595
## 30   Quadrat.1 195 Extrapolation       0 10.305180  8.438229 12.172132
## 40   Quadrat.1 264 Extrapolation       0 10.429060  8.195026 12.663094
## 41   Quadrat.2   1   Rarefaction       0  1.000000  1.000000  1.000000
## 50   Quadrat.2 222   Rarefaction       0 13.580553 12.741270 14.419837
## 60   Quadrat.2 444      Observed       0 14.000000 13.208055 14.791945
## 70   Quadrat.2 654 Extrapolation       0 14.000000 13.108614 14.891386
## 80   Quadrat.2 888 Extrapolation       0 14.000000 13.023918 14.976082
## 81   Quadrat.3   1   Rarefaction       0  1.000000  1.000000  1.000000
## 90   Quadrat.3 223   Rarefaction       0 11.437408  9.486750 13.388066
## 100  Quadrat.3 446      Observed       0 14.000000 10.703900 17.296100
## 110  Quadrat.3 657 Extrapolation       0 16.104927 11.619869 20.589986
## 120  Quadrat.3 892 Extrapolation       0 17.930966 12.181730 23.680203
## 121  Quadrat.4   1   Rarefaction       0  1.000000  1.000000  1.000000
## 130  Quadrat.4 147   Rarefaction       0 10.245584  8.617076 11.874093
## 140  Quadrat.4 294      Observed       0 12.000000  9.373415 14.626585
## 150  Quadrat.4 433 Extrapolation       0 13.214789  9.787682 16.641895
## 160  Quadrat.4 588 Extrapolation       0 14.185662 10.038285 18.333039
## 161  Quadrat.5   1   Rarefaction       0  1.000000  1.000000  1.000000
## 170  Quadrat.5 138   Rarefaction       0 15.659111 13.590975 17.727246
## 180  Quadrat.5 277      Observed       0 19.000000 16.272672 21.727328
## 190  Quadrat.5 408 Extrapolation       0 19.710680 16.209981 23.211378
## 200  Quadrat.5 554 Extrapolation       0 19.864504 15.348814 24.380195
## 201  Quadrat.6   1   Rarefaction       0  1.000000  1.000000  1.000000
## 210  Quadrat.6 232   Rarefaction       0  8.122676  6.470196  9.775156
## 220  Quadrat.6 464      Observed       0 10.000000  7.175242 12.824758
## 230  Quadrat.6 684 Extrapolation       0 11.218394  7.288549 15.148239
## 240  Quadrat.6 928 Extrapolation       0 12.187115  7.082520 17.291709
## 241  Quadrat.7   1   Rarefaction       0  1.000000  1.000000  1.000000
## 250  Quadrat.7 164   Rarefaction       0 12.252127 10.507730 13.996524
## 260  Quadrat.7 328      Observed       0 15.000000 12.464230 17.535770
## 270  Quadrat.7 483 Extrapolation       0 15.710963 12.333342 19.088584
## 280  Quadrat.7 656 Extrapolation       0 15.865031 11.541972 20.188090
## 281  Quadrat.8   1   Rarefaction       0  1.000000  1.000000  1.000000
## 290  Quadrat.8 214   Rarefaction       0 12.838973 11.559036 14.118909
## 300  Quadrat.8 428      Observed       0 14.000000 12.291802 15.708198
## 310  Quadrat.8 631 Extrapolation       0 14.211841 11.873413 16.550269
## 320  Quadrat.8 856 Extrapolation       0 14.244805 11.240242 17.249368
## 321  Quadrat.9   1   Rarefaction       0  1.000000  1.000000  1.000000
## 330  Quadrat.9  41   Rarefaction       0 12.426486 10.470280 14.382691
## 340  Quadrat.9  82      Observed       0 16.000000 13.132546 18.867454
## 350  Quadrat.9 121 Extrapolation       0 17.097502 13.324240 20.870764
## 360  Quadrat.9 164 Extrapolation       0 17.449789 12.763616 22.135962
## 361 Quadrat.10   1   Rarefaction       0  1.000000  1.000000  1.000000
## 370 Quadrat.10 125   Rarefaction       0  8.660186  7.324021  9.996352
## 380 Quadrat.10 250      Observed       0 10.000000  8.100983 11.899017
## 390 Quadrat.10 368 Extrapolation       0 10.750659  8.220012 13.281305
## 400 Quadrat.10 500 Extrapolation       0 11.260652  8.177288 14.344016
## 401 Quadrat.11   1   Rarefaction       0  1.000000  1.000000  1.000000
## 410 Quadrat.11  77   Rarefaction       0 12.378716 11.429268 13.328165
## 420 Quadrat.11 155      Observed       0 13.000000 12.089263 13.910737
## 430 Quadrat.11 228 Extrapolation       0 13.000000 11.874603 14.125397
## 440 Quadrat.11 310 Extrapolation       0 13.000000 11.639715 14.360285
##            SC    SC.LCL    SC.UCL
## 1   0.2982882 0.2243865 0.3721899
## 10  0.9681311 0.9540657 0.9821965
## 20  0.9925382 0.9783091 1.0000000
## 30  0.9971273 0.9870002 1.0000000
## 40  0.9989902 0.9923880 1.0000000
## 41  0.1177984 0.1090083 0.1265885
## 50  0.9949676 0.9922095 0.9977256
## 60  1.0000000 0.9979437 1.0000000
## 70  1.0000000 0.9990247 1.0000000
## 80  1.0000000 0.9995017 1.0000000
## 81  0.2216758 0.2016295 0.2417222
## 90  0.9876404 0.9800525 0.9952282
## 100 0.9888018 0.9822228 0.9953809
## 110 0.9911643 0.9847746 0.9975539
## 120 0.9932137 0.9876079 0.9988195
## 121 0.2072624 0.1756990 0.2388259
## 130 0.9861074 0.9772956 0.9949192
## 140 0.9898191 0.9818742 0.9977640
## 150 0.9925768 0.9861257 0.9990279
## 160 0.9947809 0.9898647 0.9996971
## 161 0.3605661 0.3057428 0.4153894
## 170 0.9576645 0.9465907 0.9687383
## 180 0.9892989 0.9776038 1.0000000
## 190 0.9977796 0.9867975 1.0000000
## 200 0.9996152 0.9903026 1.0000000
## 201 0.2695967 0.2537042 0.2854892
## 210 0.9896514 0.9830253 0.9962774
## 220 0.9935438 0.9872911 0.9997964
## 230 0.9952956 0.9893521 1.0000000
## 240 0.9966884 0.9916713 1.0000000
## 241 0.2061237 0.1767750 0.2354724
## 250 0.9755530 0.9673757 0.9837303
## 260 0.9909460 0.9818175 1.0000000
## 270 0.9981202 0.9900721 1.0000000
## 280 0.9996748 0.9931270 1.0000000
## 281 0.2280636 0.2070696 0.2490577
## 290 0.9902972 0.9858347 0.9947596
## 300 0.9976852 0.9919580 1.0000000
## 310 0.9996513 0.9953692 1.0000000
## 320 0.9999572 0.9968775 1.0000000
## 321 0.1725384 0.1158667 0.2292101
## 330 0.8625042 0.8186442 0.9063641
## 340 0.9526800 0.9109280 0.9944320
## 350 0.9855393 0.9507785 1.0000000
## 360 0.9960869 0.9684627 1.0000000
## 361 0.2881928 0.2612840 0.3151016
## 370 0.9843510 0.9757989 0.9929030
## 380 0.9920320 0.9832080 1.0000000
## 390 0.9950346 0.9887557 1.0000000
## 400 0.9970746 0.9926632 1.0000000
## 401 0.1459573 0.1151526 0.1767619
## 410 0.9750464 0.9628995 0.9871934
## 420 1.0000000 0.9900141 1.0000000
## 430 1.0000000 0.9943601 1.0000000
## 440 1.0000000 0.9964826 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage        SC   m        Method Order.q        qD     qD.LCL
## 1    Quadrat.1 0.2982883   1   Rarefaction       0  1.000000  0.8657298
## 10   Quadrat.1 0.9681311  66   Rarefaction       0  8.947706  7.2760081
## 20   Quadrat.1 0.9925382 132      Observed       0 10.000000  7.6293497
## 30   Quadrat.1 0.9971273 195 Extrapolation       0 10.305180  7.5089914
## 40   Quadrat.1 0.9989902 264 Extrapolation       0 10.429060  7.4489014
## 41   Quadrat.2 0.1177984   1   Rarefaction       0  1.000000  0.9590207
## 45   Quadrat.2 0.9824284  99   Rarefaction       0 12.373961 11.4038082
## 50   Quadrat.2 0.9949676 222   Rarefaction       0 13.580553 12.6990385
## 55   Quadrat.2 0.9986248 344   Rarefaction       0 13.937856 12.9636416
## 59   Quadrat.2 1.0000000 444      Observed       0 14.000000 12.9072002
## 60   Quadrat.3 0.2216778   1   Rarefaction       0  1.000008  0.9386104
## 69   Quadrat.3 0.9876404 223   Rarefaction       0 11.437408  5.8228676
## 79   Quadrat.3 0.9888018 446      Observed       0 14.000000  7.6186913
## 89   Quadrat.3 0.9911643 657 Extrapolation       0 16.104927  8.4119211
## 99   Quadrat.3 0.9932137 892 Extrapolation       0 17.930966  9.1041420
## 100  Quadrat.4 0.2072643   1   Rarefaction       0  1.000009  0.9117672
## 109  Quadrat.4 0.9861074 147   Rarefaction       0 10.245584  6.8337652
## 119  Quadrat.4 0.9898191 294      Observed       0 12.000000  7.7088571
## 129  Quadrat.4 0.9925768 433 Extrapolation       0 13.214789  8.3732199
## 139  Quadrat.4 0.9947809 588 Extrapolation       0 14.185662  9.0819264
## 140  Quadrat.5 0.3605678   1   Rarefaction       0  1.000005  0.8939659
## 149  Quadrat.5 0.9576645 138   Rarefaction       0 15.659111 12.7038531
## 159  Quadrat.5 0.9892989 277      Observed       0 19.000000 11.4802711
## 169  Quadrat.5 0.9977796 408 Extrapolation       0 19.710680  9.0339585
## 179  Quadrat.5 0.9996152 554 Extrapolation       0 19.864504  8.4794751
## 180  Quadrat.6 0.2695998   1   Rarefaction       0  1.000010  0.9759419
## 189  Quadrat.6 0.9896514 232   Rarefaction       0  8.122676  3.0333984
## 199  Quadrat.6 0.9935438 464      Observed       0 10.000000  2.9518951
## 209  Quadrat.6 0.9952956 684 Extrapolation       0 11.218394  3.2798062
## 219  Quadrat.6 0.9966884 928 Extrapolation       0 12.187115  3.5668134
## 220  Quadrat.7 0.2061237   1   Rarefaction       0  1.000000  0.9326281
## 229  Quadrat.7 0.9755530 164   Rarefaction       0 12.252126  9.7819088
## 239  Quadrat.7 0.9909460 328      Observed       0 15.000000  9.3506892
## 249  Quadrat.7 0.9981202 483 Extrapolation       0 15.710963  7.4235787
## 259  Quadrat.7 0.9996748 656 Extrapolation       0 15.865031  6.9357221
## 260  Quadrat.8 0.2280665   1   Rarefaction       0  1.000012  0.9473017
## 269  Quadrat.8 0.9902972 214   Rarefaction       0 12.838973 11.0915923
## 279  Quadrat.8 0.9976852 428      Observed       0 14.000000  9.9603287
## 289  Quadrat.8 0.9996513 631 Extrapolation       0 14.211841  9.4370057
## 299  Quadrat.8 0.9999572 856 Extrapolation       0 14.244805  9.3486763
## 300  Quadrat.9 0.1725400   1   Rarefaction       0  1.000009  0.7252298
## 309  Quadrat.9 0.8625042  41   Rarefaction       0 12.426484  9.4095591
## 319  Quadrat.9 0.9526800  82      Observed       0 16.000000 10.6899890
## 329  Quadrat.9 0.9855393 121 Extrapolation       0 17.097502  9.3761122
## 339  Quadrat.9 0.9960869 164 Extrapolation       0 17.449789  8.8071275
## 340 Quadrat.10 0.2881978   1   Rarefaction       0  1.000015  0.9575234
## 349 Quadrat.10 0.9843510 125   Rarefaction       0  8.660186  6.5345934
## 359 Quadrat.10 0.9920320 250      Observed       0 10.000000  6.8682056
## 369 Quadrat.10 0.9950346 368 Extrapolation       0 10.750659  7.1539713
## 379 Quadrat.10 0.9970746 500 Extrapolation       0 11.260652  7.3527730
## 380 Quadrat.11 0.1459599   1   Rarefaction       0  1.000017  0.9144488
## 384 Quadrat.11 0.9059712  35   Rarefaction       0 10.147477  8.8746384
## 389 Quadrat.11 0.9750465  77   Rarefaction       0 12.378716 11.4345167
## 394 Quadrat.11 0.9953552 120   Rarefaction       0 12.931952 11.3407788
## 398 Quadrat.11 1.0000000 155      Observed       0 13.000000 11.1008860
##        qD.UCL
## 1    1.134271
## 10  10.619403
## 20  12.370650
## 30  13.101369
## 40  13.409218
## 41   1.040979
## 45  13.344115
## 50  14.462068
## 55  14.912071
## 59  15.092800
## 60   1.061406
## 69  17.051949
## 79  20.381309
## 89  23.797934
## 99  26.757791
## 100  1.088250
## 109 13.657403
## 119 16.291143
## 129 18.056357
## 139 19.289397
## 140  1.106043
## 149 18.614368
## 159 26.519729
## 169 30.387401
## 179 31.249534
## 180  1.024078
## 189 13.211953
## 199 17.048105
## 209 19.156983
## 219 20.807416
## 220  1.067372
## 229 14.722344
## 239 20.649311
## 249 23.998348
## 259 24.794340
## 260  1.052721
## 269 14.586353
## 279 18.039671
## 289 18.986676
## 299 19.140934
## 300  1.274788
## 309 15.443410
## 319 21.310011
## 329 24.818892
## 339 26.092450
## 340  1.042508
## 349 10.785779
## 359 13.131794
## 369 14.347346
## 379 15.168531
## 380  1.085586
## 384 11.420316
## 389 13.322916
## 394 14.523125
## 398 14.899114
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.0407699 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.4966904  4.128696
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.4107232  2.547459
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.3140840 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.2713736  3.946660
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.1807775  3.115582
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.9252934 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.5824251  7.893212
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6617523  5.554310
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.5600693 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3057546  9.372766
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3692953  7.765275
## 13  Quadrat.3  Species richness 14.000000 23.977578 6.5231554 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.3110576  5.370503
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.2101264  4.099252
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.0672145 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3336024  5.854436
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3196538  4.198291
## 19  Quadrat.5  Species richness 19.000000 19.896751 4.0737704 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.3530895  4.577199
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.1892865  2.402422
## 22  Quadrat.6  Species richness 10.000000 14.490302 5.6377409 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1646019  4.034455
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1225381  3.469074
## 25  Quadrat.7  Species richness 15.000000 15.897256 3.3844306 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3314930  5.927662
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3199334  4.224399
## 28  Quadrat.8  Species richness 14.000000 14.249416 1.9456052 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3684555  5.624458
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2754614  3.844846
## 31  Quadrat.9  Species richness 16.000000 17.580488 6.2612406 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.2236455  7.070843
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.9197935  3.993049
##          UCL
## 1  14.496048
## 2   6.075686
## 3   4.157465
## 4  16.527521
## 5   5.010425
## 6   3.824217
## 7  14.813542
## 8  10.176276
## 9   8.148331
## 10 15.097716
## 11 10.571301
## 12  9.212886
## 13 36.762728
## 14  6.589826
## 15  4.922932
## 16 24.456288
## 17  7.162133
## 18  5.451311
## 19 27.881194
## 20  5.961284
## 21  3.144411
## 22 25.540071
## 23  4.679682
## 24  3.949414
## 25 22.530618
## 26  7.227091
## 27  5.478514
## 28 18.062732
## 29  7.068777
## 30  4.924635
## 31 29.852294
## 32 11.867445
## 33  7.598574
Barrow_Data_1 <- iNEXT(Barrow_Nos, q=c(1), datatype = "abundance")

Barrow_Data_1
## Compare 11 assemblages with Hill number order q = 1.
## $class: iNEXT
## 
## $DataInfo: basic data information
##    Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1   Quadrat.1 132    10 0.9925  1  1  1  3  0  0  0  1  0   0
## 2   Quadrat.2 444    14 1.0000  0  1  1  0  1  1  0  0  0   0
## 3   Quadrat.3 446    14 0.9888  5  0  0  1  0  0  0  0  0   1
## 4   Quadrat.4 294    12 0.9898  3  1  0  0  0  0  0  1  1   0
## 5   Quadrat.5 277    19 0.9893  3  5  4  1  0  1  0  1  0   0
## 6   Quadrat.6 464    10 0.9935  3  1  1  0  0  0  0  1  0   0
## 7   Quadrat.7 328    15 0.9909  3  5  0  0  0  0  0  0  0   2
## 8   Quadrat.8 428    14 0.9977  1  2  1  0  1  0  1  0  0   0
## 9   Quadrat.9  82    16 0.9527  4  5  2  1  1  1  0  0  0   0
## 10 Quadrat.10 250    10 0.9920  2  1  0  0  3  0  0  0  0   1
## 11 Quadrat.11 155    13 1.0000  0  1  1  3  1  2  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage   m        Method Order.q       qD   qD.LCL    qD.UCL        SC
## 1    Quadrat.1   1   Rarefaction       1 1.000000 1.000000  1.000000 0.2982882
## 10   Quadrat.1  66   Rarefaction       1 4.711402 3.760143  5.662661 0.9681311
## 20   Quadrat.1 132      Observed       1 4.909318 3.904383  5.914253 0.9925382
## 30   Quadrat.1 195 Extrapolation       1 4.984681 3.959598  6.009764 0.9971273
## 40   Quadrat.1 264 Extrapolation       1 5.033897 3.994794  6.073000 0.9989902
## 41   Quadrat.2   1   Rarefaction       1 1.000000 1.000000  1.000000 0.1177984
## 50   Quadrat.2 222   Rarefaction       1 9.669129 9.083650 10.254609 0.9949676
## 60   Quadrat.2 444      Observed       1 9.824330 9.226791 10.421870 1.0000000
## 70   Quadrat.2 654 Extrapolation       1 9.880874 9.279151 10.482596 1.0000000
## 80   Quadrat.2 888 Extrapolation       1 9.918790 9.314180 10.523400 1.0000000
## 81   Quadrat.3   1   Rarefaction       1 1.000000 1.000000  1.000000 0.2216758
## 90   Quadrat.3 223   Rarefaction       1 5.727900 5.310668  6.145131 0.9876404
## 100  Quadrat.3 446      Observed       1 5.827336 5.391622  6.263050 0.9888018
## 110  Quadrat.3 657 Extrapolation       1 5.874481 5.430121  6.318840 0.9911643
## 120  Quadrat.3 892 Extrapolation       1 5.910085 5.458916  6.361254 0.9932137
## 121  Quadrat.4   1   Rarefaction       1 1.000000 1.000000  1.000000 0.2072624
## 130  Quadrat.4 147   Rarefaction       1 6.194376 5.578531  6.810222 0.9861074
## 140  Quadrat.4 294      Observed       1 6.330739 5.679748  6.981730 0.9898191
## 150  Quadrat.4 433 Extrapolation       1 6.390793 5.725783  7.055802 0.9925768
## 160  Quadrat.4 588 Extrapolation       1 6.434143 5.759475  7.108810 0.9947809
## 161  Quadrat.5   1   Rarefaction       1 1.000000 1.000000  1.000000 0.3605661
## 170  Quadrat.5 138   Rarefaction       1 4.870478 4.185439  5.555517 0.9576645
## 180  Quadrat.5 277      Observed       1 5.076505 4.348155  5.804856 0.9892989
## 190  Quadrat.5 408 Extrapolation       1 5.154233 4.410024  5.898443 0.9977796
## 200  Quadrat.5 554 Extrapolation       1 5.204554 4.450272  5.958837 0.9996152
## 201  Quadrat.6   1   Rarefaction       1 1.000000 1.000000  1.000000 0.2695967
## 210  Quadrat.6 232   Rarefaction       1 4.240210 3.962798  4.517622 0.9896514
## 220  Quadrat.6 464      Observed       1 4.290540 4.003606  4.577474 0.9935438
## 230  Quadrat.6 684 Extrapolation       1 4.312906 4.021732  4.604079 0.9952956
## 240  Quadrat.6 928 Extrapolation       1 4.329034 4.034331  4.623737 0.9966884
## 241  Quadrat.7   1   Rarefaction       1 1.000000 1.000000  1.000000 0.2061237
## 250  Quadrat.7 164   Rarefaction       1 6.248599 5.709965  6.787232 0.9755530
## 260  Quadrat.7 328      Observed       1 6.415378 5.851834  6.978923 0.9909460
## 270  Quadrat.7 483 Extrapolation       1 6.481166 5.911261  7.051072 0.9981202
## 280  Quadrat.7 656 Extrapolation       1 6.523592 5.950825  7.096360 0.9996748
## 281  Quadrat.8   1   Rarefaction       1 1.000000 1.000000  1.000000 0.2280636
## 290  Quadrat.8 214   Rarefaction       1 6.136662 5.484676  6.788648 0.9902972
## 300  Quadrat.8 428      Observed       1 6.244415 5.574941  6.913890 0.9976852
## 310  Quadrat.8 631 Extrapolation       1 6.284788 5.608412  6.961164 0.9996513
## 320  Quadrat.8 856 Extrapolation       1 6.311195 5.630242  6.992148 0.9999572
## 321  Quadrat.9   1   Rarefaction       1 1.000000 1.000000  1.000000 0.1725384
## 330  Quadrat.9  41   Rarefaction       1 7.494984 6.301987  8.687981 0.8625042
## 340  Quadrat.9  82      Observed       1 8.450869 7.032717  9.869021 0.9526800
## 350  Quadrat.9 121 Extrapolation       1 8.851415 7.332048 10.370783 0.9855393
## 360  Quadrat.9 164 Extrapolation       1 9.113130 7.522099 10.704161 0.9960869
## 361 Quadrat.10   1   Rarefaction       1 1.000000 1.000000  1.000000 0.2881928
## 370 Quadrat.10 125   Rarefaction       1 4.280396 3.738913  4.821879 0.9843510
## 380 Quadrat.10 250      Observed       1 4.373262 3.808490  4.938033 0.9920320
## 390 Quadrat.10 368 Extrapolation       1 4.411537 3.837495  4.985579 0.9950346
## 400 Quadrat.10 500 Extrapolation       1 4.438123 3.857610  5.018636 0.9970746
## 401 Quadrat.11   1   Rarefaction       1 1.000000 1.000000  1.000000 0.1459573
## 410 Quadrat.11  77   Rarefaction       1 8.296187 7.235169  9.357204 0.9750464
## 420 Quadrat.11 155      Observed       1 8.680817 7.572704  9.788930 1.0000000
## 430 Quadrat.11 228 Extrapolation       1 8.816410 7.694888  9.937932 1.0000000
## 440 Quadrat.11 310 Extrapolation       1 8.907843 7.776707 10.038979 1.0000000
##        SC.LCL    SC.UCL
## 1   0.2280502 0.3685263
## 10  0.9543563 0.9819059
## 20  0.9782344 1.0000000
## 30  0.9867012 1.0000000
## 40  0.9915765 1.0000000
## 41  0.1071873 0.1284095
## 50  0.9924174 0.9975177
## 60  0.9978829 1.0000000
## 70  0.9992010 1.0000000
## 80  0.9997222 1.0000000
## 81  0.2056266 0.2377250
## 90  0.9807715 0.9945092
## 100 0.9813010 0.9963026
## 110 0.9844459 0.9978826
## 120 0.9876476 0.9987798
## 121 0.1810981 0.2334268
## 130 0.9766127 0.9956021
## 140 0.9802838 0.9993544
## 150 0.9844813 1.0000000
## 160 0.9883411 1.0000000
## 161 0.3113414 0.4097908
## 170 0.9487169 0.9666121
## 180 0.9794733 0.9991245
## 190 0.9880179 1.0000000
## 200 0.9917148 1.0000000
## 201 0.2526354 0.2865580
## 210 0.9834377 0.9958650
## 220 0.9870466 1.0000000
## 230 0.9892945 1.0000000
## 240 0.9915656 1.0000000
## 241 0.1842334 0.2280139
## 250 0.9675948 0.9835112
## 260 0.9820009 0.9998910
## 270 0.9900023 1.0000000
## 280 0.9929656 1.0000000
## 281 0.1996284 0.2564989
## 290 0.9862939 0.9943005
## 300 0.9933993 1.0000000
## 310 0.9967514 1.0000000
## 320 0.9980135 1.0000000
## 321 0.1320913 0.2129855
## 330 0.8237317 0.9012767
## 340 0.9098902 0.9954698
## 350 0.9492043 1.0000000
## 360 0.9676046 1.0000000
## 361 0.2576992 0.3186863
## 370 0.9765636 0.9921383
## 380 0.9829106 1.0000000
## 390 0.9874710 1.0000000
## 400 0.9912614 1.0000000
## 401 0.1148089 0.1771056
## 410 0.9641671 0.9859258
## 420 0.9907542 1.0000000
## 430 0.9955281 1.0000000
## 440 0.9976839 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage        SC   m        Method Order.q       qD    qD.LCL    qD.UCL
## 1    Quadrat.1 0.2982883   1   Rarefaction       1 1.000000 0.8698992  1.130101
## 10   Quadrat.1 0.9681311  66   Rarefaction       1 4.711402 3.7720384  5.650765
## 20   Quadrat.1 0.9925382 132      Observed       1 4.909318 3.8899196  5.928716
## 30   Quadrat.1 0.9971273 195 Extrapolation       1 4.984681 3.9435228  6.025839
## 40   Quadrat.1 0.9989902 264 Extrapolation       1 5.033897 3.9844456  6.083348
## 41   Quadrat.2 0.1177984   1   Rarefaction       1 1.000000 0.9613424  1.038658
## 45   Quadrat.2 0.9824284  99   Rarefaction       1 9.293222 8.7417542  9.844690
## 50   Quadrat.2 0.9949676 222   Rarefaction       1 9.669129 9.0896958 10.248563
## 55   Quadrat.2 0.9986248 344   Rarefaction       1 9.779881 9.1848870 10.374874
## 59   Quadrat.2 1.0000000 444      Observed       1 9.824330 9.2276656 10.420995
## 60   Quadrat.3 0.2216778   1   Rarefaction       1 1.000008 0.9596079  1.040407
## 69   Quadrat.3 0.9876404 223   Rarefaction       1 5.727900 5.2257731  6.230026
## 79   Quadrat.3 0.9888018 446      Observed       1 5.827336 5.3218448  6.332827
## 89   Quadrat.3 0.9911643 657 Extrapolation       1 5.874481 5.3740216  6.374940
## 99   Quadrat.3 0.9932137 892 Extrapolation       1 5.910085 5.4161650  6.404005
## 100  Quadrat.4 0.2072643   1   Rarefaction       1 1.000008 0.9384814  1.061534
## 109  Quadrat.4 0.9861074 147   Rarefaction       1 6.194376 5.4686563  6.920096
## 119  Quadrat.4 0.9898191 294      Observed       1 6.330739 5.6211830  7.040295
## 129  Quadrat.4 0.9925768 433 Extrapolation       1 6.390793 5.6880060  7.093580
## 139  Quadrat.4 0.9947809 588 Extrapolation       1 6.434143 5.7371307  7.131154
## 140  Quadrat.5 0.3605678   1   Rarefaction       1 1.000004 0.9213204  1.078688
## 149  Quadrat.5 0.9576645 138   Rarefaction       1 4.870478 4.1628406  5.578116
## 159  Quadrat.5 0.9892989 277      Observed       1 5.076505 4.3421273  5.810884
## 169  Quadrat.5 0.9977796 408 Extrapolation       1 5.154233 4.4098402  5.898627
## 179  Quadrat.5 0.9996152 554 Extrapolation       1 5.204554 4.4512276  5.957881
## 180  Quadrat.6 0.2695998   1   Rarefaction       1 1.000009 0.9732419  1.026776
## 189  Quadrat.6 0.9896514 232   Rarefaction       1 4.240210 3.9213937  4.559027
## 199  Quadrat.6 0.9935438 464      Observed       1 4.290540 3.9822049  4.598875
## 209  Quadrat.6 0.9952956 684 Extrapolation       1 4.312906 4.0058158  4.619995
## 219  Quadrat.6 0.9966884 928 Extrapolation       1 4.329034 4.0237075  4.634360
## 220  Quadrat.7 0.2061237   1   Rarefaction       1 1.000000 0.9519803  1.048020
## 229  Quadrat.7 0.9755530 164   Rarefaction       1 6.248599 5.6558278  6.841369
## 239  Quadrat.7 0.9909460 328      Observed       1 6.415378 5.8647570  6.966000
## 249  Quadrat.7 0.9981202 483 Extrapolation       1 6.481166 5.9414248  7.020908
## 259  Quadrat.7 0.9996748 656 Extrapolation       1 6.523592 5.9731608  7.074024
## 260  Quadrat.8 0.2280665   1   Rarefaction       1 1.000011 0.9364733  1.063548
## 269  Quadrat.8 0.9902972 214   Rarefaction       1 6.136662 5.4759668  6.797358
## 279  Quadrat.8 0.9976852 428      Observed       1 6.244415 5.5655413  6.923290
## 289  Quadrat.8 0.9996513 631 Extrapolation       1 6.284788 5.5957651  6.973811
## 299  Quadrat.8 0.9999572 856 Extrapolation       1 6.311195 5.6173325  7.005057
## 300  Quadrat.9 0.1725400   1   Rarefaction       1 1.000008 0.8980461  1.101971
## 309  Quadrat.9 0.8625042  41   Rarefaction       1 7.494984 6.1659310  8.824036
## 319  Quadrat.9 0.9526800  82      Observed       1 8.450869 6.8760237 10.025714
## 329  Quadrat.9 0.9855393 121 Extrapolation       1 8.851415 7.1544843 10.548347
## 339  Quadrat.9 0.9960869 164 Extrapolation       1 9.113130 7.3846215 10.841639
## 340 Quadrat.10 0.2881978   1   Rarefaction       1 1.000014 0.9525175  1.047510
## 349 Quadrat.10 0.9843510 125   Rarefaction       1 4.280396 3.7287149  4.832077
## 359 Quadrat.10 0.9920320 250      Observed       1 4.373262 3.8012635  4.945260
## 369 Quadrat.10 0.9950346 368 Extrapolation       1 4.411537 3.8322333  4.990841
## 379 Quadrat.10 0.9970746 500 Extrapolation       1 4.438123 3.8539672  5.022279
## 380 Quadrat.11 0.1459599   1   Rarefaction       1 1.000017 0.9072042  1.092829
## 384 Quadrat.11 0.9059712  35   Rarefaction       1 7.431555 6.4654176  8.397692
## 389 Quadrat.11 0.9750465  77   Rarefaction       1 8.296187 7.3147014  9.277672
## 394 Quadrat.11 0.9953552 120   Rarefaction       1 8.573161 7.5623942  9.583927
## 398 Quadrat.11 1.0000000 155      Observed       1 8.680817 7.6708676  9.690767
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 10.000000 10.496212 2.1021836 10.000000
## 2   Quadrat.1 Shannon diversity  4.909318  5.102191 0.5211681  4.080720
## 3   Quadrat.1 Simpson diversity  3.293762  3.352462 0.4199852  2.529306
## 4  Quadrat.10  Species richness 10.000000 11.992000 2.3633781 10.000000
## 5  Quadrat.10 Shannon diversity  4.373262  4.478543 0.3091254  3.872668
## 6  Quadrat.10 Simpson diversity  3.435954  3.469900 0.2087957  3.060668
## 7  Quadrat.11  Species richness 13.000000 13.000000 0.6784089 13.000000
## 8  Quadrat.11 Shannon diversity  8.680817  9.034744 0.5802050  7.897563
## 9  Quadrat.11 Simpson diversity  6.602088  6.851320 0.6661695  5.545652
## 10  Quadrat.2  Species richness 14.000000 14.000000 0.5786921 14.000000
## 11  Quadrat.2 Shannon diversity  9.824330  9.972034 0.3218745  9.341171
## 12  Quadrat.2 Simpson diversity  8.348268  8.489081 0.3688872  7.766075
## 13  Quadrat.3  Species richness 14.000000 23.977578 6.8534538 14.000000
## 14  Quadrat.3 Shannon diversity  5.827336  5.980165 0.2810357  5.429345
## 15  Quadrat.3 Simpson diversity  4.475856  4.511092 0.1931473  4.132530
## 16  Quadrat.4  Species richness 12.000000 16.484694 4.6771678 12.000000
## 17  Quadrat.4 Shannon diversity  6.330739  6.508285 0.3623052  5.798179
## 18  Quadrat.4 Simpson diversity  4.762839  4.824801 0.3506156  4.137607
## 19  Quadrat.5  Species richness 19.000000 19.896751 3.7499589 19.000000
## 20  Quadrat.5 Shannon diversity  5.076505  5.269242 0.4335765  4.419447
## 21  Quadrat.5 Simpson diversity  2.755773  2.773417 0.2142646  2.353466
## 22  Quadrat.6  Species richness 10.000000 14.490302 5.5760854 10.000000
## 23  Quadrat.6 Shannon diversity  4.290540  4.357068 0.1723429  4.019282
## 24  Quadrat.6 Simpson diversity  3.687712  3.709244 0.1388154  3.437171
## 25  Quadrat.7  Species richness 15.000000 15.897256 4.2278534 15.000000
## 26  Quadrat.7 Shannon diversity  6.415378  6.577376 0.3518315  5.887799
## 27  Quadrat.7 Simpson diversity  4.795151  4.851456 0.3205302  4.223229
## 28  Quadrat.8  Species richness 14.000000 14.249416 1.4792156 14.000000
## 29  Quadrat.8 Shannon diversity  6.244415  6.346618 0.3451594  5.670118
## 30  Quadrat.8 Simpson diversity  4.350337  4.384741 0.2633434  3.868597
## 31  Quadrat.9  Species richness 16.000000 17.580488 7.5130661 16.000000
## 32  Quadrat.9 Shannon diversity  8.450869  9.469144 1.1735942  7.168942
## 33  Quadrat.9 Simpson diversity  5.475570  5.795812 0.8794702  4.072082
##          UCL
## 1  14.616416
## 2   6.123662
## 3   4.175618
## 4  16.624136
## 5   5.084417
## 6   3.879132
## 7  14.329657
## 8  10.171925
## 9   8.156989
## 10 15.134216
## 11 10.602896
## 12  9.212086
## 13 37.410101
## 14  6.530985
## 15  4.889654
## 16 25.651774
## 17  7.218390
## 18  5.511995
## 19 27.246535
## 20  6.119036
## 21  3.193367
## 22 25.419228
## 23  4.694854
## 24  3.981317
## 25 24.183697
## 26  7.266953
## 27  5.479684
## 28 17.148625
## 29  7.023118
## 30  4.900885
## 31 32.305827
## 32 11.769347
## 33  7.519541

#Now to look at further things, such as sample coverage#

Barrowout1 <- estimateD(Barrow_Nos, q = c(0,1,2), datatype = "abundance", base="size")
Barrowout1
##    Assemblage   m        Method Order.q        SC        qD    qD.LCL    qD.UCL
## 1   Quadrat.1 164 Extrapolation       0 0.9954051 10.190652  8.100828 12.280477
## 2   Quadrat.1 164 Extrapolation       1 0.9954051  4.952234  3.987533  5.916936
## 3   Quadrat.1 164 Extrapolation       2 0.9954051  3.305054  2.533973  4.076134
## 4   Quadrat.2 164   Rarefaction       0 0.9912442 13.189205 12.416490 13.961920
## 5   Quadrat.2 164   Rarefaction       1 0.9912442  9.559224  9.117205 10.001243
## 6   Quadrat.2 164   Rarefaction       2 0.9912442  8.118355  7.642962  8.593748
## 7   Quadrat.3 164   Rarefaction       0 0.9861054 10.668601  9.078462 12.258740
## 8   Quadrat.3 164   Rarefaction       1 0.9861054  5.668334  5.241128  6.095539
## 9   Quadrat.3 164   Rarefaction       2 0.9861054  4.416538  4.116465  4.716611
## 10  Quadrat.4 164   Rarefaction       0 0.9866832 10.476948  8.934794 12.019101
## 11  Quadrat.4 164   Rarefaction       1 0.9866832  6.220335  5.553406  6.887263
## 12  Quadrat.4 164   Rarefaction       2 0.9866832  4.714842  3.976765  5.452918
## 13  Quadrat.5 164   Rarefaction       0 0.9662006 16.649438 14.397445 18.901431
## 14  Quadrat.5 164   Rarefaction       1 0.9662006  4.932905  4.138787  5.727023
## 15  Quadrat.5 164   Rarefaction       2 0.9662006  2.743747  2.339642  3.147852
## 16  Quadrat.6 164   Rarefaction       0 0.9872702  7.343957  6.010975  8.676939
## 17  Quadrat.6 164   Rarefaction       1 0.9872702  4.205418  3.896950  4.513886
## 18  Quadrat.6 164   Rarefaction       2 0.9872702  3.648964  3.385984  3.911944
## 19  Quadrat.7 164   Rarefaction       0 0.9755530 12.252127 10.500287 14.003967
## 20  Quadrat.7 164   Rarefaction       1 0.9755530  6.248599  5.542857  6.954340
## 21  Quadrat.7 164   Rarefaction       2 0.9755530  4.740137  4.115473  5.364800
## 22  Quadrat.8 164   Rarefaction       0 0.9865650 12.266054 11.160187 13.371921
## 23  Quadrat.8 164   Rarefaction       1 0.9865650  6.073900  5.477058  6.670742
## 24  Quadrat.8 164   Rarefaction       2 0.9865650  4.296076  3.836414  4.755738
## 25  Quadrat.9 164 Extrapolation       0 0.9960869 17.449789 12.563565 22.336013
## 26  Quadrat.9 164 Extrapolation       1 0.9960869  9.113130  6.689178 11.537083
## 27  Quadrat.9 164 Extrapolation       2 0.9960869  5.631141  3.906147  7.356135
## 28 Quadrat.10 164   Rarefaction       0 0.9884901  9.181189  7.630874 10.731503
## 29 Quadrat.10 164   Rarefaction       1 0.9884901  4.322982  3.805836  4.840128
## 30 Quadrat.10 164   Rarefaction       2 0.9884901  3.418417  3.061483  3.775351
## 31 Quadrat.11 164 Extrapolation       0 1.0000000 13.000000 12.069427 13.930573
## 32 Quadrat.11 164 Extrapolation       1 1.0000000  8.701280  7.589417  9.813144
## 33 Quadrat.11 164 Extrapolation       2 1.0000000  6.615295  5.391803  7.838786
Barrowout2 <- estimateD(Barrow_Nos, q = c(0,1,2), datatype = "abundance", base="coverage")
Barrowout2
##    Assemblage        m        Method Order.q        SC        qD    qD.LCL
## 1   Quadrat.1 138.2628 Extrapolation       0 0.9932137 10.044922  6.342696
## 2   Quadrat.1 138.2628 Extrapolation       1 0.9932137  4.918588  3.960696
## 3   Quadrat.1 138.2628 Extrapolation       2 0.9932137  3.296376  2.544970
## 4   Quadrat.2 190.4990   Rarefaction       0 0.9932137 13.394898 12.672915
## 5   Quadrat.2 190.4990   Rarefaction       1 0.9932137  9.617527  9.011628
## 6   Quadrat.2 190.4990   Rarefaction       2 0.9932137  8.167971  7.476919
## 7   Quadrat.3 892.0000 Extrapolation       0 0.9932137 17.930966  6.764204
## 8   Quadrat.3 892.0000 Extrapolation       1 0.9932137  5.910085  5.365996
## 9   Quadrat.3 892.0000 Extrapolation       2 0.9932137  4.493405  4.164549
## 10  Quadrat.4 472.4666 Extrapolation       0 0.9932137 13.495319  8.423662
## 11  Quadrat.4 472.4666 Extrapolation       1 0.9932137  6.403789  5.668152
## 12  Quadrat.4 472.4666 Extrapolation       2 0.9932137  4.786056  4.121641
## 13  Quadrat.5 314.9374 Extrapolation       0 0.9932137 19.328057 10.629086
## 14  Quadrat.5 314.9374 Extrapolation       1 0.9932137  5.103273  4.271010
## 15  Quadrat.5 314.9374 Extrapolation       2 0.9932137  2.757887  2.337956
## 16  Quadrat.6 431.6331   Rarefaction       0 0.9932137  9.785694  3.630680
## 17  Quadrat.6 431.6331   Rarefaction       1 0.9932137  4.286286  3.925709
## 18  Quadrat.6 431.6331   Rarefaction       2 0.9932137  3.686107  3.394856
## 19  Quadrat.7 356.4264 Extrapolation       0 0.9932137 15.224732  9.675363
## 20  Quadrat.7 356.4264 Extrapolation       1 0.9932137  6.430142  5.793599
## 21  Quadrat.7 356.4264 Extrapolation       2 0.9932137  4.799593  4.248940
## 22  Quadrat.8 274.3834   Rarefaction       0 0.9932137 13.332443 10.663237
## 23  Quadrat.8 274.3834   Rarefaction       1 0.9932137  6.183540  5.624736
## 24  Quadrat.8 274.3834   Rarefaction       2 0.9932137  4.331310  3.910415
## 25  Quadrat.9 145.8877 Extrapolation       0 0.9932137 17.353825 10.081748
## 26  Quadrat.9 145.8877 Extrapolation       1 0.9932137  9.020112  6.737161
## 27  Quadrat.9 145.8877 Extrapolation       2 0.9932137  5.611348  3.972748
## 28 Quadrat.10 290.0508 Extrapolation       0 0.9932137 10.295420  6.594716
## 29 Quadrat.10 290.0508 Extrapolation       1 0.9932137  4.388231  3.822873
## 30 Quadrat.10 290.0508 Extrapolation       2 0.9932137  3.440602  3.029648
## 31 Quadrat.11 111.6350   Rarefaction       0 0.9932137 12.883437 11.681553
## 32 Quadrat.11 111.6350   Rarefaction       1 0.9932137  8.536622  7.560174
## 33 Quadrat.11 111.6350   Rarefaction       2 0.9932137  6.510090  5.512620
##       qD.UCL
## 1  13.747147
## 2   5.876480
## 3   4.047783
## 4  14.116882
## 5  10.223426
## 6   8.859024
## 7  29.097729
## 8   6.454175
## 9   4.822261
## 10 18.566977
## 11  7.139427
## 12  5.450471
## 13 28.027029
## 14  5.935537
## 15  3.177818
## 16 15.940708
## 17  4.646863
## 18  3.977359
## 19 20.774101
## 20  7.066685
## 21  5.350247
## 22 16.001650
## 23  6.742345
## 24  4.752206
## 25 24.625901
## 26 11.303063
## 27  7.249947
## 28 13.996123
## 29  4.953588
## 30  3.851555
## 31 14.085322
## 32  9.513070
## 33  7.507559

#Looking at species evenness using the vegan package#

H <- diversity(Barrow_Nos)

Bevenness <- H/log(specnumber(Barrow_Nos))

summary(Bevenness)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##  0.1435  0.6500  0.7629  0.7022  0.8691  1.0000      22
H1 <- diversity(Barrow_Nos$Quadrat.1)

Bevenness1 <- H1/log(specnumber(Barrow_Nos$Quadrat.1))

summary(Bevenness1)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.691   0.691   0.691   0.691   0.691   0.691
H2 <- diversity(Barrow_Nos$Quadrat.2)

Bevenness2 <- H2/log(specnumber(Barrow_Nos$Quadrat.2))

summary(Bevenness2)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8658  0.8658  0.8658  0.8658  0.8658  0.8658
H3 <- diversity(Barrow_Nos$Quadrat.3)

Bevenness3 <- H3/log(specnumber(Barrow_Nos$Quadrat.3))

summary(Bevenness3)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6679  0.6679  0.6679  0.6679  0.6679  0.6679
H4 <- diversity(Barrow_Nos$Quadrat.4)

Bevenness4 <- H4/log(specnumber(Barrow_Nos$Quadrat.4))

summary(Bevenness4)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7427  0.7427  0.7427  0.7427  0.7427  0.7427
H5 <- diversity(Barrow_Nos$Quadrat.5)

Bevenness5 <- H5/log(specnumber(Barrow_Nos$Quadrat.5))

summary(Bevenness5)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.5518  0.5518  0.5518  0.5518  0.5518  0.5518
H6 <- diversity(Barrow_Nos$Quadrat.6)

Bevenness6 <- H6/log(specnumber(Barrow_Nos$Quadrat.6))

summary(Bevenness6)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6325  0.6325  0.6325  0.6325  0.6325  0.6325
H7 <- diversity(Barrow_Nos$Quadrat.7)

Bevenness7 <- H7/log(specnumber(Barrow_Nos$Quadrat.7))

summary(Bevenness7)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6864  0.6864  0.6864  0.6864  0.6864  0.6864
H8 <- diversity(Barrow_Nos$Quadrat.8)

Bevenness8 <- H8/log(specnumber(Barrow_Nos$Quadrat.8))

summary(Bevenness8)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6941  0.6941  0.6941  0.6941  0.6941  0.6941
H9 <- diversity(Barrow_Nos$Quadrat.9)

Bevenness9 <- H9/log(specnumber(Barrow_Nos$Quadrat.9))

summary(Bevenness9)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7698  0.7698  0.7698  0.7698  0.7698  0.7698
H10 <- diversity(Barrow_Nos$Quadrat.10)

Bevenness10 <- H10/log(specnumber(Barrow_Nos$Quadrat.10))

summary(Bevenness10)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6408  0.6408  0.6408  0.6408  0.6408  0.6408
H11 <- diversity(Barrow_Nos$Quadrat.11)

Bevenness11 <- H11/log(specnumber(Barrow_Nos$Quadrat.11))

summary(Bevenness11)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8426  0.8426  0.8426  0.8426  0.8426  0.8426

##Now to generate graphs to better visually examine species curves etc##

Barrow_Data_Graph1 <- ggiNEXT(x = Barrow_Data, se=TRUE, type = 1,
                              facet.var = "None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Barrow_Data_Graph1
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 11. Consider
## specifying shapes manually if you must have them.
## Warning: Removed 5 rows containing missing values (`geom_point()`).

g7 <- Barrow_Data_Graph1 + theme_hc(style = "darkunica") +
  scale_colour_hc("darkunica")
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
g7
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 11. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 5 rows containing missing values (`geom_point()`).

Barrow_Data_Graph2 <- ggiNEXT(x = Barrow_Data, se=TRUE, type = 1,
                              facet.var="None", grey= TRUE) 
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Barrow_Data_Graph2
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 11. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 5 rows containing missing values (`geom_point()`).

plot(Barrow_Data, type=1)

Barrow_Data_Graph3 <- ggiNEXT(x = Barrow_Data, se=TRUE, type = 2,
                              facet.var="None", grey = TRUE) 
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Barrow_Data_Graph3
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 11. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 5 rows containing missing values (`geom_point()`).

plot(Barrow_Data, type=2)

Barrow_Data_Graph4 <- ggiNEXT(x = Barrow_Data, se=TRUE, type = 3,
                              facet.var="None", grey= TRUE) 
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Barrow_Data_Graph4
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 11. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 5 rows containing missing values (`geom_point()`).

plot(Barrow_Data, type=3)

##Fallin Data##

urlfile2 <- 'https://raw.githubusercontent.com/Savannankvm/Biodiversity-analyses-for-six-study-sites/PhD-files/Fallin_Abundance_Data.csv'

Fallin_Nos <-read.csv(urlfile2)

print(Fallin_Nos)
##     Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5
## 1           0         9         1         0         0
## 2           0         0         0         0         0
## 3           0         0         0         0         0
## 4           0         0         0         0         0
## 5           0         0         0         0         0
## 6          81        18         8        82        55
## 7           0         0         0         0         0
## 8           0         0         0         0         0
## 9           0         0         0         2        42
## 10          0         0         0         0        10
## 11          0         0         0         0         0
## 12          1         0         8        16         0
## 13          0         0        12         0         0
## 14          0         0         0         0         0
## 15          0         0         0         0         0
## 16          0         0         0         0         0
## 17          0         0         0         0         0
## 18          0         0         0         0         0
## 19          0         0         0         0         0
## 20          0         0         0         0         0
## 21          0         0        10         0         0
## 22          0         0        10         0         0
## 23          0        10         0         0         0
## 24          0         0         0         0         0
## 25          0         0        10        10        30
## 26          0        20         0         0        30
## 27          0         0         0         0         0
## 28          0         0         0         0         0
## 29          0         0         0         0         0
## 30          0         0         0         0         0
## 31          0         0         0         0         0
## 32          0         0         0         0         0
## 33          0         0         0         0         0
## 34          0         0         0         0         0
## 35          0         0         0         0         0
## 36          0         6         0         0         0
## 37          0         0         0         0         0
## 38          0         0        10         0         0
## 39          0         0         0         0         0
## 40          0         0         0         0         0
## 41          4         0         0         1         0
## 42          0         0         0         0         0
## 43          1         0         0         0         0
## 44          0         0         0         0         0
## 45          0         0         0         0         0
## 46          0         0         0         0         0
## 47          0         0         0         0         0
## 48         30        20         0        10        16
## 49          0         0         0         0         0
## 50          0         0         0         0         0
## 51          0         0         0         0         0
## 52          0         0         0         0         0
## 53          3         0         6         0         1
## 54          0         0         0         0         0
## 55          0         0         0         0         0
## 56          0         5         0         0         0
## 57          0         0         0         0         0
## 58          0         0        10         0         0
## 59          0         0        10         0         0
## 60          0         0         0         0         0
## 61         67        38        65       117        68
## 62          0         0         0         0         0
## 63          0         0         0         0         0
## 64          0         0         0         0         0
## 65          0         0         0         0         0
## 66          0         0         0         0         0
## 67          0         0         0         0         0
## 68          0         0         0         0         0
## 69          0         0         0         0         0
## 70          0         0         0         0         0
## 71          0         0         0         0         0
## 72         30        80         0        28        36
## 73          0         0         0         0         0
## 74          0         0         0         0         0
## 75         50        80       110       160        90
## 76         11        24         2         4         1
## 77          0        10        60        10        20
## 78          0         0         0         0         0
## 79          0        20         0         0       120
## 80          0         0         0         0         0
## 81          0         0         0         0         0
## 82          0         0         0         0         0
## 83          0         0         0         0         0
## 84          0         0         0         0         0
## 85         20        15         0         7         1
## 86          0         0         0         0         0
## 87          0         0         0         0         0
## 88          0         0        10         0         0
## 89         69       120        92         1         0
## 90          0         0         0         0         0
## 91          0         0         0         0         0
## 92          0         0         0         0         0
## 93          0         0         0         0         0
## 94          0         0         0         0         0
## 95          0         0         0         0         0
## 96          0         0         0         0         0
## 97          0         0         0         0         0
## 98          0         0         0         0         0
## 99          0         0         0         0         0
## 100        13         0         0        22        36
## 101       110        10         0         0       120
## 102         0         0         0         0         0
## 103         0         0         0         0         0
## 104         0         0         0         0         0
## 105         0         0         0         0         0
## 106         0        40         0         0         0
## 107         0         0         0         0         0
## 108         1         0         2         0         0
## 109        40         0       150       150        90
## 110         0         0         0         0         0
## 111         0         0         0         0         2
## 112         0         0         0         0         0
## 113         0         0         0         0         0
## 114         0         0         0         0         0
## 115         0         0         0         0         0
## 116         0         0         0         0         0
## 117       160         0        30       150        30
## 118        20         0         0        20         0
## 119         0         0         1         0         0
## 120         0         0         0         0         0
## 121         0         0         0         0         0
## 122         0         0         0         0         0
## 123         0         0         0         0         0
## 124         0         0         0         0         0
## 125         0         0         0         0         0
## 126         0         0         0         0         0
## 127         0         0         0         0         0
## 128         0         0         0         0         0
## 129         0         0         0        30         0
## 130         0         0         0         0         0
## 131         0         0         0         0         0
## 132         0         0         0         0         0
## 133         0         0         0         0         0
## 134         0         0         0         0         0
## 135         0         0         0         0         0
## 136         0         0         0         0         0
## 137         0         0         0         0         0
## 138         0         0         0         0         0
## 139         0         0         2         0         0
## 140         0         0         0         0         0
## 141         0         0         0         0         0
## 142         0         0        20         0         0
## 143         0         0         0         0         0

#colSums to establish sample size for each of the quadrats.

colSums(Fallin_Nos)
## Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5 
##       711       525       639       820       798

#Setting m to sample size for Quadrat 1. This will give me observed #qD value that will be most representative for Quadrat and Community. Will do the same #for the other communities below.

m <- c(711)

Fallin_Datam <- iNEXT(Fallin_Nos, q=c(0), datatype= "abundance", size = m)

Fallin_Datam
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 711    18 0.9958  3  0  1  1  0  0  0  0  0   0
## 2  Quadrat_2 525    17 1.0000  0  0  0  0  1  1  0  0  1   3
## 3  Quadrat_3 639    23 0.9969  2  3  0  0  0  1  0  2  0   7
## 4  Quadrat_4 820    18 0.9976  2  1  0  1  0  0  1  0  0   3
## 5  Quadrat_5 798    19 0.9962  3  1  0  0  0  0  0  0  0   1
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD   qD.LCL   qD.UCL        SC
## 1   Quadrat_1 711      Observed       0 18.00000 15.98054 20.01946 0.9957865
## 2   Quadrat_2 524   Rarefaction       0 17.00000 16.72283 17.27717 1.0000000
## 3   Quadrat_2 525      Observed       0 17.00000 16.72282 17.27718 1.0000000
## 4   Quadrat_2 526 Extrapolation       0 17.00000 16.72282 17.27718 1.0000000
## 5   Quadrat_2 711 Extrapolation       0 17.00000 16.72282 17.27718 1.0000000
## 6   Quadrat_3 638   Rarefaction       0 22.99687 20.83079 25.16295 0.9968701
## 7   Quadrat_3 639      Observed       0 23.00000 20.83262 25.16738 0.9968848
## 8   Quadrat_3 640 Extrapolation       0 23.00312 20.83419 25.17204 0.9968993
## 9   Quadrat_3 711 Extrapolation       0 23.19079 20.91200 25.46958 0.9977777
## 10  Quadrat_4 711   Rarefaction       0 17.71632 15.95137 19.48127 0.9972284
## 11  Quadrat_4 819   Rarefaction       0 17.99756 16.09978 19.89534 0.9975610
## 12  Quadrat_4 820      Observed       0 18.00000 16.10098 19.89902 0.9975640
## 13  Quadrat_4 821 Extrapolation       0 18.00244 16.10211 19.90276 0.9975669
## 14  Quadrat_5 711   Rarefaction       0 18.66117 16.91521 20.40712 0.9959702
## 15  Quadrat_5 797   Rarefaction       0 18.99624 17.09901 20.89347 0.9962406
## 16  Quadrat_5 798      Observed       0 19.00000 17.10098 20.89902 0.9962437
## 17  Quadrat_5 799 Extrapolation       0 19.00376 17.10280 20.90471 0.9962469
##       SC.LCL    SC.UCL
## 1  0.9924373 0.9991358
## 2  0.9994720 1.0000000
## 3  1.0000000 1.0000000
## 4  1.0000000 1.0000000
## 5  1.0000000 1.0000000
## 6  0.9937817 0.9999586
## 7  0.9935498 1.0000000
## 8  0.9935670 1.0000000
## 9  0.9946163 1.0000000
## 10 0.9954080 0.9990488
## 11 0.9956240 0.9994980
## 12 0.9955752 0.9995527
## 13 0.9955805 0.9995533
## 14 0.9934150 0.9985253
## 15 0.9935097 0.9989715
## 16 0.9933644 0.9991231
## 17 0.9933683 0.9991255
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD   qD.LCL   qD.UCL
## 1   Quadrat_1 0.9957865 711      Observed       0 18.00000 15.07118 20.92882
## 2   Quadrat_2 1.0000000 525      Observed       0 17.00000 16.72282 17.27718
## 3   Quadrat_3 0.9968701 638   Rarefaction       0 22.99559 19.55202 26.43915
## 4   Quadrat_3 0.9968848 639      Observed       0 23.00000 19.55185 26.44815
## 5   Quadrat_3 0.9968993 640 Extrapolation       0 23.00312 19.54927 26.45696
## 6   Quadrat_3 0.9977777 711 Extrapolation       0 23.19079 19.37454 27.00705
## 7   Quadrat_4 0.9972284 711   Rarefaction       0 17.71632 15.25091 20.18173
## 8   Quadrat_4 0.9975610 818   Rarefaction       0 17.99617 15.46800 20.52434
## 9   Quadrat_4 0.9975640 820      Observed       0 18.00000 15.47030 20.52970
## 10  Quadrat_4 0.9975669 821 Extrapolation       0 18.00244 15.47284 20.53203
## 11  Quadrat_5 0.9959702 711   Rarefaction       0 18.66117 15.04095 22.28139
## 12  Quadrat_5 0.9962406 796   Rarefaction       0 18.99407 15.31022 22.67793
## 13  Quadrat_5 0.9962437 798      Observed       0 19.00000 15.31400 22.68600
## 14  Quadrat_5 0.9962469 799 Extrapolation       0 19.00376 15.31667 22.69084
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 18.000000 20.995781 3.2731675 18.000000
## 2   Quadrat_1 Shannon diversity 10.537842 10.696181 0.3393021 10.031162
## 3   Quadrat_1 Simpson diversity  8.351716  8.439099 0.3507053  7.751729
## 4   Quadrat_2  Species richness 17.000000 17.000000 0.0000000 17.000000
## 5   Quadrat_2 Shannon diversity 11.247195 11.422020 0.4156465 10.607367
## 6   Quadrat_2 Simpson diversity  8.349490  8.468263 0.4462573  7.593615
## 7   Quadrat_3  Species richness 23.000000 23.665623 2.6096152 23.000000
## 8   Quadrat_3 Shannon diversity 10.877508 11.082181 0.4908834 10.120067
## 9   Quadrat_3 Simpson diversity  7.673620  7.754736 0.3980580  6.974557
## 10  Quadrat_4  Species richness 18.000000 19.997561 2.2332675 18.000000
## 11  Quadrat_4 Shannon diversity  9.098377  9.209640 0.2613348  8.697433
## 12  Quadrat_4 Simpson diversity  7.137398  7.191288 0.1955626  6.807992
## 13  Quadrat_5  Species richness 19.000000 23.494361 4.2403201 19.000000
## 14  Quadrat_5 Shannon diversity 12.511066 12.694857 0.3122613 12.082836
## 15  Quadrat_5 Simpson diversity 10.531256 10.658723 0.3390233  9.994250
##          UCL
## 1  27.411071
## 2  11.361201
## 3   9.126468
## 4  17.000000
## 5  12.236672
## 6   9.342911
## 7  28.780375
## 8  12.044295
## 9   8.534916
## 10 24.374685
## 11  9.721847
## 12  7.574584
## 13 31.805236
## 14 13.306878
## 15 11.323196
n <- c(525)

Fallin_Datan <- iNEXT(Fallin_Nos, q=c(0), datatype= "abundance", size = n)

Fallin_Datan
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 711    18 0.9958  3  0  1  1  0  0  0  0  0   0
## 2  Quadrat_2 525    17 1.0000  0  0  0  0  1  1  0  0  1   3
## 3  Quadrat_3 639    23 0.9969  2  3  0  0  0  1  0  2  0   7
## 4  Quadrat_4 820    18 0.9976  2  1  0  1  0  0  1  0  0   3
## 5  Quadrat_5 798    19 0.9962  3  1  0  0  0  0  0  0  0   1
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD   qD.LCL   qD.UCL        SC
## 1   Quadrat_1 525   Rarefaction       0 17.19293 15.26113 19.12473 0.9953969
## 2   Quadrat_1 710   Rarefaction       0 17.99578 15.75751 20.23405 0.9957806
## 3   Quadrat_1 711      Observed       0 18.00000 15.76004 20.23996 0.9957865
## 4   Quadrat_1 712 Extrapolation       0 18.00421 15.76242 20.24600 0.9957925
## 5   Quadrat_2 525      Observed       0 17.00000 17.00000 17.00000 1.0000000
## 6   Quadrat_3 525   Rarefaction       0 22.54837 20.79724 24.29949 0.9952054
## 7   Quadrat_3 638   Rarefaction       0 22.99687 20.99530 24.99844 0.9968701
## 8   Quadrat_3 639      Observed       0 23.00000 20.99613 25.00387 0.9968848
## 9   Quadrat_3 640 Extrapolation       0 23.00312 20.99665 25.00958 0.9968993
## 10  Quadrat_4 525   Rarefaction       0 17.13397 15.68023 18.58770 0.9964402
## 11  Quadrat_4 819   Rarefaction       0 17.99756 16.10453 19.89059 0.9975610
## 12  Quadrat_4 820      Observed       0 18.00000 16.10553 19.89447 0.9975640
## 13  Quadrat_4 821 Extrapolation       0 18.00244 16.10641 19.89846 0.9975669
## 14  Quadrat_5 525   Rarefaction       0 17.85691 16.08020 19.63363 0.9953845
## 15  Quadrat_5 797   Rarefaction       0 18.99624 16.61451 21.37797 0.9962406
## 16  Quadrat_5 798      Observed       0 19.00000 16.61593 21.38407 0.9962437
## 17  Quadrat_5 799 Extrapolation       0 19.00376 16.61710 21.39041 0.9962469
##       SC.LCL    SC.UCL
## 1  0.9925192 0.9982746
## 2  0.9925576 0.9990035
## 3  0.9924279 0.9991452
## 4  0.9924357 0.9991492
## 5  1.0000000 1.0000000
## 6  0.9913898 0.9990210
## 7  0.9929760 1.0000000
## 8  0.9928464 1.0000000
## 9  0.9928620 1.0000000
## 10 0.9941714 0.9987090
## 11 0.9950869 1.0000000
## 12 0.9950020 1.0000000
## 13 0.9950077 1.0000000
## 14 0.9924974 0.9982717
## 15 0.9928529 0.9996283
## 16 0.9926657 0.9998218
## 17 0.9926704 0.9998234
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD   qD.LCL   qD.UCL
## 1   Quadrat_1 0.9953969 525   Rarefaction       0 17.19293 13.77116 20.61469
## 2   Quadrat_1 0.9957806 708   Rarefaction       0 17.98785 14.34429 21.63141
## 3   Quadrat_1 0.9957865 711      Observed       0 18.00000 14.35257 21.64743
## 4   Quadrat_1 0.9957925 712 Extrapolation       0 18.00421 14.35336 21.65507
## 5   Quadrat_2 1.0000000 525      Observed       0 17.00000 17.00000 17.00000
## 6   Quadrat_3 0.9952054 525   Rarefaction       0 22.54837 18.63010 26.46663
## 7   Quadrat_3 0.9968701 638   Rarefaction       0 22.99559 18.09443 27.89674
## 8   Quadrat_3 0.9968848 639      Observed       0 23.00000 18.08987 27.91013
## 9   Quadrat_3 0.9968993 640 Extrapolation       0 23.00312 18.08371 27.92252
## 10  Quadrat_4 0.9964402 525   Rarefaction       0 17.13397 14.46801 19.79993
## 11  Quadrat_4 0.9975610 818   Rarefaction       0 17.99617 14.87545 21.11690
## 12  Quadrat_4 0.9975640 820      Observed       0 18.00000 14.87803 21.12197
## 13  Quadrat_4 0.9975669 821 Extrapolation       0 18.00244 14.87915 21.12572
## 14  Quadrat_5 0.9953845 525   Rarefaction       0 17.85691 13.25850 22.45533
## 15  Quadrat_5 0.9962406 796   Rarefaction       0 18.99407 13.75508 24.23306
## 16  Quadrat_5 0.9962437 798      Observed       0 19.00000 13.75815 24.24185
## 17  Quadrat_5 0.9962469 799 Extrapolation       0 19.00376 13.76215 24.24536
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 18.000000 20.995781 3.1509487 18.000000
## 2   Quadrat_1 Shannon diversity 10.537842 10.696181 0.3570947  9.996289
## 3   Quadrat_1 Simpson diversity  8.351716  8.439099 0.3998817  7.655345
## 4   Quadrat_2  Species richness 17.000000 17.000000 0.1000000 17.000000
## 5   Quadrat_2 Shannon diversity 11.247195 11.422020 0.4884945 10.464588
## 6   Quadrat_2 Simpson diversity  8.349490  8.468263 0.5192568  7.450539
## 7   Quadrat_3  Species richness 23.000000 23.665623 2.4820391 23.000000
## 8   Quadrat_3 Shannon diversity 10.877508 11.082181 0.4436091 10.212723
## 9   Quadrat_3 Simpson diversity  7.673620  7.754736 0.3432254  7.082027
## 10  Quadrat_4  Species richness 18.000000 19.997561 2.4736019 18.000000
## 11  Quadrat_4 Shannon diversity  9.098377  9.209640 0.2894883  8.642254
## 12  Quadrat_4 Simpson diversity  7.137398  7.191288 0.2414209  6.718112
## 13  Quadrat_5  Species richness 19.000000 23.494361 5.1569149 19.000000
## 14  Quadrat_5 Shannon diversity 12.511066 12.694857 0.2565998 12.191931
## 15  Quadrat_5 Simpson diversity 10.531256 10.658723 0.2932944 10.083876
##          UCL
## 1  27.171527
## 2  11.396074
## 3   9.222852
## 4  17.195996
## 5  12.379451
## 6   9.485988
## 7  28.530331
## 8  11.951639
## 9   8.427446
## 10 24.845732
## 11  9.777027
## 12  7.664464
## 13 33.601728
## 14 13.197784
## 15 11.233570
o <- c(639)

Fallin_Datao <- iNEXT(Fallin_Nos, q=c(0), datatype= "abundance", size = o)

Fallin_Datao
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 711    18 0.9958  3  0  1  1  0  0  0  0  0   0
## 2  Quadrat_2 525    17 1.0000  0  0  0  0  1  1  0  0  1   3
## 3  Quadrat_3 639    23 0.9969  2  3  0  0  0  1  0  2  0   7
## 4  Quadrat_4 820    18 0.9976  2  1  0  1  0  0  1  0  0   3
## 5  Quadrat_5 798    19 0.9962  3  1  0  0  0  0  0  0  0   1
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD   qD.LCL   qD.UCL        SC
## 1   Quadrat_1 639   Rarefaction       0 17.69511 15.43495 19.95526 0.9957335
## 2   Quadrat_1 710   Rarefaction       0 17.99578 15.57137 20.42019 0.9957806
## 3   Quadrat_1 711      Observed       0 18.00000 15.57323 20.42677 0.9957865
## 4   Quadrat_1 712 Extrapolation       0 18.00421 15.57507 20.43336 0.9957925
## 5   Quadrat_2 524   Rarefaction       0 17.00000 16.99887 17.00113 1.0000000
## 6   Quadrat_2 525      Observed       0 17.00000 17.00000 17.00000 1.0000000
## 7   Quadrat_2 526 Extrapolation       0 17.00000 16.99947 17.00053 1.0000000
## 8   Quadrat_2 639 Extrapolation       0 17.00000 16.95127 17.04873 1.0000000
## 9   Quadrat_3 639      Observed       0 23.00000 21.13052 24.86948 0.9968848
## 10  Quadrat_4 639   Rarefaction       0 17.50769 15.89123 19.12415 0.9969729
## 11  Quadrat_4 819   Rarefaction       0 17.99756 16.09026 19.90487 0.9975610
## 12  Quadrat_4 820      Observed       0 18.00000 16.09110 19.90890 0.9975640
## 13  Quadrat_4 821 Extrapolation       0 18.00244 16.09163 19.91324 0.9975669
## 14  Quadrat_5 639   Rarefaction       0 18.36276 15.75390 20.97161 0.9957437
## 15  Quadrat_5 797   Rarefaction       0 18.99624 15.96863 22.02385 0.9962406
## 16  Quadrat_5 798      Observed       0 19.00000 15.96984 22.03016 0.9962437
## 17  Quadrat_5 799 Extrapolation       0 19.00376 15.97068 22.03684 0.9962469
##       SC.LCL    SC.UCL
## 1  0.9922546 0.9992124
## 2  0.9921989 0.9993623
## 3  0.9920946 0.9994784
## 4  0.9921028 0.9994821
## 5  0.9988686 1.0000000
## 6  0.9994740 1.0000000
## 7  0.9994760 1.0000000
## 8  0.9996593 1.0000000
## 9  0.9938345 0.9999350
## 10 0.9944479 0.9994978
## 11 0.9949655 1.0000000
## 12 0.9946994 1.0000000
## 13 0.9947048 1.0000000
## 14 0.9924877 0.9989998
## 15 0.9929959 0.9994853
## 16 0.9926146 0.9998728
## 17 0.9926201 0.9998736
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD   qD.LCL   qD.UCL
## 1   Quadrat_1 0.9957335 639   Rarefaction       0 17.69511 14.16813 21.22208
## 2   Quadrat_1 0.9957806 708   Rarefaction       0 17.98785 14.42107 21.55462
## 3   Quadrat_1 0.9957865 711      Observed       0 18.00000 14.42913 21.57087
## 4   Quadrat_1 0.9957925 712 Extrapolation       0 18.00421 14.43005 21.57838
## 5   Quadrat_2 1.0000000 525      Observed       0 17.00000 16.86167 17.13833
## 6   Quadrat_3 0.9968848 639      Observed       0 23.00000 20.12728 25.87272
## 7   Quadrat_4 0.9969729 639   Rarefaction       0 17.50769 13.93282 21.08255
## 8   Quadrat_4 0.9975610 818   Rarefaction       0 17.99617 14.17283 21.81952
## 9   Quadrat_4 0.9975640 820      Observed       0 18.00000 14.17495 21.82505
## 10  Quadrat_4 0.9975669 821 Extrapolation       0 18.00244 14.17619 21.82869
## 11  Quadrat_5 0.9957437 639   Rarefaction       0 18.36276 13.82097 22.90454
## 12  Quadrat_5 0.9962406 796   Rarefaction       0 18.99407 14.20761 23.78054
## 13  Quadrat_5 0.9962437 798      Observed       0 19.00000 14.21118 23.78882
## 14  Quadrat_5 0.9962469 799 Extrapolation       0 19.00376 14.21458 23.79293
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 18.000000 20.995781 3.3419772 18.000000
## 2   Quadrat_1 Shannon diversity 10.537842 10.696181 0.3914681  9.928918
## 3   Quadrat_1 Simpson diversity  8.351716  8.439099 0.3889767  7.676718
## 4   Quadrat_2  Species richness 17.000000 17.000000 0.1407053 17.000000
## 5   Quadrat_2 Shannon diversity 11.247195 11.422020 0.4126974 10.613147
## 6   Quadrat_2 Simpson diversity  8.349490  8.468263 0.4588317  7.568970
## 7   Quadrat_3  Species richness 23.000000 23.665623 3.0826636 23.000000
## 8   Quadrat_3 Shannon diversity 10.877508 11.082181 0.4571960 10.186093
## 9   Quadrat_3 Simpson diversity  7.673620  7.754736 0.3537791  7.061342
## 10  Quadrat_4  Species richness 18.000000 19.997561 2.8934624 18.000000
## 11  Quadrat_4 Shannon diversity  9.098377  9.209640 0.3269323  8.568865
## 12  Quadrat_4 Simpson diversity  7.137398  7.191288 0.2558758  6.689781
## 13  Quadrat_5  Species richness 19.000000 23.494361 3.8481549 19.000000
## 14  Quadrat_5 Shannon diversity 12.511066 12.694857 0.3695457 11.970561
## 15  Quadrat_5 Simpson diversity 10.531256 10.658723 0.4355828  9.804996
##          UCL
## 1  27.545935
## 2  11.463445
## 3   9.201479
## 4  17.275777
## 5  12.230892
## 6   9.367557
## 7  29.707533
## 8  11.978268
## 9   8.448131
## 10 25.668643
## 11  9.850416
## 12  7.692795
## 13 31.036606
## 14 13.419154
## 15 11.512450
p <- c(820)

Fallin_Datap <- iNEXT(Fallin_Nos, q=c(0), datatype= "abundance", size = p)

Fallin_Datap
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 711    18 0.9958  3  0  1  1  0  0  0  0  0   0
## 2  Quadrat_2 525    17 1.0000  0  0  0  0  1  1  0  0  1   3
## 3  Quadrat_3 639    23 0.9969  2  3  0  0  0  1  0  2  0   7
## 4  Quadrat_4 820    18 0.9976  2  1  0  1  0  0  1  0  0   3
## 5  Quadrat_5 798    19 0.9962  3  1  0  0  0  0  0  0  0   1
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD   qD.LCL   qD.UCL        SC
## 1   Quadrat_1 710   Rarefaction       0 17.99578 16.02751 19.96405 0.9957806
## 2   Quadrat_1 711      Observed       0 18.00000 16.02966 19.97034 0.9957865
## 3   Quadrat_1 712 Extrapolation       0 18.00421 16.03166 19.97676 0.9957925
## 4   Quadrat_1 820 Extrapolation       0 18.42607 16.21451 20.63764 0.9963858
## 5   Quadrat_2 524   Rarefaction       0 17.00000 16.99869 17.00131 1.0000000
## 6   Quadrat_2 525      Observed       0 17.00000 17.00000 17.00000 1.0000000
## 7   Quadrat_2 526 Extrapolation       0 17.00000 17.00000 17.00000 1.0000000
## 8   Quadrat_2 820 Extrapolation       0 17.00000 17.00000 17.00000 1.0000000
## 9   Quadrat_3 638   Rarefaction       0 22.99687 21.19952 24.79422 0.9968701
## 10  Quadrat_3 639      Observed       0 23.00000 21.20105 24.79895 0.9968848
## 11  Quadrat_3 640 Extrapolation       0 23.00312 21.20256 24.80367 0.9968993
## 12  Quadrat_3 820 Extrapolation       0 23.38087 21.26247 25.49927 0.9986673
## 13  Quadrat_4 820      Observed       0 18.00000 16.01066 19.98934 0.9975640
## 14  Quadrat_5 797   Rarefaction       0 18.99624 15.95701 22.03547 0.9962406
## 15  Quadrat_5 798      Observed       0 19.00000 15.95848 22.04152 0.9962437
## 16  Quadrat_5 799 Extrapolation       0 19.00376 15.95962 22.04789 0.9962469
## 17  Quadrat_5 820 Extrapolation       0 19.08192 15.98309 22.18074 0.9963122
##       SC.LCL    SC.UCL
## 1  0.9927629 0.9987983
## 2  0.9926376 0.9989354
## 3  0.9926451 0.9989398
## 4  0.9934159 0.9993556
## 5  0.9986915 1.0000000
## 6  1.0000000 1.0000000
## 7  1.0000000 1.0000000
## 8  1.0000000 1.0000000
## 9  0.9934851 1.0000000
## 10 0.9935006 1.0000000
## 11 0.9935161 1.0000000
## 12 0.9955697 1.0000000
## 13 0.9947974 1.0000000
## 14 0.9932530 0.9992282
## 15 0.9928911 0.9995964
## 16 0.9928957 0.9995981
## 17 0.9929899 0.9996345
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD   qD.LCL   qD.UCL
## 1   Quadrat_1 0.9957806 708   Rarefaction       0 17.98785 14.61472 21.36097
## 2   Quadrat_1 0.9957865 711      Observed       0 18.00000 14.62456 21.37544
## 3   Quadrat_1 0.9957925 712 Extrapolation       0 18.00421 14.62579 21.38264
## 4   Quadrat_1 0.9963858 820 Extrapolation       0 18.42607 14.76409 22.08806
## 5   Quadrat_2 1.0000000 525      Observed       0 17.00000 17.00000 17.00000
## 6   Quadrat_3 0.9968701 638   Rarefaction       0 22.99559 19.72336 26.26781
## 7   Quadrat_3 0.9968848 639      Observed       0 23.00000 19.72117 26.27883
## 8   Quadrat_3 0.9968993 640 Extrapolation       0 23.00312 19.71724 26.28899
## 9   Quadrat_3 0.9986673 820 Extrapolation       0 23.38087 19.19038 27.57136
## 10  Quadrat_4 0.9975640 820      Observed       0 18.00000 14.71917 21.28083
## 11  Quadrat_5 0.9962406 796   Rarefaction       0 18.99407 12.72293 25.26522
## 12  Quadrat_5 0.9962437 798      Observed       0 19.00000 12.72745 25.27255
## 13  Quadrat_5 0.9962469 799 Extrapolation       0 19.00376 12.73726 25.27026
## 14  Quadrat_5 0.9963122 820 Extrapolation       0 19.08192 12.76436 25.39948
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 18.000000 20.995781 2.6765791 18.000000
## 2   Quadrat_1 Shannon diversity 10.537842 10.696181 0.3423202 10.025246
## 3   Quadrat_1 Simpson diversity  8.351716  8.439099 0.4080958  7.639246
## 4   Quadrat_2  Species richness 17.000000 17.000000 0.0000000 17.000000
## 5   Quadrat_2 Shannon diversity 11.247195 11.422020 0.3882739 10.661017
## 6   Quadrat_2 Simpson diversity  8.349490  8.468263 0.4360577  7.613606
## 7   Quadrat_3  Species richness 23.000000 23.665623 2.9381189 23.000000
## 8   Quadrat_3 Shannon diversity 10.877508 11.082181 0.4912499 10.119349
## 9   Quadrat_3 Simpson diversity  7.673620  7.754736 0.3781209  7.013633
## 10  Quadrat_4  Species richness 18.000000 19.997561 2.1899090 18.000000
## 11  Quadrat_4 Shannon diversity  9.098377  9.209640 0.2455599  8.728352
## 12  Quadrat_4 Simpson diversity  7.137398  7.191288 0.1996344  6.800012
## 13  Quadrat_5  Species richness 19.000000 23.494361 4.5108444 19.000000
## 14  Quadrat_5 Shannon diversity 12.511066 12.694857 0.3209155 12.065875
## 15  Quadrat_5 Simpson diversity 10.531256 10.658723 0.3772578  9.919311
##          UCL
## 1  26.241779
## 2  11.367117
## 3   9.238952
## 4  17.000000
## 5  12.183022
## 6   9.322921
## 7  29.424231
## 8  12.045013
## 9   8.495840
## 10 24.289704
## 11  9.690929
## 12  7.582564
## 13 32.335453
## 14 13.323840
## 15 11.398135
q <- c(798)

Fallin_Dataq <- iNEXT(Fallin_Nos, q=c(0), datatype= "abundance", size = q)

Fallin_Dataq
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 711    18 0.9958  3  0  1  1  0  0  0  0  0   0
## 2  Quadrat_2 525    17 1.0000  0  0  0  0  1  1  0  0  1   3
## 3  Quadrat_3 639    23 0.9969  2  3  0  0  0  1  0  2  0   7
## 4  Quadrat_4 820    18 0.9976  2  1  0  1  0  0  1  0  0   3
## 5  Quadrat_5 798    19 0.9962  3  1  0  0  0  0  0  0  0   1
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD   qD.LCL   qD.UCL        SC
## 1   Quadrat_1 710   Rarefaction       0 17.99578 15.65020 20.34136 0.9957806
## 2   Quadrat_1 711      Observed       0 18.00000 15.65205 20.34795 0.9957865
## 3   Quadrat_1 712 Extrapolation       0 18.00421 15.65371 20.35472 0.9957925
## 4   Quadrat_1 798 Extrapolation       0 18.34526 15.77534 20.91518 0.9962721
## 5   Quadrat_2 524   Rarefaction       0 17.00000 16.99947 17.00053 1.0000000
## 6   Quadrat_2 525      Observed       0 17.00000 17.00000 17.00000 1.0000000
## 7   Quadrat_2 526 Extrapolation       0 17.00000 17.00000 17.00000 1.0000000
## 8   Quadrat_2 798 Extrapolation       0 17.00000 17.00000 17.00000 1.0000000
## 9   Quadrat_3 638   Rarefaction       0 22.99687 21.08266 24.91108 0.9968701
## 10  Quadrat_3 639      Observed       0 23.00000 21.08413 24.91587 0.9968848
## 11  Quadrat_3 640 Extrapolation       0 23.00312 21.08559 24.92064 0.9968993
## 12  Quadrat_3 798 Extrapolation       0 23.34991 21.13156 25.56826 0.9985224
## 13  Quadrat_4 798   Rarefaction       0 17.94565 15.70336 20.18795 0.9974984
## 14  Quadrat_4 819   Rarefaction       0 17.99756 15.71613 20.27899 0.9975610
## 15  Quadrat_4 820      Observed       0 18.00000 15.71671 20.28329 0.9975640
## 16  Quadrat_4 821 Extrapolation       0 18.00244 15.71718 20.28769 0.9975669
## 17  Quadrat_5 798      Observed       0 19.00000 16.27814 21.72186 0.9962437
##       SC.LCL    SC.UCL
## 1  0.9922742 0.9992870
## 2  0.9920535 0.9995196
## 3  0.9920623 0.9995226
## 4  0.9927731 0.9997712
## 5  0.9994720 1.0000000
## 6  1.0000000 1.0000000
## 7  1.0000000 1.0000000
## 8  1.0000000 1.0000000
## 9  0.9934783 1.0000000
## 10 0.9934931 1.0000000
## 11 0.9935078 1.0000000
## 12 0.9952639 1.0000000
## 13 0.9947530 1.0000000
## 14 0.9947916 1.0000000
## 15 0.9946627 1.0000000
## 16 0.9946682 1.0000000
## 17 0.9930249 0.9994626
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD   qD.LCL   qD.UCL
## 1   Quadrat_1 0.9957806 708   Rarefaction       0 17.98785 14.10774 21.86796
## 2   Quadrat_1 0.9957865 711      Observed       0 18.00000 14.11684 21.88316
## 3   Quadrat_1 0.9957925 712 Extrapolation       0 18.00421 14.11768 21.89075
## 4   Quadrat_1 0.9962721 798 Extrapolation       0 18.34526 14.20935 22.48117
## 5   Quadrat_2 1.0000000 525      Observed       0 17.00000 17.00000 17.00000
## 6   Quadrat_3 0.9968701 638   Rarefaction       0 22.99559 19.00256 26.98861
## 7   Quadrat_3 0.9968848 639      Observed       0 23.00000 19.00019 26.99981
## 8   Quadrat_3 0.9968993 640 Extrapolation       0 23.00312 18.99561 27.01062
## 9   Quadrat_3 0.9985224 798 Extrapolation       0 23.34991 18.45383 28.24599
## 10  Quadrat_4 0.9974984 798   Rarefaction       0 17.94565 13.60229 22.28901
## 11  Quadrat_4 0.9975610 818   Rarefaction       0 17.99617 13.68632 22.30602
## 12  Quadrat_4 0.9975640 820      Observed       0 18.00000 13.68812 22.31188
## 13  Quadrat_4 0.9975669 821 Extrapolation       0 18.00244 13.69005 22.31483
## 14  Quadrat_5 0.9962437 798      Observed       0 19.00000 11.77365 26.22635
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 18.000000 20.995781 2.5797839 18.000000
## 2   Quadrat_1 Shannon diversity 10.537842 10.696181 0.3164605 10.075930
## 3   Quadrat_1 Simpson diversity  8.351716  8.439099 0.3339319  7.784604
## 4   Quadrat_2  Species richness 17.000000 17.000000 0.1794070 17.000000
## 5   Quadrat_2 Shannon diversity 11.247195 11.422020 0.4856249 10.470212
## 6   Quadrat_2 Simpson diversity  8.349490  8.468263 0.4938911  7.500255
## 7   Quadrat_3  Species richness 23.000000 23.665623 2.7767448 23.000000
## 8   Quadrat_3 Shannon diversity 10.877508 11.082181 0.4592343 10.182098
## 9   Quadrat_3 Simpson diversity  7.673620  7.754736 0.3543317  7.060259
## 10  Quadrat_4  Species richness 18.000000 19.997561 2.7697791 18.000000
## 11  Quadrat_4 Shannon diversity  9.098377  9.209640 0.2929990  8.635373
## 12  Quadrat_4 Simpson diversity  7.137398  7.191288 0.2218285  6.756512
## 13  Quadrat_5  Species richness 19.000000 23.494361 6.4976740 19.000000
## 14  Quadrat_5 Shannon diversity 12.511066 12.694857 0.3705154 11.968661
## 15  Quadrat_5 Simpson diversity 10.531256 10.658723 0.3879325  9.898389
##          UCL
## 1  26.052064
## 2  11.316433
## 3   9.093593
## 4  17.351631
## 5  12.373827
## 6   9.436272
## 7  29.107943
## 8  11.982263
## 9   8.449214
## 10 25.426228
## 11  9.783908
## 12  7.626064
## 13 36.229568
## 14 13.421054
## 15 11.419057

#Now to run the analysis again for Fallin without specificying the size, can do this for #looking at the other diversity indices

Fallin_Data <- iNEXT(Fallin_Nos, q=c(0), datatype= "abundance")

Fallin_Data
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 711    18 0.9958  3  0  1  1  0  0  0  0  0   0
## 2  Quadrat_2 525    17 1.0000  0  0  0  0  1  1  0  0  1   3
## 3  Quadrat_3 639    23 0.9969  2  3  0  0  0  1  0  2  0   7
## 4  Quadrat_4 820    18 0.9976  2  1  0  1  0  0  1  0  0   3
## 5  Quadrat_5 798    19 0.9962  3  1  0  0  0  0  0  0  0   1
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage    m        Method Order.q       qD   qD.LCL   qD.UCL         SC
## 1    Quadrat_1    1   Rarefaction       0  1.00000  1.00000  1.00000 0.11849607
## 10   Quadrat_1  355   Rarefaction       0 16.31000 14.82167 17.79833 0.99400865
## 20   Quadrat_1  711      Observed       0 18.00000 15.85845 20.14155 0.99578653
## 30   Quadrat_1 1048 Extrapolation       0 19.13147 16.19933 22.06361 0.99737790
## 40   Quadrat_1 1422 Extrapolation       0 19.89447 16.19687 23.59207 0.99845104
## 41   Quadrat_2    1   Rarefaction       0  1.00000  1.00000  1.00000 0.11808797
## 50   Quadrat_2  262   Rarefaction       0 16.94907 16.60823 17.28992 0.99889192
## 60   Quadrat_2  525      Observed       0 17.00000 16.72282 17.27718 1.00000000
## 70   Quadrat_2  774 Extrapolation       0 17.00000 16.72282 17.27718 1.00000000
## 80   Quadrat_2 1050 Extrapolation       0 17.00000 16.72282 17.27718 1.00000000
## 81   Quadrat_3    1   Rarefaction       0  1.00000  1.00000  1.00000 0.12895345
## 90   Quadrat_3  319   Rarefaction       0 21.21760 19.83377 22.60142 0.99148671
## 100  Quadrat_3  639      Observed       0 23.00000 21.11923 24.88077 0.99688476
## 110  Quadrat_3  942 Extrapolation       0 23.50496 21.19783 25.81210 0.99924808
## 120  Quadrat_3 1278 Extrapolation       0 23.63241 20.91129 26.35352 0.99984454
## 121  Quadrat_4    1   Rarefaction       0  1.00000  1.00000  1.00000 0.13905715
## 130  Quadrat_4  410   Rarefaction       0 16.67786 15.32155 18.03418 0.99553952
## 140  Quadrat_4  820      Observed       0 18.00000 15.89687 20.10313 0.99756395
## 150  Quadrat_4 1208 Extrapolation       0 18.75339 15.93197 21.57481 0.99848272
## 160  Quadrat_4 1640 Extrapolation       0 19.26315 15.80136 22.72494 0.99910437
## 161  Quadrat_5    1   Rarefaction       0  1.00000  1.00000  1.00000 0.09381987
## 170  Quadrat_5  399   Rarefaction       0 17.24938 15.44530 19.05345 0.99496536
## 180  Quadrat_5  798      Observed       0 19.00000 16.22367 21.77633 0.99624374
## 190  Quadrat_5 1176 Extrapolation       0 20.21788 16.56135 23.87441 0.99726161
## 200  Quadrat_5 1596 Extrapolation       0 21.18817 16.67576 25.70057 0.99807255
##         SC.LCL     SC.UCL
## 1   0.10705886 0.12993327
## 10  0.99084152 0.99717579
## 20  0.99226313 0.99930992
## 30  0.99465870 1.00000000
## 40  0.99643358 1.00000000
## 41  0.10602596 0.13014998
## 50  0.99711842 1.00000000
## 60  1.00000000 1.00000000
## 70  1.00000000 1.00000000
## 80  1.00000000 1.00000000
## 81  0.11737095 0.14053595
## 90  0.98841964 0.99455378
## 100 0.99371316 1.00000000
## 110 0.99687917 1.00000000
## 120 0.99817566 1.00000000
## 121 0.12884632 0.14926798
## 130 0.99285842 0.99822062
## 140 0.99480880 1.00000000
## 150 0.99645732 1.00000000
## 160 0.99765049 1.00000000
## 161 0.08824497 0.09939476
## 170 0.99157185 0.99835887
## 180 0.99296866 0.99951883
## 190 0.99455739 0.99996584
## 200 0.99593744 1.00000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage         SC    m        Method Order.q        qD     qD.LCL
## 1    Quadrat_1 0.11849715    1   Rarefaction       0  1.000009  0.9547203
## 10   Quadrat_1 0.99400865  355   Rarefaction       0 16.309997 13.8351620
## 20   Quadrat_1 0.99578653  711      Observed       0 18.000000 14.5744879
## 30   Quadrat_1 0.99737790 1048 Extrapolation       0 19.131471 14.8395080
## 40   Quadrat_1 0.99845104 1422 Extrapolation       0 19.894470 14.9456555
## 41   Quadrat_2 0.11808836    1   Rarefaction       0  1.000003  0.9398288
## 45   Quadrat_2 0.98313198  117   Rarefaction       0 16.112326 15.6497955
## 50   Quadrat_2 0.99889192  262   Rarefaction       0 16.949072 16.6746816
## 55   Quadrat_2 0.99997119  407   Rarefaction       0 16.999345 16.7221711
## 59   Quadrat_2 1.00000000  525      Observed       0 17.000000 16.7228192
## 60   Quadrat_3 0.12895345    1   Rarefaction       0  1.000000  0.9616279
## 69   Quadrat_3 0.99148671  319   Rarefaction       0 21.217597 19.3891731
## 79   Quadrat_3 0.99688476  639      Observed       0 23.000000 20.3006433
## 89   Quadrat_3 0.99924808  942 Extrapolation       0 23.504962 20.0175933
## 99   Quadrat_3 0.99984454 1278 Extrapolation       0 23.632406 19.8924815
## 100  Quadrat_4 0.13905905    1   Rarefaction       0  1.000013  0.9639310
## 109  Quadrat_4 0.99553952  410   Rarefaction       0 16.677864 14.4288030
## 119  Quadrat_4 0.99756395  820      Observed       0 18.000000 14.5059798
## 129  Quadrat_4 0.99848272 1208 Extrapolation       0 18.753392 14.6631126
## 139  Quadrat_4 0.99910437 1640 Extrapolation       0 19.263148 14.7722037
## 140  Quadrat_5 0.09381987    1   Rarefaction       0  1.000000  0.9724142
## 149  Quadrat_5 0.99496536  399   Rarefaction       0 17.249377 13.3355966
## 159  Quadrat_5 0.99624374  798      Observed       0 19.000000 13.9693487
## 169  Quadrat_5 0.99726161 1176 Extrapolation       0 20.217880 14.4462993
## 179  Quadrat_5 0.99807255 1596 Extrapolation       0 21.188165 15.0551922
##        qD.UCL
## 1    1.045297
## 10  18.784832
## 20  21.425512
## 30  23.423434
## 40  24.843284
## 41   1.060178
## 45  16.574857
## 50  17.223462
## 55  17.276519
## 59  17.277181
## 60   1.038372
## 69  23.046022
## 79  25.699357
## 89  26.992331
## 99  27.372331
## 100  1.036095
## 109 18.926925
## 119 21.494020
## 129 22.843672
## 139 23.754092
## 140  1.027586
## 149 21.163158
## 159 24.030651
## 169 25.989461
## 179 27.321138
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 18.000000 20.995781 3.3166724 18.000000
## 2   Quadrat_1 Shannon diversity 10.537842 10.696181 0.2890815 10.129592
## 3   Quadrat_1 Simpson diversity  8.351716  8.439099 0.3505210  7.752090
## 4   Quadrat_2  Species richness 17.000000 17.000000 0.0000000 17.000000
## 5   Quadrat_2 Shannon diversity 11.247195 11.422020 0.4316300 10.576040
## 6   Quadrat_2 Simpson diversity  8.349490  8.468263 0.4818153  7.523923
## 7   Quadrat_3  Species richness 23.000000 23.665623 2.8100777 23.000000
## 8   Quadrat_3 Shannon diversity 10.877508 11.082181 0.4836387 10.134266
## 9   Quadrat_3 Simpson diversity  7.673620  7.754736 0.3617445  7.045730
## 10  Quadrat_4  Species richness 18.000000 19.997561 2.7870183 18.000000
## 11  Quadrat_4 Shannon diversity  9.098377  9.209640 0.2783747  8.664036
## 12  Quadrat_4 Simpson diversity  7.137398  7.191288 0.2193769  6.761317
## 13  Quadrat_5  Species richness 19.000000 23.494361 4.5088587 19.000000
## 14  Quadrat_5 Shannon diversity 12.511066 12.694857 0.2911877 12.124140
## 15  Quadrat_5 Simpson diversity 10.531256 10.658723 0.3384654  9.995343
##          UCL
## 1  27.496339
## 2  11.262771
## 3   9.126107
## 4  17.000000
## 5  12.267999
## 6   9.412604
## 7  29.173274
## 8  12.030095
## 9   8.463743
## 10 25.460017
## 11  9.755245
## 12  7.621259
## 13 32.331561
## 14 13.265575
## 15 11.322103
F1 <- diversity(Fallin_Nos$Quadrat_1)

#Now to do other analyses to generate further biodiversity indices for Fallin, including coverage

Fallin2 <- estimateD(Fallin_Nos, q = c(0,1,2), datatype = "abundance", base="coverage")
Fallin2
##    Assemblage         m        Method Order.q        SC        qD    qD.LCL
## 1   Quadrat_1 1266.6741 Extrapolation       0 0.9980725 19.625362 14.996248
## 2   Quadrat_1 1266.6741 Extrapolation       1 0.9980725 10.621084 10.126700
## 3   Quadrat_1 1266.6741 Extrapolation       2 0.9980725  8.389826  7.742133
## 4   Quadrat_2  232.8222   Rarefaction       0 0.9980725 16.905394 16.826185
## 5   Quadrat_2  232.8222   Rarefaction       1 0.9980725 11.022989 10.207929
## 6   Quadrat_2  232.8222   Rarefaction       2 0.9980725  8.205068  7.231886
## 7   Quadrat_3  741.3429 Extrapolation       0 0.9980725 23.253791 19.245390
## 8   Quadrat_3  741.3429 Extrapolation       1 0.9980725 10.909101  9.895418
## 9   Quadrat_3  741.3429 Extrapolation       2 0.9980725  7.684717  6.837757
## 10  Quadrat_4 1011.9098 Extrapolation       0 0.9980725 18.417051 15.178425
## 11  Quadrat_4 1011.9098 Extrapolation       1 0.9980725  9.121107  8.590401
## 12  Quadrat_4 1011.9098 Extrapolation       2 0.9980725  7.147556  6.749009
## 13  Quadrat_5 1596.0000 Extrapolation       0 0.9980725 21.188165 15.699138
## 14  Quadrat_5 1596.0000 Extrapolation       1 0.9980725 12.621079 11.894762
## 15  Quadrat_5 1596.0000 Extrapolation       2 0.9980725 10.594606  9.902558
##       qD.UCL
## 1  24.254477
## 2  11.115468
## 3   9.037519
## 4  16.984603
## 5  11.838048
## 6   9.178249
## 7  27.262193
## 8  11.922784
## 9   8.531677
## 10 21.655676
## 11  9.651813
## 12  7.546104
## 13 26.677192
## 14 13.347397
## 15 11.286655

#Now to do vegan analyses for species evenness for Fallin data

Fevenness1 <- F1/log(specnumber(Fallin_Nos$Quadrat_1))

summary(Fevenness1)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8148  0.8148  0.8148  0.8148  0.8148  0.8148
F2 <- diversity(Fallin_Nos$Quadrat_2)

Fevenness2 <- F2/log(specnumber(Fallin_Nos$Quadrat_2))

summary(Fevenness2)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8542  0.8542  0.8542  0.8542  0.8542  0.8542
F3 <- diversity(Fallin_Nos$Quadrat_3)

Fevenness3 <- F3/log(specnumber(Fallin_Nos$Quadrat_3))

summary(Fevenness3)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7612  0.7612  0.7612  0.7612  0.7612  0.7612
F4 <- diversity(Fallin_Nos$Quadrat_4)

Fevenness4 <- F4/log(specnumber(Fallin_Nos$Quadrat_4))

summary(Fevenness4)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7639  0.7639  0.7639  0.7639  0.7639  0.7639
F5 <- diversity(Fallin_Nos$Quadrat_5)

Fevenness5 <- F5/log(specnumber(Fallin_Nos$Quadrat_5))

summary(Fevenness5)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8581  0.8581  0.8581  0.8581  0.8581  0.8581

#Now to generate some graphs for Fallin data for better visualisation, including to visualise species curves#

Fallin_Data_Graph1 <- ggiNEXT(x = Fallin_Data, se=TRUE, color.var="Order.q")

Fallin_Data_Graph1

Fallin_Data_Graph1.1 <- ggiNEXT(x = Fallin_Data, se=TRUE, type = 1,
                                facet.var="None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Fallin_Data_Graph1.1

Falling <- Fallin_Data_Graph1.1 + theme_hc(style = "darkunica") +
  scale_colour_hc("darkunica")
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Falling

Fallin_Data_Graph2 <- ggiNEXT(x = Fallin_Data, se=TRUE, type = 1,
                              facet.var="None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Fallin_Data_Graph2

Fallin_Data_Graph3 <- ggiNEXT(x = Fallin_Data, se=TRUE, type = 2,
                              facet.var="None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Fallin_Data_Graph3

Falling3 <- Fallin_Data_Graph3 + theme_hc(style = "darkunica") +
  scale_colour_hc("darkunica")
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Falling3

Fallin_Data_Graph4 <- ggiNEXT(x = Fallin_Data, se=TRUE, type = 3,
                              facet.var="None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Fallin_Data_Graph4

Falling4 <- Fallin_Data_Graph4 + theme_hc(style = "darkunica") +
  scale_colour_hc("darkunica")
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Falling4

##Addiewell Data##

##Loading the Addiewell data##

urlfile3 <- 'https://raw.githubusercontent.com/Savannankvm/Biodiversity-analyses-for-six-study-sites/PhD-files/Addiewell_Abundance_Data.csv'

Addiewell_Nos <-read.csv(urlfile3)

print(Addiewell_Nos)
##     Quadrat.1 Quadrat.2 Quadrat.3 Quadrat.4 Quadrat.5
## 1           1         0         0         0        14
## 2           0         0         0         0         0
## 3           0         0         0         0         0
## 4           0         0         0         0         0
## 5           0         0         0         0         0
## 6           0         0         0         0         0
## 7           0         0         0         0         0
## 8           0         0         0         0        11
## 9           0         0         3         1         0
## 10          0         0        10         0         0
## 11          0         0         0         0         0
## 12          0         0         0         0         0
## 13          0         0         0         0         0
## 14          0         0         0         0         0
## 15          0         0         0         0         0
## 16         10         0         0         0         0
## 17         10        80         0         0       150
## 18         10         0         0        10        10
## 19          0         0         0         0         0
## 20          0         0         0         0         0
## 21          0         0         0         0         0
## 22          0         0         0         0         0
## 23          0         0         0         0         0
## 24          0         0        10         0         0
## 25         30       120       150        90         0
## 26        130        80        30       110        10
## 27          0         0         0         0         0
## 28          0         0         0         0         0
## 29          0         0         1         0         9
## 30          0         0         0         0         0
## 31          0         0         0         0         0
## 32          0         2         0         0         0
## 33          0         0         0         0         0
## 34          0         0         0         0         0
## 35          0         0         0         0         0
## 36          0         0         0         0         0
## 37          0         0         4         0         0
## 38          0         0         0         0         0
## 39          0         0         0         0         0
## 40          4         0         3         0         0
## 41          0         0         0         0         0
## 42          0         0         0         0        16
## 43          0         0         0         0        12
## 44          0         0        22         0         1
## 45          0         0         0         0         1
## 46          0         0         0         0         0
## 47          0         0         0         0         0
## 48          0         0         0        50         0
## 49          8         1         0         0         0
## 50          0         0         0         0         0
## 51          0         0         0         0         0
## 52          0         0         0         0         0
## 53          0         0         0         0         0
## 54          0         0         0         0         0
## 55          0         0         0         0         0
## 56          0         0         0         0         0
## 57         27         0         0         0         0
## 58          0         0         0         0         0
## 59          0         0         0         0         0
## 60          0         0         0         0         0
## 61          0         0         0         0         0
## 62          0         0         0         0         0
## 63          0         0         0         0         0
## 64          0         0         0         0         0
## 65          0         0         0         0         0
## 66          0         0         0         0         0
## 67          0         0         0         0         0
## 68          0         0         0         0         0
## 69          0         8         0         0         1
## 70          0         0         0         0         0
## 71          5        14        36         0         0
## 72          0         0         0         0         0
## 73          0         0         0       143         1
## 74          0         0         0         0         0
## 75          0         0         1        90         0
## 76          0         0         0         0         0
## 77          0         0         0        20        50
## 78          0         0         0        60         0
## 79          0         0         0         0        10
## 80          0         0         0         0         0
## 81         10        60         0        30        10
## 82          0         0        30         0        18
## 83          0         0         0         0         0
## 84          0         0         0         0         0
## 85          0         0         0         0         0
## 86          0         0         0         0         0
## 87          0         0         0         0         0
## 88          0         0         0         0         0
## 89          0         0         0         0         0
## 90          0         0         1         0         0
## 91          0         0         0         0         0
## 92          0         0         0         0         0
## 93          0         0         2         0         0
## 94          0         0         0         0         2
## 95          0         0         0         0         0
## 96          0         0         0         0         0
## 97          0         0         0         0         0
## 98          0         0         0         0         0
## 99          0         0         0         0         0
## 100         0         0         0         0         8
## 101         0         0         0        60         0
## 102         0         0         0         0         0
## 103         0         0         0         0         0
## 104         0         0         0        10         0
## 105         0         0         0        10         0
## 106         0         0         0         0         0
## 107         0         0         0         0         4
## 108         0         0         0         0         0
## 109         0         0         0        10         0
## 110         8         4         0         0         0
## 111         0         0         0         0         0
## 112         0         0         0         0         0
## 113         5         0        23         0         0
## 114         0         0         0         0         0
## 115         0         0         0         0         4
## 116         0         0         4         0         0
## 117       130       160       110       110         0
## 118         0         0         0         0         0
## 119         3         0         0         0         0
## 120         0         0         0         0         0
## 121         0         0        10        10         0
## 122         0         0         0         0         0
## 123         0         0         0         0         0
## 124         0         0         0         0         0
## 125         0         3         0         0         0
## 126         0         0         0         0         0
## 127         0         0         0         0         0
## 128         0         1         0         0         0
## 129         0         0        20        10         0
## 130         0         0         0         0         0
## 131         0         0         0         0         0
## 132         0         0         0         0         0
## 133         0         0         0         0         0
## 134         0         0         5         0         1
## 135         0         0        35         0         0
## 136         0         0         1         0         0
## 137         0         0         0         0         0
## 138         1         0         0         0        52
## 139         0         0         0         0         0
## 140         0         0       110         0         0
## 141        28         0         0         0         0
## 142         0         0         0         0         0
## 143         0         0         0         0         0

#colSums to establish sample size for each of the quadrats.

colSums(Addiewell_Nos)
## Quadrat.1 Quadrat.2 Quadrat.3 Quadrat.4 Quadrat.5 
##       420       533       621       824       395

#Setting m to sample size for Quadrat 1. This will give me observed #qD value that will be most representative for Quadrat and Community. Will do the same #for the other communities below.

m <- c(420)

Addiewell_Datam <- iNEXT(Addiewell_Nos, q=c(0), datatype= "abundance", size = m)

Addiewell_Datam
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat.1 420    17 0.9953  2  0  1  1  2  0  0  2  0   4
## 2  Quadrat.2 533    12 0.9963  2  1  1  1  0  0  0  1  0   0
## 3  Quadrat.3 621    23 0.9936  4  1  2  2  1  0  0  0  0   3
## 4  Quadrat.4 824    17 1.0000  1  0  0  0  0  0  0  0  0   6
## 5  Quadrat.5 395    22 0.9874  5  1  0  2  0  0  0  1  1   4
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 420      Observed       0 17.00000 15.582772 18.41723 0.9952607
## 2   Quadrat.2 420   Rarefaction       0 11.52008  9.720600 13.31956 0.9951412
## 3   Quadrat.2 532   Rarefaction       0 11.99625  9.866985 14.12551 0.9962477
## 4   Quadrat.2 533      Observed       0 12.00000  9.867623 14.13238 0.9962547
## 5   Quadrat.2 534 Extrapolation       0 12.00375  9.867865 14.13963 0.9962617
## 6   Quadrat.3 420   Rarefaction       0 21.50880 19.089807 23.92779 0.9910028
## 7   Quadrat.3 620   Rarefaction       0 22.99356 19.859039 26.12808 0.9935588
## 8   Quadrat.3 621      Observed       0 23.00000 19.861808 26.13819 0.9935640
## 9   Quadrat.3 622 Extrapolation       0 23.00644 19.864389 26.14848 0.9935692
## 10  Quadrat.4 420   Rarefaction       0 16.50516 15.795169 17.21515 0.9986738
## 11  Quadrat.4 823   Rarefaction       0 16.99879 16.022180 17.97539 0.9987864
## 12  Quadrat.4 824      Observed       0 17.00000 16.022822 17.97718 1.0000000
## 13  Quadrat.4 825 Extrapolation       0 17.00000 16.022822 17.97718 1.0000000
## 14  Quadrat.5 394   Rarefaction       0 21.98734 18.680746 25.29394 0.9873418
## 15  Quadrat.5 395      Observed       0 22.00000 18.687056 25.31294 0.9873546
## 16  Quadrat.5 396 Extrapolation       0 22.01265 18.693351 25.33194 0.9873674
## 17  Quadrat.5 420 Extrapolation       0 22.31232 18.839860 25.78477 0.9876714
##       SC.LCL    SC.UCL
## 1  0.9909590 0.9995625
## 2  0.9906998 0.9995826
## 3  0.9914930 1.0000000
## 4  0.9910385 1.0000000
## 5  0.9910488 1.0000000
## 6  0.9857041 0.9963015
## 7  0.9880481 0.9990694
## 8  0.9877873 0.9993407
## 9  0.9877902 0.9993481
## 10 0.9973938 0.9999539
## 11 0.9977076 0.9998652
## 12 1.0000000 1.0000000
## 13 1.0000000 1.0000000
## 14 0.9796803 0.9950032
## 15 0.9796908 0.9950184
## 16 0.9797013 0.9950336
## 17 0.9799525 0.9953902
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9952607 420      Observed       0 17.00000 15.196298 18.80370
## 2   Quadrat.2 0.9951412 420   Rarefaction       0 11.52008  6.836787 16.20338
## 3   Quadrat.2 0.9962477 531   Rarefaction       0 11.99369  6.789630 17.19774
## 4   Quadrat.2 0.9962547 533      Observed       0 12.00000  6.792467 17.20753
## 5   Quadrat.2 0.9962617 534 Extrapolation       0 12.00375  6.793103 17.21439
## 6   Quadrat.3 0.9910028 420   Rarefaction       0 21.50880 13.016106 30.00149
## 7   Quadrat.3 0.9935588 620   Rarefaction       0 22.99315 12.227294 33.75900
## 8   Quadrat.3 0.9935640 621      Observed       0 23.00000 12.228869 33.77113
## 9   Quadrat.3 0.9935692 622 Extrapolation       0 23.00644 12.231578 33.78129
## 10  Quadrat.4 0.9986738 420   Rarefaction       0 16.50516 15.690211 17.32011
## 11  Quadrat.4 0.9987864 800   Rarefaction       0 16.97117 15.988634 17.95370
## 12  Quadrat.4 1.0000000 824      Observed       0 17.00000 16.022822 17.97718
## 13  Quadrat.5 0.9873418 394   Rarefaction       0 21.98355 12.673092 31.29401
## 14  Quadrat.5 0.9873546 395      Observed       0 22.00000 12.681182 31.31882
## 15  Quadrat.5 0.9873674 396 Extrapolation       0 22.01265 12.686203 31.33909
## 16  Quadrat.5 0.9876714 420 Extrapolation       0 22.31232 12.790731 31.83390
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat.1  Species richness 17.000000 17.997619  1.5171731 17.000000
## 2   Quadrat.1 Shannon diversity  7.331452  7.490633  0.4272095  6.653317
## 3   Quadrat.1 Simpson diversity  4.791135  4.834881  0.2828891  4.280429
## 4   Quadrat.2  Species richness 12.000000 13.996248  2.4994278 12.000000
## 5   Quadrat.2 Shannon diversity  5.936430  6.014410  0.1964995  5.629278
## 6   Quadrat.2 Simpson diversity  5.011183  5.049254  0.1760017  4.704297
## 7   Quadrat.3  Species richness 23.000000 30.987118  7.9131110 23.000000
## 8   Quadrat.3 Shannon diversity 10.402538 10.660309  0.4875661  9.704697
## 9   Quadrat.3 Simpson diversity  7.301456  7.376427  0.3907707  6.610531
## 10  Quadrat.4  Species richness 17.000000 17.000000  0.4852366 17.000000
## 11  Quadrat.4 Shannon diversity 11.213290 11.324644  0.2943362 10.747756
## 12  Quadrat.4 Simpson diversity  9.371649  9.467959  0.2995201  8.880910
## 13  Quadrat.5  Species richness 22.000000 34.468354 10.1896597 22.000000
## 14  Quadrat.5 Shannon diversity  9.244176  9.633365  0.6729454  8.314416
## 15  Quadrat.5 Simpson diversity  5.319457  5.378421  0.4911000  4.415883
##          UCL
## 1  20.971224
## 2   8.327948
## 3   5.389334
## 4  18.895036
## 5   6.399542
## 6   5.394211
## 7  46.496530
## 8  11.615921
## 9   8.142324
## 10 17.951046
## 11 11.901532
## 12 10.055007
## 13 54.439721
## 14 10.952313
## 15  6.340960
n <- c(533)

Addiewell_Datan <- iNEXT(Addiewell_Nos, q=c(0), datatype= "abundance", size = n)

Addiewell_Datan
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat.1 420    17 0.9953  2  0  1  1  2  0  0  2  0   4
## 2  Quadrat.2 533    12 0.9963  2  1  1  1  0  0  0  1  0   0
## 3  Quadrat.3 621    23 0.9936  4  1  2  2  1  0  0  0  0   3
## 4  Quadrat.4 824    17 1.0000  1  0  0  0  0  0  0  0  0   6
## 5  Quadrat.5 395    22 0.9874  5  1  0  2  0  0  0  1  1   4
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 419   Rarefaction       0 16.99524 15.436563 18.55391 0.9952381
## 2   Quadrat.1 420      Observed       0 17.00000 15.438040 18.56196 0.9952607
## 3   Quadrat.1 421 Extrapolation       0 17.00474 15.439499 18.56998 0.9952832
## 4   Quadrat.1 533 Extrapolation       0 17.41515 15.490223 19.34008 0.9972329
## 5   Quadrat.2 533      Observed       0 12.00000  9.942466 14.05753 0.9962547
## 6   Quadrat.3 533   Rarefaction       0 22.40695 18.706597 26.10730 0.9928810
## 7   Quadrat.3 620   Rarefaction       0 22.99356 18.853946 27.13317 0.9935588
## 8   Quadrat.3 621      Observed       0 23.00000 18.855319 27.14468 0.9935640
## 9   Quadrat.3 622 Extrapolation       0 23.00644 18.856557 27.15631 0.9935692
## 10  Quadrat.4 533   Rarefaction       0 16.64668 15.908612 17.38475 0.9987808
## 11  Quadrat.4 823   Rarefaction       0 16.99879 16.092065 17.90551 0.9987864
## 12  Quadrat.4 824      Observed       0 17.00000 16.092713 17.90729 1.0000000
## 13  Quadrat.4 825 Extrapolation       0 17.00000 16.092682 17.90732 1.0000000
## 14  Quadrat.5 394   Rarefaction       0 21.98734 18.462396 25.51229 0.9873418
## 15  Quadrat.5 395      Observed       0 22.00000 18.468067 25.53193 0.9873546
## 16  Quadrat.5 396 Extrapolation       0 22.01265 18.473719 25.55157 0.9873674
## 17  Quadrat.5 533 Extrapolation       0 23.62922 19.080142 28.17829 0.9890070
##       SC.LCL    SC.UCL
## 1  0.9902529 1.0000000
## 2  0.9901144 1.0000000
## 3  0.9901510 1.0000000
## 4  0.9933260 1.0000000
## 5  0.9915397 1.0000000
## 6  0.9867802 0.9989818
## 7  0.9873556 0.9997619
## 8  0.9872178 0.9999101
## 9  0.9872216 0.9999167
## 10 0.9976544 0.9999072
## 11 0.9976331 0.9999397
## 12 0.9996644 1.0000000
## 13 0.9996652 1.0000000
## 14 0.9786457 0.9960378
## 15 0.9786521 0.9960571
## 16 0.9786586 0.9960763
## 17 0.9799826 0.9980313
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9952381 418   Rarefaction       0 16.99178 14.505977 19.47759
## 2   Quadrat.1 0.9952607 420      Observed       0 17.00000 14.508573 19.49143
## 3   Quadrat.1 0.9952832 421 Extrapolation       0 17.00474 14.507673 19.50181
## 4   Quadrat.1 0.9972329 533 Extrapolation       0 17.41515 14.409219 20.42108
## 5   Quadrat.2 0.9962547 533      Observed       0 12.00000  7.776227 16.22377
## 6   Quadrat.3 0.9928810 533   Rarefaction       0 22.40695 10.410389 34.40351
## 7   Quadrat.3 0.9935588 620   Rarefaction       0 22.99315 10.245564 35.74073
## 8   Quadrat.3 0.9935640 621      Observed       0 23.00000 10.246950 35.75305
## 9   Quadrat.3 0.9935692 622 Extrapolation       0 23.00644 10.247914 35.76496
## 10  Quadrat.4 0.9987808 533   Rarefaction       0 16.64668 15.808892 17.48447
## 11  Quadrat.4 0.9987864 800   Rarefaction       0 16.97117 16.047791 17.89454
## 12  Quadrat.4 1.0000000 824      Observed       0 17.00000 16.069505 17.93050
## 13  Quadrat.5 0.9873418 394   Rarefaction       0 21.98355 12.926733 31.04037
## 14  Quadrat.5 0.9873546 395      Observed       0 22.00000 12.934297 31.06570
## 15  Quadrat.5 0.9873674 396 Extrapolation       0 22.01265 12.939509 31.08578
## 16  Quadrat.5 0.9890070 533 Extrapolation       0 23.62922 13.440676 33.81776
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat.1  Species richness 17.000000 17.997619  1.2733565 17.000000
## 2   Quadrat.1 Shannon diversity  7.331452  7.490633  0.4227210  6.662115
## 3   Quadrat.1 Simpson diversity  4.791135  4.834881  0.2990490  4.248756
## 4   Quadrat.2  Species richness 12.000000 13.996248  2.6873168 12.000000
## 5   Quadrat.2 Shannon diversity  5.936430  6.014410  0.1959176  5.630418
## 6   Quadrat.2 Simpson diversity  5.011183  5.049254  0.1801781  4.696111
## 7   Quadrat.3  Species richness 23.000000 30.987118  9.0863592 23.000000
## 8   Quadrat.3 Shannon diversity 10.402538 10.660309  0.4808580  9.717844
## 9   Quadrat.3 Simpson diversity  7.301456  7.376427  0.3737002  6.643988
## 10  Quadrat.4  Species richness 17.000000 17.000000  0.4923660 17.000000
## 11  Quadrat.4 Shannon diversity 11.213290 11.324644  0.2780127 10.779749
## 12  Quadrat.4 Simpson diversity  9.371649  9.467959  0.3119682  8.856512
## 13  Quadrat.5  Species richness 22.000000 34.468354 10.5707761 22.000000
## 14  Quadrat.5 Shannon diversity  9.244176  9.633365  0.6090072  8.439732
## 15  Quadrat.5 Simpson diversity  5.319457  5.378421  0.4479466  4.500462
##          UCL
## 1  20.493352
## 2   8.319151
## 3   5.421006
## 4  19.263292
## 5   6.398401
## 6   5.402397
## 7  48.796054
## 8  11.602773
## 9   8.108866
## 10 17.965020
## 11 11.869539
## 12 10.079405
## 13 55.186695
## 14 10.826997
## 15  6.256381
o <- c(621)

Addiewell_Datao <- iNEXT(Addiewell_Nos, q=c(0), datatype= "abundance", size = o)

Addiewell_Datao
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat.1 420    17 0.9953  2  0  1  1  2  0  0  2  0   4
## 2  Quadrat.2 533    12 0.9963  2  1  1  1  0  0  0  1  0   0
## 3  Quadrat.3 621    23 0.9936  4  1  2  2  1  0  0  0  0   3
## 4  Quadrat.4 824    17 1.0000  1  0  0  0  0  0  0  0  0   6
## 5  Quadrat.5 395    22 0.9874  5  1  0  2  0  0  0  1  1   4
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD   qD.LCL   qD.UCL        SC
## 1   Quadrat.1 419   Rarefaction       0 16.99524 15.55400 18.43648 0.9952381
## 2   Quadrat.1 420      Observed       0 17.00000 15.55646 18.44354 0.9952607
## 3   Quadrat.1 421 Extrapolation       0 17.00474 15.55858 18.45090 0.9952832
## 4   Quadrat.1 621 Extrapolation       0 17.61455 15.65384 19.57525 0.9981802
## 5   Quadrat.2 532   Rarefaction       0 11.99625 10.02807 13.96443 0.9962477
## 6   Quadrat.2 533      Observed       0 12.00000 10.02966 13.97034 0.9962547
## 7   Quadrat.2 534 Extrapolation       0 12.00375 10.03091 13.97658 0.9962617
## 8   Quadrat.2 621 Extrapolation       0 12.30408 10.11009 14.49807 0.9968252
## 9   Quadrat.3 621      Observed       0 23.00000 19.23430 26.76570 0.9935640
## 10  Quadrat.4 621   Rarefaction       0 16.75364 15.98271 17.52456 0.9987862
## 11  Quadrat.4 823   Rarefaction       0 16.99879 16.07599 17.92159 0.9987864
## 12  Quadrat.4 824      Observed       0 17.00000 16.07644 17.92356 1.0000000
## 13  Quadrat.4 825 Extrapolation       0 17.00000 16.07641 17.92359 1.0000000
## 14  Quadrat.5 394   Rarefaction       0 21.98734 18.05642 25.91826 0.9873418
## 15  Quadrat.5 395      Observed       0 22.00000 18.06012 25.93988 0.9873546
## 16  Quadrat.5 396 Extrapolation       0 22.01265 18.06381 25.96148 0.9873674
## 17  Quadrat.5 621 Extrapolation       0 24.55514 18.58015 30.53013 0.9899460
##       SC.LCL    SC.UCL
## 1  0.9907670 0.9997092
## 2  0.9905002 1.0000000
## 3  0.9905359 1.0000000
## 4  0.9951066 1.0000000
## 5  0.9921086 1.0000000
## 6  0.9918174 1.0000000
## 7  0.9918297 1.0000000
## 8  0.9927944 1.0000000
## 9  0.9870667 1.0000000
## 10 0.9976826 0.9998898
## 11 0.9975889 0.9999839
## 12 0.9996644 1.0000000
## 13 0.9996652 1.0000000
## 14 0.9774539 0.9972296
## 15 0.9774656 0.9972436
## 16 0.9774772 0.9972576
## 17 0.9801911 0.9997010
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9952381 418   Rarefaction       0 16.99178 14.569378 19.41419
## 2   Quadrat.1 0.9952607 420      Observed       0 17.00000 14.571694 19.42831
## 3   Quadrat.1 0.9952832 421 Extrapolation       0 17.00474 14.571133 19.43835
## 4   Quadrat.1 0.9981802 621 Extrapolation       0 17.61455 14.491591 20.73750
## 5   Quadrat.2 0.9962477 531   Rarefaction       0 11.99369  8.533274 15.45410
## 6   Quadrat.2 0.9962547 533      Observed       0 12.00000  8.537482 15.46252
## 7   Quadrat.2 0.9962617 534 Extrapolation       0 12.00375  8.538710 15.46878
## 8   Quadrat.2 0.9968252 621 Extrapolation       0 12.30408  8.643911 15.96425
## 9   Quadrat.3 0.9935640 621      Observed       0 23.00000 10.388734 35.61127
## 10  Quadrat.4 0.9987862 621   Rarefaction       0 16.75364 15.887699 17.61957
## 11  Quadrat.4 0.9987864 800   Rarefaction       0 16.97117 16.016698 17.92563
## 12  Quadrat.4 1.0000000 824      Observed       0 17.00000 16.052805 17.94719
## 13  Quadrat.5 0.9873418 394   Rarefaction       0 21.98355  8.723317 35.24378
## 14  Quadrat.5 0.9873546 395      Observed       0 22.00000  8.730122 35.26988
## 15  Quadrat.5 0.9873674 396 Extrapolation       0 22.01265  8.732863 35.29243
## 16  Quadrat.5 0.9899460 621 Extrapolation       0 24.55514  9.312823 39.79746
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat.1  Species richness 17.000000 17.997619  1.8258693 17.000000
## 2   Quadrat.1 Shannon diversity  7.331452  7.490633  0.4025133  6.701721
## 3   Quadrat.1 Simpson diversity  4.791135  4.834881  0.2743079  4.297248
## 4   Quadrat.2  Species richness 12.000000 13.996248  2.3434945 12.000000
## 5   Quadrat.2 Shannon diversity  5.936430  6.014410  0.2038624  5.614847
## 6   Quadrat.2 Simpson diversity  5.011183  5.049254  0.1747301  4.706789
## 7   Quadrat.3  Species richness 23.000000 30.987118  6.0817005 23.000000
## 8   Quadrat.3 Shannon diversity 10.402538 10.660309  0.4339261  9.809829
## 9   Quadrat.3 Simpson diversity  7.301456  7.376427  0.3662643  6.658562
## 10  Quadrat.4  Species richness 17.000000 17.000000  0.4942747 17.000000
## 11  Quadrat.4 Shannon diversity 11.213290 11.324644  0.3011566 10.734388
## 12  Quadrat.4 Simpson diversity  9.371649  9.467959  0.3049806  8.870207
## 13  Quadrat.5  Species richness 22.000000 34.468354 11.3257461 22.000000
## 14  Quadrat.5 Shannon diversity  9.244176  9.633365  0.6905111  8.279988
## 15  Quadrat.5 Simpson diversity  5.319457  5.378421  0.4838036  4.430184
##          UCL
## 1  21.576257
## 2   8.279544
## 3   5.372515
## 4  18.589412
## 5   6.413973
## 6   5.391719
## 7  42.907032
## 8  11.510788
## 9   8.094292
## 10 17.968761
## 11 11.914900
## 12 10.065710
## 13 56.666409
## 14 10.986741
## 15  6.326659
p <- c(824)

Addiewell_Datap <- iNEXT(Addiewell_Nos, q=c(0), datatype= "abundance", size = p)

Addiewell_Datap
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat.1 420    17 0.9953  2  0  1  1  2  0  0  2  0   4
## 2  Quadrat.2 533    12 0.9963  2  1  1  1  0  0  0  1  0   0
## 3  Quadrat.3 621    23 0.9936  4  1  2  2  1  0  0  0  0   3
## 4  Quadrat.4 824    17 1.0000  1  0  0  0  0  0  0  0  0   6
## 5  Quadrat.5 395    22 0.9874  5  1  0  2  0  0  0  1  1   4
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 419   Rarefaction       0 16.99524 15.408801 18.58168 0.9952381
## 2   Quadrat.1 420      Observed       0 17.00000 15.411661 18.58834 0.9952607
## 3   Quadrat.1 421 Extrapolation       0 17.00474 15.414183 18.59530 0.9952832
## 4   Quadrat.1 824 Extrapolation       0 17.85192 15.513971 20.18986 0.9993078
## 5   Quadrat.2 532   Rarefaction       0 11.99625  9.698187 14.29431 0.9962477
## 6   Quadrat.2 533      Observed       0 12.00000  9.699267 14.30073 0.9962547
## 7   Quadrat.2 534 Extrapolation       0 12.00375  9.700114 14.30738 0.9962617
## 8   Quadrat.2 824 Extrapolation       0 12.84045  9.728173 15.95273 0.9978315
## 9   Quadrat.3 620   Rarefaction       0 22.99356 18.679937 27.30718 0.9935588
## 10  Quadrat.3 621      Observed       0 23.00000 18.681176 27.31882 0.9935640
## 11  Quadrat.3 622 Extrapolation       0 23.00644 18.682407 27.33046 0.9935692
## 12  Quadrat.3 824 Extrapolation       0 24.20570 18.786276 29.62512 0.9945355
## 13  Quadrat.4 824      Observed       0 17.00000 16.062122 17.93788 1.0000000
## 14  Quadrat.5 394   Rarefaction       0 21.98734 18.301551 25.67313 0.9873418
## 15  Quadrat.5 395      Observed       0 22.00000 18.306614 25.69339 0.9873546
## 16  Quadrat.5 396 Extrapolation       0 22.01265 18.311405 25.71389 0.9873674
## 17  Quadrat.5 824 Extrapolation       0 26.40055 19.328288 33.47281 0.9918176
##       SC.LCL    SC.UCL
## 1  0.9908473 0.9996289
## 2  0.9906312 0.9998902
## 3  0.9906669 0.9998995
## 4  0.9975973 1.0000000
## 5  0.9920523 1.0000000
## 6  0.9916075 1.0000000
## 7  0.9916210 1.0000000
## 8  0.9945809 1.0000000
## 9  0.9866841 1.0000000
## 10 0.9866857 1.0000000
## 11 0.9866873 1.0000000
## 12 0.9875708 1.0000000
## 13 1.0000000 1.0000000
## 14 0.9782194 0.9964642
## 15 0.9779993 0.9967100
## 16 0.9780093 0.9967256
## 17 0.9832734 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9952381 418   Rarefaction       0 16.99178 14.989556 18.99401
## 2   Quadrat.1 0.9952607 420      Observed       0 17.00000 14.993429 19.00657
## 3   Quadrat.1 0.9952832 421 Extrapolation       0 17.00474 14.994666 19.01481
## 4   Quadrat.1 0.9993078 824 Extrapolation       0 17.85192 15.126700 20.57714
## 5   Quadrat.2 0.9962477 531   Rarefaction       0 11.99369  8.059019 15.92835
## 6   Quadrat.2 0.9962547 533      Observed       0 12.00000  8.062645 15.93736
## 7   Quadrat.2 0.9962617 534 Extrapolation       0 12.00375  8.063892 15.94360
## 8   Quadrat.2 0.9978315 824 Extrapolation       0 12.84045  8.264952 17.41595
## 9   Quadrat.3 0.9935588 620   Rarefaction       0 22.99315  7.549295 38.43700
## 10  Quadrat.3 0.9935640 621      Observed       0 23.00000  7.549603 38.45040
## 11  Quadrat.3 0.9935692 622 Extrapolation       0 23.00644  7.550361 38.46251
## 12  Quadrat.3 0.9945355 824 Extrapolation       0 24.20570  7.556016 40.85538
## 13  Quadrat.4 1.0000000 824      Observed       0 17.00000 16.062122 17.93788
## 14  Quadrat.5 0.9873418 394   Rarefaction       0 21.98355 11.735555 32.23155
## 15  Quadrat.5 0.9873546 395      Observed       0 22.00000 11.743255 32.25674
## 16  Quadrat.5 0.9873674 396 Extrapolation       0 22.01265 11.750365 32.27493
## 17  Quadrat.5 0.9918176 824 Extrapolation       0 26.40055 13.099643 39.70145
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 17.000000 17.997619 1.4901997 17.000000
## 2   Quadrat.1 Shannon diversity  7.331452  7.490633 0.4391352  6.629943
## 3   Quadrat.1 Simpson diversity  4.791135  4.834881 0.3126308  4.222136
## 4   Quadrat.2  Species richness 12.000000 13.996248 3.1665387 12.000000
## 5   Quadrat.2 Shannon diversity  5.936430  6.014410 0.2083685  5.606015
## 6   Quadrat.2 Simpson diversity  5.011183  5.049254 0.1761846  4.703938
## 7   Quadrat.3  Species richness 23.000000 30.987118 8.9257216 23.000000
## 8   Quadrat.3 Shannon diversity 10.402538 10.660309 0.4937985  9.692481
## 9   Quadrat.3 Simpson diversity  7.301456  7.376427 0.4050483  6.582547
## 10  Quadrat.4  Species richness 17.000000 17.000000 0.4605662 17.000000
## 11  Quadrat.4 Shannon diversity 11.213290 11.324644 0.2707923 10.793901
## 12  Quadrat.4 Simpson diversity  9.371649  9.467959 0.2736255  8.931662
## 13  Quadrat.5  Species richness 22.000000 34.468354 9.3148375 22.000000
## 14  Quadrat.5 Shannon diversity  9.244176  9.633365 0.6688512  8.322440
## 15  Quadrat.5 Simpson diversity  5.319457  5.378421 0.4619844  4.472948
##          UCL
## 1  20.918357
## 2   8.351322
## 3   5.447626
## 4  20.202549
## 5   6.422804
## 6   5.394569
## 7  48.481210
## 8  11.628136
## 9   8.170307
## 10 17.902693
## 11 11.855387
## 12 10.004255
## 13 52.725101
## 14 10.944289
## 15  6.283894
q <- c(395)

Addiewell_Dataq <- iNEXT(Addiewell_Nos, q=c(0), datatype= "abundance", size = q)

Addiewell_Dataq
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat.1 420    17 0.9953  2  0  1  1  2  0  0  2  0   4
## 2  Quadrat.2 533    12 0.9963  2  1  1  1  0  0  0  1  0   0
## 3  Quadrat.3 621    23 0.9936  4  1  2  2  1  0  0  0  0   3
## 4  Quadrat.4 824    17 1.0000  1  0  0  0  0  0  0  0  0   6
## 5  Quadrat.5 395    22 0.9874  5  1  0  2  0  0  0  1  1   4
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q       qD    qD.LCL   qD.UCL        SC
## 1   Quadrat.1 395   Rarefaction       0 16.88075 15.411901 18.34961 0.9952138
## 2   Quadrat.1 419   Rarefaction       0 16.99524 15.452015 18.53846 0.9952381
## 3   Quadrat.1 420      Observed       0 17.00000 15.453678 18.54632 0.9952607
## 4   Quadrat.1 421 Extrapolation       0 17.00474 15.454830 18.55465 0.9952832
## 5   Quadrat.2 395   Rarefaction       0 11.39406  9.895696 12.89242 0.9947830
## 6   Quadrat.2 532   Rarefaction       0 11.99625 10.171817 13.82068 0.9962477
## 7   Quadrat.2 533      Observed       0 12.00000 10.172940 13.82706 0.9962547
## 8   Quadrat.2 534 Extrapolation       0 12.00375 10.174053 13.83344 0.9962617
## 9   Quadrat.3 395   Rarefaction       0 21.27582 18.909720 23.64192 0.9903687
## 10  Quadrat.3 620   Rarefaction       0 22.99356 19.774643 26.21247 0.9935588
## 11  Quadrat.3 621      Observed       0 23.00000 19.777017 26.22298 0.9935640
## 12  Quadrat.3 622 Extrapolation       0 23.00644 19.779384 26.23349 0.9935692
## 13  Quadrat.4 395   Rarefaction       0 16.47102 15.816945 17.12510 0.9985918
## 14  Quadrat.4 823   Rarefaction       0 16.99879 16.075656 17.92192 0.9987864
## 15  Quadrat.4 824      Observed       0 17.00000 16.076441 17.92356 1.0000000
## 16  Quadrat.4 825 Extrapolation       0 17.00000 16.076441 17.92356 1.0000000
## 17  Quadrat.5 395      Observed       0 22.00000 18.706994 25.29301 0.9873546
##       SC.LCL    SC.UCL
## 1  0.9907077 0.9997199
## 2  0.9908676 0.9996086
## 3  0.9905966 0.9999248
## 4  0.9906348 0.9999316
## 5  0.9912620 0.9983041
## 6  0.9922297 1.0000000
## 7  0.9922379 1.0000000
## 8  0.9922460 1.0000000
## 9  0.9848046 0.9959327
## 10 0.9875973 0.9995203
## 11 0.9876016 0.9995263
## 12 0.9876060 0.9995323
## 13 0.9971246 1.0000000
## 14 0.9977325 0.9998403
## 15 1.0000000 1.0000000
## 16 1.0000000 1.0000000
## 17 0.9787735 0.9959357
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q       qD    qD.LCL   qD.UCL
## 1   Quadrat.1 0.9952138 395   Rarefaction       0 16.88075 14.743465 19.01804
## 2   Quadrat.1 0.9952381 418   Rarefaction       0 16.99178 14.840962 19.14260
## 3   Quadrat.1 0.9952607 420      Observed       0 17.00000 14.844253 19.15575
## 4   Quadrat.1 0.9952832 421 Extrapolation       0 17.00474 14.844793 19.16469
## 5   Quadrat.2 0.9947830 395   Rarefaction       0 11.39406  8.108635 14.67948
## 6   Quadrat.2 0.9962477 531   Rarefaction       0 11.99369  8.165934 15.82144
## 7   Quadrat.2 0.9962547 533      Observed       0 12.00000  8.169258 15.83074
## 8   Quadrat.2 0.9962617 534 Extrapolation       0 12.00375  8.170343 15.83715
## 9   Quadrat.3 0.9903687 395   Rarefaction       0 21.27582 14.409598 28.14205
## 10  Quadrat.3 0.9935588 620   Rarefaction       0 22.99315 12.906402 33.07989
## 11  Quadrat.3 0.9935640 621      Observed       0 23.00000 12.907599 33.09240
## 12  Quadrat.3 0.9935692 622 Extrapolation       0 23.00644 12.909760 33.10311
## 13  Quadrat.4 0.9985918 395   Rarefaction       0 16.47102 15.704047 17.23800
## 14  Quadrat.4 0.9987864 800   Rarefaction       0 16.97117 16.063812 17.87852
## 15  Quadrat.4 1.0000000 824      Observed       0 17.00000 16.076441 17.92356
## 16  Quadrat.5 0.9873546 395      Observed       0 22.00000 13.730915 30.26909
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 17.000000 17.997619 1.3115798 17.000000
## 2   Quadrat.1 Shannon diversity  7.331452  7.490633 0.3946414  6.717150
## 3   Quadrat.1 Simpson diversity  4.791135  4.834881 0.2749649  4.295960
## 4   Quadrat.2  Species richness 12.000000 13.996248 2.8142308 12.000000
## 5   Quadrat.2 Shannon diversity  5.936430  6.014410 0.2130885  5.596764
## 6   Quadrat.2 Simpson diversity  5.011183  5.049254 0.1858988  4.684899
## 7   Quadrat.3  Species richness 23.000000 30.987118 7.6170672 23.000000
## 8   Quadrat.3 Shannon diversity 10.402538 10.660309 0.4444157  9.789270
## 9   Quadrat.3 Simpson diversity  7.301456  7.376427 0.3793833  6.632850
## 10  Quadrat.4  Species richness 17.000000 17.000000 0.4878317 17.000000
## 11  Quadrat.4 Shannon diversity 11.213290 11.324644 0.2838687 10.768272
## 12  Quadrat.4 Simpson diversity  9.371649  9.467959 0.2897072  8.900143
## 13  Quadrat.5  Species richness 22.000000 34.468354 9.5354789 22.000000
## 14  Quadrat.5 Shannon diversity  9.244176  9.633365 0.6741604  8.312034
## 15  Quadrat.5 Simpson diversity  5.319457  5.378421 0.4894171  4.419181
##          UCL
## 1  20.568268
## 2   8.264115
## 3   5.373802
## 4  19.512039
## 5   6.432055
## 6   5.413609
## 7  45.916295
## 8  11.531348
## 9   8.120005
## 10 17.956133
## 11 11.881017
## 12 10.035774
## 13 53.157550
## 14 10.954695
## 15  6.337661

#Now to run the analysis again without specificying the size, can do this for #looking at the other diversity indices

Addiewell_Data <- iNEXT(Addiewell_Nos, q=c(0), datatype= "abundance")

print(Addiewell_Data)
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat.1 420    17 0.9953  2  0  1  1  2  0  0  2  0   4
## 2  Quadrat.2 533    12 0.9963  2  1  1  1  0  0  0  1  0   0
## 3  Quadrat.3 621    23 0.9936  4  1  2  2  1  0  0  0  0   3
## 4  Quadrat.4 824    17 1.0000  1  0  0  0  0  0  0  0  0   6
## 5  Quadrat.5 395    22 0.9874  5  1  0  2  0  0  0  1  1   4
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage    m        Method Order.q       qD    qD.LCL   qD.UCL        SC
## 1    Quadrat.1    1   Rarefaction       0  1.00000  1.000000  1.00000 0.2068303
## 10   Quadrat.1  210   Rarefaction       0 15.74247 14.842238 16.64271 0.9903942
## 20   Quadrat.1  420      Observed       0 17.00000 15.619197 18.38080 0.9952607
## 30   Quadrat.1  619 Extrapolation       0 17.61088 15.542656 19.67910 0.9981628
## 40   Quadrat.1  840 Extrapolation       0 17.86261 15.247166 20.47805 0.9993586
## 41   Quadrat.2    1   Rarefaction       0  1.00000  1.000000  1.00000 0.1980491
## 50   Quadrat.2  266   Rarefaction       0 10.55658  9.266041 11.84712 0.9919188
## 60   Quadrat.2  533      Observed       0 12.00000 10.089048 13.91095 0.9962547
## 70   Quadrat.2  786 Extrapolation       0 12.75496 10.095158 15.41476 0.9976711
## 80   Quadrat.2 1066 Extrapolation       0 13.26256  9.787479 16.73764 0.9986235
## 81   Quadrat.3    1   Rarefaction       0  1.00000  1.000000  1.00000 0.1355670
## 90   Quadrat.3  310   Rarefaction       0 20.33802 17.888887 22.78715 0.9873470
## 100  Quadrat.3  621      Observed       0 23.00000 18.934575 27.06543 0.9935640
## 110  Quadrat.3  915 Extrapolation       0 24.68536 19.166518 30.20420 0.9949220
## 120  Quadrat.3 1242 Extrapolation       0 26.14561 19.145397 33.14583 0.9960987
## 121  Quadrat.4    1   Rarefaction       0  1.00000  1.000000  1.00000 0.1056194
## 130  Quadrat.4  412   Rarefaction       0 16.49445 15.876197 17.11271 0.9986518
## 140  Quadrat.4  824      Observed       0 17.00000 16.013242 17.98676 1.0000000
## 150  Quadrat.4 1214 Extrapolation       0 17.00000 16.013242 17.98676 1.0000000
## 160  Quadrat.4 1648 Extrapolation       0 17.00000 16.013242 17.98676 1.0000000
## 161  Quadrat.5    1   Rarefaction       0  1.00000  1.000000  1.00000 0.1859282
## 170  Quadrat.5  197   Rarefaction       0 19.10887 17.240812 20.97693 0.9818432
## 180  Quadrat.5  395      Observed       0 22.00000 18.280176 25.71982 0.9873546
## 190  Quadrat.5  582 Extrapolation       0 24.15497 18.578191 29.73175 0.9895402
## 200  Quadrat.5  790 Extrapolation       0 26.11735 18.531217 33.70348 0.9915304
##        SC.LCL    SC.UCL
## 1   0.1835853 0.2300754
## 10  0.9859521 0.9948363
## 20  0.9900781 1.0000000
## 30  0.9947053 1.0000000
## 40  0.9970496 1.0000000
## 41  0.1830569 0.2130412
## 50  0.9878882 0.9959493
## 60  0.9918926 1.0000000
## 70  0.9937926 1.0000000
## 80  0.9954838 1.0000000
## 81  0.1223704 0.1487635
## 90  0.9807024 0.9939917
## 100 0.9875506 0.9995774
## 110 0.9891427 1.0000000
## 120 0.9909499 1.0000000
## 121 0.0978555 0.1133833
## 130 0.9972999 1.0000000
## 140 1.0000000 1.0000000
## 150 1.0000000 1.0000000
## 160 1.0000000 1.0000000
## 161 0.1501893 0.2216670
## 170 0.9716026 0.9920839
## 180 0.9763057 0.9984035
## 190 0.9786846 1.0000000
## 200 0.9815134 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage        SC    m        Method Order.q        qD     qD.LCL
## 1    Quadrat.1 0.2068303    1   Rarefaction       0  1.000000  0.9412638
## 10   Quadrat.1 0.9903942  210   Rarefaction       0 15.742475 14.3840593
## 20   Quadrat.1 0.9952607  420      Observed       0 17.000000 14.4608618
## 30   Quadrat.1 0.9981628  619 Extrapolation       0 17.610880 14.3404467
## 40   Quadrat.1 0.9993586  840 Extrapolation       0 17.862607 14.2532645
## 41   Quadrat.2 0.1980518    1   Rarefaction       0  1.000013  0.9712751
## 50   Quadrat.2 0.9919188  266   Rarefaction       0 10.556580  7.3677502
## 60   Quadrat.2 0.9962547  533      Observed       0 12.000000  7.0452165
## 70   Quadrat.2 0.9976711  786 Extrapolation       0 12.754957  7.1217379
## 80   Quadrat.2 0.9986235 1066 Extrapolation       0 13.262559  7.1476446
## 81   Quadrat.3 0.1355670    1   Rarefaction       0  1.000000  0.9527542
## 90   Quadrat.3 0.9873470  310   Rarefaction       0 20.338019 15.2953807
## 100  Quadrat.3 0.9935640  621      Observed       0 23.000000 12.9231919
## 110  Quadrat.3 0.9949220  915 Extrapolation       0 24.685359 13.2672052
## 120  Quadrat.3 0.9960987 1242 Extrapolation       0 26.145614 13.6086664
## 121  Quadrat.4 0.1056194    1   Rarefaction       0  1.000000  0.9723682
## 125  Quadrat.4 0.9910949  183   Rarefaction       0 15.736145 15.2360537
## 130  Quadrat.4 0.9986518  412   Rarefaction       0 16.494455 15.7233483
## 135  Quadrat.4 0.9987863  640   Rarefaction       0 16.776697 15.8234128
## 140  Quadrat.4 1.0000000  824      Observed       0 17.000000 16.0132416
## 141  Quadrat.5 0.1859282    1   Rarefaction       0  1.000000  0.8560309
## 150  Quadrat.5 0.9818432  197   Rarefaction       0 19.108869  9.2541964
## 160  Quadrat.5 0.9873546  395      Observed       0 22.000000  7.4583627
## 170  Quadrat.5 0.9895402  582 Extrapolation       0 24.154971  7.7940180
## 180  Quadrat.5 0.9915304  790 Extrapolation       0 26.117349  8.2759770
##        qD.UCL
## 1    1.058736
## 10  17.100890
## 20  19.539138
## 30  20.881313
## 40  21.471949
## 41   1.028750
## 50  13.745409
## 60  16.954784
## 70  18.388176
## 80  19.377473
## 81   1.047246
## 90  25.380658
## 100 33.076808
## 110 36.103513
## 120 38.682562
## 121  1.027632
## 125 16.236237
## 130 17.265561
## 135 17.729982
## 140 17.986758
## 141  1.143969
## 150 28.963541
## 160 36.541637
## 170 40.515925
## 180 43.958720
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat.1  Species richness 17.000000 17.997619 1.6916433 17.000000
## 2   Quadrat.1 Shannon diversity  7.331452  7.490633 0.4080371  6.690894
## 3   Quadrat.1 Simpson diversity  4.791135  4.834881 0.2929942  4.260623
## 4   Quadrat.2  Species richness 12.000000 13.996248 3.1511865 12.000000
## 5   Quadrat.2 Shannon diversity  5.936430  6.014410 0.2204109  5.582412
## 6   Quadrat.2 Simpson diversity  5.011183  5.049254 0.1864013  4.683914
## 7   Quadrat.3  Species richness 23.000000 30.987118 6.1673167 23.000000
## 8   Quadrat.3 Shannon diversity 10.402538 10.660309 0.4798053  9.719908
## 9   Quadrat.3 Simpson diversity  7.301456  7.376427 0.3667080  6.657693
## 10  Quadrat.4  Species richness 17.000000 17.000000 0.4916109 17.000000
## 11  Quadrat.4 Shannon diversity 11.213290 11.324644 0.2643650 10.806498
## 12  Quadrat.4 Simpson diversity  9.371649  9.467959 0.2827086  8.913860
## 13  Quadrat.5  Species richness 22.000000 34.468354 9.2701545 22.000000
## 14  Quadrat.5 Shannon diversity  9.244176  9.633365 0.6094670  8.438831
## 15  Quadrat.5 Simpson diversity  5.319457  5.378421 0.4296377  4.536347
##          UCL
## 1  21.313179
## 2   8.290371
## 3   5.409139
## 4  20.172460
## 5   6.446407
## 6   5.414594
## 7  43.074836
## 8  11.600710
## 9   8.095162
## 10 17.963540
## 11 11.842790
## 12 10.022057
## 13 52.637523
## 14 10.827898
## 15  6.220496

##Now to do further analyses for initial biodiversity indices for Addiewell, including sample coverage

A1 <- diversity(Addiewell_Nos$Quadrat.1)

Addiewell2 <- estimateD(Addiewell_Nos, q = c(0,1,2), datatype = "abundance", base="coverage")
Addiewell2
##    Assemblage        m        Method Order.q        SC        qD    qD.LCL
## 1   Quadrat.1 226.2999   Rarefaction       0 0.9915304 15.889971 14.418400
## 2   Quadrat.1 226.2999   Rarefaction       1 0.9915304  7.197444  6.296685
## 3   Quadrat.1 226.2999   Rarefaction       2 0.9915304  4.754314  4.082784
## 4   Quadrat.2 254.0636   Rarefaction       0 0.9915304 10.457635  8.062079
## 5   Quadrat.2 254.0636   Rarefaction       1 0.9915304  5.858901  5.495032
## 6   Quadrat.2 254.0636   Rarefaction       2 0.9915304  4.970042  4.617688
## 7   Quadrat.3 444.1923   Rarefaction       0 0.9915304 21.720179 12.574855
## 8   Quadrat.3 444.1923   Rarefaction       1 0.9915304 10.315575  9.331317
## 9   Quadrat.3 444.1923   Rarefaction       2 0.9915304  7.272036  6.448958
## 10  Quadrat.4 186.9737   Rarefaction       0 0.9915304 15.770875 15.287802
## 11  Quadrat.4 186.9737   Rarefaction       1 0.9915304 10.826412 10.239085
## 12  Quadrat.4 186.9737   Rarefaction       2 0.9915304  9.057737  8.453411
## 13  Quadrat.5 790.0000 Extrapolation       0 0.9915304 26.117349 10.306162
## 14  Quadrat.5 790.0000 Extrapolation       1 0.9915304  9.459618  8.073684
## 15  Quadrat.5 790.0000 Extrapolation       2 0.9915304  5.348777  4.338191
##       qD.UCL
## 1  17.361541
## 2   8.098203
## 3   5.425844
## 4  12.853191
## 5   6.222770
## 6   5.322395
## 7  30.865503
## 8  11.299833
## 9   8.095115
## 10 16.253948
## 11 11.413738
## 12  9.662063
## 13 41.928535
## 14 10.845551
## 15  6.359363

#Running vegan analyses for species evenness for Addiewell data#

Aevenness1 <- A1/log(specnumber(Addiewell_Nos$Quadrat.1))

summary(Aevenness1)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7031  0.7031  0.7031  0.7031  0.7031  0.7031
A2 <- diversity(Addiewell_Nos$Quadrat.2)

Aevenness2 <- A2/log(specnumber(Addiewell_Nos$Quadrat.2))

summary(Aevenness2)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7168  0.7168  0.7168  0.7168  0.7168  0.7168
A3 <- diversity(Addiewell_Nos$Quadrat.3)

Aevenness3 <- A3/log(specnumber(Addiewell_Nos$Quadrat.3))

summary(Aevenness3)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7469  0.7469  0.7469  0.7469  0.7469  0.7469
A4 <- diversity(Addiewell_Nos$Quadrat.4)

Aevenness4 <- A4/log(specnumber(Addiewell_Nos$Quadrat.4))

summary(Aevenness4)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8531  0.8531  0.8531  0.8531  0.8531  0.8531
A5 <- diversity(Addiewell_Nos$Quadrat.5)

Aevenness5 <- A5/log(specnumber(Addiewell_Nos$Quadrat.5))

summary(Aevenness5)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7195  0.7195  0.7195  0.7195  0.7195  0.7195

#Now to create some graphs for better visualisation of the data, including species curves#

Addiewell_Data_Graph1 <- ggiNEXT(x = Addiewell_Data, se=TRUE, color.var="Order.q")

Addiewell_Data_Graph1

Addiewell_Data_Graph1.1 <- ggiNEXT(x = Addiewell_Data, se=TRUE,
                                   facet.var = "None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Addiewell_Data_Graph1.1

Addiewell_Data_Graph2 <- ggiNEXT(x = Addiewell_Data, se=TRUE, type = 1,
                                 facet.var = "None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Addiewell_Data_Graph2

Addiewellg2 <- Addiewell_Data_Graph2 + theme_hc(style = "darkunica") +
  scale_colour_hc("darkunica")
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Addiewellg2

Addiewell_Data_Graph2.1 <- ggiNEXT(x = Addiewell_Data, se=TRUE, type = 1,
                                   facet.var="None", grey=TRUE) 
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Addiewell_Data_Graph2.1

Addiewell_Data_Graph3 <- ggiNEXT(x = Addiewell_Data, se=TRUE, type = 2,
                                 facet.var="None", grey = TRUE) 
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Addiewell_Data_Graph3

Addiewell_Data_Graph4 <- ggiNEXT(x = Addiewell_Data, se=TRUE, type = 3,
                                 facet.var="None", grey = TRUE) 
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Addiewell_Data_Graph4

#Hodbarrow Data#

#Loading the Hodbarrow data#

urlfile4 <- 'https://raw.githubusercontent.com/Savannankvm/Biodiversity-analyses-for-six-study-sites/PhD-files/Hodbarrow_Abundance_Data.csv'

Hodbarrow_Nos <-read.csv(urlfile4)

print(Hodbarrow_Nos)
##     Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5 Quadrat_6 Quadrat_7
## 1           0         0         0         0         0         0         0
## 2           0         0         0         0         0         0         0
## 3           0         0         0         0         0         0         0
## 4           0         0         0         0         0         0         0
## 5           0         0         0         0         0         0         0
## 6           0         0         0         7         0         0         0
## 7           0        70       189         0         0         0         0
## 8           0         0         0         0         0         0         0
## 9           0         0         0         0         0         0         0
## 10          0         0         0         0         0         0         0
## 11          0         0         0         0         0         0         0
## 12          0         0         1         0         0         0         0
## 13          0         0         0         0         0         0         0
## 14          0         0         0         0         0         0         0
## 15          0         0         0         0         0         0         0
## 16          0         0         0         0         0         0         0
## 17          0         0         0         0         0         0         0
## 18          0         0         0         0         0         0         0
## 19          0         0         0         0         0         0         0
## 20          0         0         0         0         0         0         0
## 21          0         0         0         0         0         0         0
## 22          0         0         0         0         0         0         0
## 23          0         0         0         0         0         0         0
## 24          0         0        60         0         0         0         0
## 25          0         0         0         0         0         0         0
## 26          0         0         0         0         0         0         0
## 27          0         0         0        42         0         0         0
## 28          0         0         0         0         0         0         0
## 29          0         0         0         0         3         0         2
## 30          0         0         1         0         0         0         0
## 31          0         0         0         3         2         1         7
## 32          0         0         0         0         1         0         0
## 33          0         0         0         0         0         0         0
## 34          0         4         0         4         5         0         1
## 35          0         0         0         0         0         0         0
## 36          0         0         0         1         0         0         0
## 37          0         0         0         0         0         0         0
## 38          0         0         0         0         0         0         0
## 39          0         0         0         0         0         0         0
## 40          0         0         0         0         0         0         0
## 41          0         0         0         0         0         0         0
## 42          0         0         0         0         0         0         0
## 43          0         0         0         0         0         0        10
## 44          0         0         0         0         0         0         0
## 45          0         0         0         0         0         0         0
## 46          0         0         0         0         0         0         0
## 47          0         0         0         0         0         0         0
## 48          0         0         0         0         0         0         0
## 49          0         0         0         0         0         0         0
## 50          0         0         0        10         0         0         0
## 51          0         0         0        31         0         0         0
## 52          0         0         0         0         0         0         0
## 53          0         0         0         0        36         0        31
## 54          0         0         0         0         0         0         0
## 55         10         0         4         2        44         0        33
## 56          0         0         0         0         0         0         0
## 57          0         0         0         0         0         0         0
## 58          0         0         0         0         0         0         0
## 59          0         0         0         0         0         0         0
## 60          0         0         0         0         0         0         0
## 61          0         0         0         0         0         0         0
## 62          0         0         0         0         0         0         0
## 63          0         0         0         0         0         0         0
## 64          0         0         0         0         0         0         0
## 65          0         0         0         0         0         0         0
## 66          0         0         0         0         0         0         0
## 67          0         0         0         0         0         0         0
## 68          0         0         0         0         0         0         0
## 69          0         0         0         0         0         0         0
## 70          0         0         0         0         0         0         0
## 71         47         0         0         0        23        78        10
## 72          0         0         0        18         0         0         0
## 73          0         0         0         0         0         0         0
## 74          0         0         0         0         0         0         0
## 75          0         0         0         0         0         0         0
## 76          0         0         0         0         0         0         0
## 77          0         0         0       160         0         0         0
## 78          0         0         0         0         0         0         0
## 79          0         0         0         0         0         0         0
## 80          0         0         0         0         0         0         0
## 81          0         0         0         0         0         0         0
## 82          0         0         0         0         0         0         0
## 83          0         0         0         0        16         2        43
## 84          0         0         0         0         0         0         0
## 85          2         0         2         1         6         0         0
## 86          0         2         0         0         1         6         6
## 87          0         0         0         0         0         0         0
## 88          0         0         0         0         0         0         0
## 89          0         0         0         0        57         0        20
## 90          0         0         0         0         0         0         0
## 91          2         0         0         0         0         0         0
## 92          0         0         0        91         0         0         0
## 93          0         0         0         0         0         0         0
## 94          0         5         1       111         2         0         0
## 95          0         0         0         0         0         0         0
## 96          0         0         0         0         0         0         0
## 97          0         0         0         0         0         0         0
## 98          2         0         0        91        39         0         0
## 99          0         0         0         0        50         0         0
## 100         0         0         0         5        20         0        29
## 101         0         0         0         0         0         0         0
## 102         0        69        46         0        55         0         0
## 103         0         0         0         0         0         0         0
## 104         0         0         0         0         0         0         0
## 105         0         0         0         0         0         0         0
## 106         0         0         0         0         0         0         0
## 107         0         0         0         0         0         0         0
## 108         0         0         0         0         0         0         2
## 109         0         0         0         0         0         0         0
## 110         0         0         0         0         0         0         0
## 111         0         0         0         0         0         0         0
## 112         0         0         0         0         0         0         0
## 113         0         0         0         0         0         0         0
## 114         0         0         0         0         0         0         0
## 115         0         0         0         0         0         0         0
## 116         0         0         0         0         0         0         0
## 117         0         0         0         0         0         0         0
## 118         0         0         0         0         0         0         0
## 119         0         0         0         0         0         0         0
## 120         0         0         0         0         0         0         0
## 121         0         0         0         0         0         0         0
## 122         0         0         0         0         0         0         0
## 123         0         0         0         0         0         0         0
## 124         0         0         0         0         0         0         0
## 125         0         0         0         0         0         0         0
## 126         0         0         0         0         0         0         0
## 127         0         0         0         0         0         0         0
## 128         0         0         0         0         0         2         1
## 129         0         0         0         0         0         0         0
## 130         0       216       253         0         0         7         0
## 131       150        30        60         0        70         0         0
## 132         0         0         0         0         0         0         0
## 133         0         0         0         0         0         0         0
## 134         0         0         0         0         0         0        21
## 135         0         0         0         0         0         0         0
## 136         0         0         0         0         0         0         0
## 137         0         0         0         0         3         0         0
## 138         0         0         0         0         0         0         0
## 139         0         0         0         0         0         0         0
## 140         0         0         0         0         0         0         0
## 141         0         0         0         0         0         0         0
## 142         0         0         0         0         0         0         0
## 143         0         0         0         0         0        10         0

#colSums to establish sample size for each of the quadrats.

colSums(Hodbarrow_Nos)
## Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5 Quadrat_6 Quadrat_7 
##       213       396       617       577       433       106       216

#Setting m to sample size for Quadrat 1. This will give me observed #qD value that will be most representative for Quadrat and Community. Will do the same #for the other communities below.

m <- c(213)

Hodbarrow_Datam <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance", size = m)

Hodbarrow_Datam
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 213      Observed       0  6.000000  4.796348  7.203652 1.0000000
## 2   Quadrat_2 213   Rarefaction       0  6.721814  5.896149  7.547479 0.9961347
## 3   Quadrat_2 395   Rarefaction       0  7.000000  6.066901  7.933099 1.0000000
## 4   Quadrat_2 396      Observed       0  7.000000  6.066311  7.933689 1.0000000
## 5   Quadrat_2 397 Extrapolation       0  7.000000  6.065954  7.934046 1.0000000
## 6   Quadrat_3 213   Rarefaction       0  7.424413  6.113825  8.735001 0.9912065
## 7   Quadrat_3 616   Rarefaction       0  9.995138  7.127895 12.862380 0.9951378
## 8   Quadrat_3 617      Observed       0 10.000000  7.129267 12.870733 0.9951430
## 9   Quadrat_3 618 Extrapolation       0 10.004857  7.130327 12.879387 0.9951483
## 10  Quadrat_4 213   Rarefaction       0 12.785465 11.270779 14.300151 0.9881773
## 11  Quadrat_4 576   Rarefaction       0 14.996534 12.731948 17.261119 0.9965338
## 12  Quadrat_4 577      Observed       0 15.000000 12.733598 17.266402 0.9965398
## 13  Quadrat_4 578 Extrapolation       0 15.003460 12.734690 17.272230 0.9965458
## 14  Quadrat_5 213   Rarefaction       0 16.158389 14.925337 17.391441 0.9859379
## 15  Quadrat_5 432   Rarefaction       0 17.995381 16.150928 19.839834 0.9953811
## 16  Quadrat_5 433      Observed       0 18.000000 16.152883 19.847117 0.9954023
## 17  Quadrat_5 434 Extrapolation       0 18.004598 16.154811 19.854384 0.9954235
## 18  Quadrat_6 105   Rarefaction       0  6.990566  5.395727  8.585405 0.9905660
## 19  Quadrat_6 106      Observed       0  7.000000  5.398390  8.601610 0.9909122
## 20  Quadrat_6 107 Extrapolation       0  7.009088  5.399445  8.618731 0.9912457
## 21  Quadrat_6 213 Extrapolation       0  7.243108  4.711550  9.774665 0.9998336
## 22  Quadrat_7 213   Rarefaction       0 13.971964 12.193609 15.750319 0.9905685
## 23  Quadrat_7 215   Rarefaction       0 13.990741 12.201012 15.780469 0.9907407
## 24  Quadrat_7 216      Observed       0 14.000000 12.204536 15.795464 0.9908261
## 25  Quadrat_7 217 Extrapolation       0 14.009174 12.207608 15.810740 0.9909106
##       SC.LCL    SC.UCL
## 1  0.9924224 1.0000000
## 2  0.9929010 0.9993684
## 3  0.9973544 1.0000000
## 4  0.9980077 1.0000000
## 5  0.9980178 1.0000000
## 6  0.9861023 0.9963107
## 7  0.9906541 0.9996214
## 8  0.9903565 0.9999295
## 9  0.9903646 0.9999320
## 10 0.9832072 0.9931475
## 11 0.9922762 1.0000000
## 12 0.9918970 1.0000000
## 13 0.9919066 1.0000000
## 14 0.9808238 0.9910520
## 15 0.9900143 1.0000000
## 16 0.9900362 1.0000000
## 17 0.9900579 1.0000000
## 18 0.9729493 1.0000000
## 19 0.9723586 1.0000000
## 20 0.9728467 1.0000000
## 21 0.9909834 1.0000000
## 22 0.9800659 1.0000000
## 23 0.9801763 1.0000000
## 24 0.9798682 1.0000000
## 25 0.9799937 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 1.0000000 213      Observed       0  6.000000  4.194228  7.805772
## 2   Quadrat_2 0.9961347 213   Rarefaction       0  6.721814  5.699172  7.744456
## 3   Quadrat_2 1.0000000 396      Observed       0  7.000000  5.923179  8.076821
## 4   Quadrat_3 0.9912065 213   Rarefaction       0  7.424413  4.161120 10.687705
## 5   Quadrat_3 0.9951378 616   Rarefaction       0  9.992800  4.201307 15.784293
## 6   Quadrat_3 0.9951430 617      Observed       0 10.000000  4.205265 15.794735
## 7   Quadrat_3 0.9951483 618 Extrapolation       0 10.004857  4.206911 15.802803
## 8   Quadrat_4 0.9881773 213   Rarefaction       0 12.785465 10.673642 14.897288
## 9   Quadrat_4 0.9965338 576   Rarefaction       0 14.995943 10.906152 19.085734
## 10  Quadrat_4 0.9965398 577      Observed       0 15.000000 10.907808 19.092192
## 11  Quadrat_4 0.9965458 578 Extrapolation       0 15.003460 10.909016 19.097905
## 12  Quadrat_5 0.9859379 213   Rarefaction       0 16.158389 14.146234 18.170543
## 13  Quadrat_5 0.9953811 431   Rarefaction       0 17.993045 13.756134 22.229956
## 14  Quadrat_5 0.9954023 433      Observed       0 18.000000 13.756458 22.243542
## 15  Quadrat_5 0.9954235 434 Extrapolation       0 18.004598 13.753359 22.255837
## 16  Quadrat_6 0.9905660 104   Rarefaction       0  6.981784  4.015808  9.947760
## 17  Quadrat_6 0.9909122 106      Observed       0  7.000000  4.011680  9.988320
## 18  Quadrat_6 0.9912457 107 Extrapolation       0  7.009088  3.997300 10.020876
## 19  Quadrat_6 0.9998336 213 Extrapolation       0  7.243108  3.583949 10.902267
## 20  Quadrat_7 0.9905685 213   Rarefaction       0 13.971964 10.858781 17.085147
## 21  Quadrat_7 0.9907407 215   Rarefaction       0 13.988843 10.863824 17.113863
## 22  Quadrat_7 0.9908261 216      Observed       0 14.000000 10.862711 17.137289
## 23  Quadrat_7 0.9909106 217 Extrapolation       0 14.009174 10.859738 17.158610
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 0.93387866  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.13258626  2.121905
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.09994436  1.639126
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.41970329  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.17059438  3.237126
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.16192170  2.433316
## 7   Quadrat_3  Species richness 10.000000 14.492707 5.72216594 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.14823526  4.053562
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.13689956  3.236200
## 10  Quadrat_4  Species richness 15.000000 16.996534 2.94725990 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.30265986  6.755151
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.24739997  5.329521
## 13  Quadrat_5  Species richness 18.000000 18.997691 2.92611034 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.42588946 10.503447
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.38731393  8.948996
## 16  Quadrat_6  Species richness  7.000000  7.247642 2.02387273  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.32590333  2.124220
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.18181723  1.446950
## 19  Quadrat_7  Species richness 14.000000 14.995370 2.52916675 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.47641099  8.745177
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.46189098  7.299657
##          UCL
## 1   7.830369
## 2   2.641634
## 3   2.030900
## 4   7.822603
## 5   3.905844
## 6   3.068038
## 7  25.707946
## 8   4.634634
## 9   3.772836
## 10 22.773057
## 11  7.941556
## 12  6.299311
## 13 24.732761
## 14 12.172903
## 15 10.467238
## 16 11.214359
## 17  3.401738
## 18  2.159660
## 19 19.952446
## 20 10.612674
## 21  9.110237
n <- c(396)

Hodbarrow_Datan <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance", size = n)

Hodbarrow_Datan
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 212   Rarefaction       0  6.000000  5.092853  6.907147 1.0000000
## 2   Quadrat_1 213      Observed       0  6.000000  5.092713  6.907287 1.0000000
## 3   Quadrat_1 214 Extrapolation       0  6.000000  5.092250  6.907750 1.0000000
## 4   Quadrat_1 396 Extrapolation       0  6.000000  4.861288  7.138712 1.0000000
## 5   Quadrat_2 396      Observed       0  7.000000  6.179849  7.820151 1.0000000
## 6   Quadrat_3 396   Rarefaction       0  8.781349  6.521438 11.041260 0.9936874
## 7   Quadrat_3 616   Rarefaction       0  9.995138  6.850974 13.139301 0.9951378
## 8   Quadrat_3 617      Observed       0 10.000000  6.851832 13.148168 0.9951430
## 9   Quadrat_3 618 Extrapolation       0 10.004857  6.852438 13.157276 0.9951483
## 10  Quadrat_4 396   Rarefaction       0 14.231402 12.682491 15.780312 0.9946438
## 11  Quadrat_4 576   Rarefaction       0 14.996534 13.217727 16.775341 0.9965338
## 12  Quadrat_4 577      Observed       0 15.000000 13.219884 16.780116 0.9965398
## 13  Quadrat_4 578 Extrapolation       0 15.003460 13.222033 16.784887 0.9965458
## 14  Quadrat_5 396   Rarefaction       0 17.813697 15.780172 19.847222 0.9945169
## 15  Quadrat_5 432   Rarefaction       0 17.995381 15.876927 20.113835 0.9953811
## 16  Quadrat_5 433      Observed       0 18.000000 15.879051 20.120949 0.9954023
## 17  Quadrat_5 434 Extrapolation       0 18.004598 15.881047 20.128148 0.9954235
## 18  Quadrat_6 105   Rarefaction       0  6.990566  5.244251  8.736881 0.9905660
## 19  Quadrat_6 106      Observed       0  7.000000  5.242935  8.757065 0.9909122
## 20  Quadrat_6 107 Extrapolation       0  7.009088  5.237766  8.780410 0.9912457
## 21  Quadrat_6 396 Extrapolation       0  7.247637  3.773306 10.721967 0.9999998
## 22  Quadrat_7 215   Rarefaction       0 13.990741 11.793338 16.188143 0.9907407
## 23  Quadrat_7 216      Observed       0 14.000000 11.796741 16.203259 0.9908261
## 24  Quadrat_7 217 Extrapolation       0 14.009174 11.799550 16.218798 0.9909106
## 25  Quadrat_7 396 Extrapolation       0 14.807371 11.592326 18.022417 0.9982673
##       SC.LCL    SC.UCL
## 1  0.9936793 1.0000000
## 2  0.9933048 1.0000000
## 3  0.9933655 1.0000000
## 4  0.9982380 1.0000000
## 5  0.9982064 1.0000000
## 6  0.9888247 0.9985500
## 7  0.9902128 1.0000000
## 8  0.9900472 1.0000000
## 9  0.9900541 1.0000000
## 10 0.9916314 0.9976562
## 11 0.9931294 0.9999382
## 12 0.9931374 0.9999422
## 13 0.9931455 0.9999461
## 14 0.9897121 0.9993218
## 15 0.9904700 1.0000000
## 16 0.9903608 1.0000000
## 17 0.9903834 1.0000000
## 18 0.9725575 1.0000000
## 19 0.9704054 1.0000000
## 20 0.9709462 1.0000000
## 21 0.9977201 1.0000000
## 22 0.9807519 1.0000000
## 23 0.9806587 1.0000000
## 24 0.9807839 1.0000000
## 25 0.9925409 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 1.0000000 213      Observed       0  6.000000  4.651698  7.348302
## 2   Quadrat_2 1.0000000 396      Observed       0  7.000000  6.059033  7.940967
## 3   Quadrat_3 0.9936874 396   Rarefaction       0  8.781349  2.190807 15.371891
## 4   Quadrat_3 0.9951378 616   Rarefaction       0  9.992800  2.369329 17.616270
## 5   Quadrat_3 0.9951430 617      Observed       0 10.000000  2.372535 17.627465
## 6   Quadrat_3 0.9951483 618 Extrapolation       0 10.004857  2.373621 17.636093
## 7   Quadrat_4 0.9946438 396   Rarefaction       0 14.231401 11.888126 16.574677
## 8   Quadrat_4 0.9965338 576   Rarefaction       0 14.995943 12.179676 17.812210
## 9   Quadrat_4 0.9965398 577      Observed       0 15.000000 12.181633 17.818367
## 10  Quadrat_4 0.9965458 578 Extrapolation       0 15.003460 12.184722 17.822198
## 11  Quadrat_5 0.9945170 396   Rarefaction       0 17.813697 14.056946 21.570449
## 12  Quadrat_5 0.9953811 431   Rarefaction       0 17.993045 14.007117 21.978973
## 13  Quadrat_5 0.9954023 433      Observed       0 18.000000 14.007990 21.992010
## 14  Quadrat_5 0.9954235 434 Extrapolation       0 18.004598 14.005350 22.003845
## 15  Quadrat_6 0.9905660 104   Rarefaction       0  6.981784  4.021079  9.942490
## 16  Quadrat_6 0.9909122 106      Observed       0  7.000000  4.013677  9.986323
## 17  Quadrat_6 0.9912457 107 Extrapolation       0  7.009088  3.996940 10.021236
## 18  Quadrat_6 0.9999998 396 Extrapolation       0  7.247637  3.518959 10.976314
## 19  Quadrat_7 0.9907407 215   Rarefaction       0 13.988843 10.667108 17.310579
## 20  Quadrat_7 0.9908261 216      Observed       0 14.000000 10.665610 17.334390
## 21  Quadrat_7 0.9909106 217 Extrapolation       0 14.009174 10.661292 17.357056
## 22  Quadrat_7 0.9982673 396 Extrapolation       0 14.807371 10.230067 19.384676
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 0.9159977  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.1585277  2.071061
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.1009107  1.637232
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.4341566  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.1537871  3.270068
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.1541357  2.448577
## 7   Quadrat_3  Species richness 10.000000 14.492707 5.0128406 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.1462546  4.057444
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.1263121  3.256951
## 10  Quadrat_4  Species richness 15.000000 16.996534 2.7603942 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.3029794  6.754525
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.2463020  5.331673
## 13  Quadrat_5  Species richness 18.000000 18.997691 3.1170676 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.4176406 10.519614
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.3742111  8.974677
## 16  Quadrat_6  Species richness  7.000000  7.247642 1.9574404  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.3298583  2.116469
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.2072210  1.397160
## 19  Quadrat_7  Species richness 14.000000 14.995370 1.9192839 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.4753343  8.747287
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.4748080  7.274340
##          UCL
## 1   7.795322
## 2   2.692478
## 3   2.032794
## 4   7.850931
## 5   3.872902
## 6   3.052778
## 7  24.317694
## 8   4.630752
## 9   3.752085
## 10 22.406807
## 11  7.942182
## 12  6.297159
## 13 25.107031
## 14 12.156735
## 15 10.441557
## 16 11.084154
## 17  3.409490
## 18  2.209451
## 19 18.757098
## 20 10.610563
## 21  9.135554
o <- c(617)

Hodbarrow_Datao <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance", size = o)

Hodbarrow_Datao
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 212   Rarefaction       0  6.000000  4.898006  7.101994 1.0000000
## 2   Quadrat_1 213      Observed       0  6.000000  4.896948  7.103052 1.0000000
## 3   Quadrat_1 214 Extrapolation       0  6.000000  4.895243  7.104757 1.0000000
## 4   Quadrat_1 617 Extrapolation       0  6.000000  4.325913  7.674087 1.0000000
## 5   Quadrat_2 395   Rarefaction       0  7.000000  6.208701  7.791299 1.0000000
## 6   Quadrat_2 396      Observed       0  7.000000  6.208055  7.791945 1.0000000
## 7   Quadrat_2 397 Extrapolation       0  7.000000  6.207605  7.792395 1.0000000
## 8   Quadrat_2 617 Extrapolation       0  7.000000  6.107186  7.892814 1.0000000
## 9   Quadrat_3 617      Observed       0 10.000000  7.396198 12.603802 0.9951430
## 10  Quadrat_4 576   Rarefaction       0 14.996534 12.894927 17.098140 0.9965338
## 11  Quadrat_4 577      Observed       0 15.000000 12.896868 17.103132 0.9965398
## 12  Quadrat_4 578 Extrapolation       0 15.003460 12.898615 17.108305 0.9965458
## 13  Quadrat_4 617 Extrapolation       0 15.133831 12.963329 17.304334 0.9967717
## 14  Quadrat_5 432   Rarefaction       0 17.995381 16.126216 19.864546 0.9953811
## 15  Quadrat_5 433      Observed       0 18.000000 16.127590 19.872410 0.9954023
## 16  Quadrat_5 434 Extrapolation       0 18.004598 16.128938 19.880257 0.9954235
## 17  Quadrat_5 617 Extrapolation       0 18.571214 16.078725 21.063703 0.9980347
## 18  Quadrat_6 105   Rarefaction       0  6.990566  5.356912  8.624220 0.9905660
## 19  Quadrat_6 106      Observed       0  7.000000  5.355403  8.644597 0.9909122
## 20  Quadrat_6 107 Extrapolation       0  7.009088  5.351892  8.666283 0.9912457
## 21  Quadrat_6 617 Extrapolation       0  7.247642  3.276088 11.219195 1.0000000
## 22  Quadrat_7 215   Rarefaction       0 13.990741 12.677105 15.304377 0.9907407
## 23  Quadrat_7 216      Observed       0 14.000000 12.681346 15.318654 0.9908261
## 24  Quadrat_7 217 Extrapolation       0 14.009174 12.685138 15.333210 0.9909106
## 25  Quadrat_7 617 Extrapolation       0 14.971079 11.829771 18.112387 0.9997761
##       SC.LCL    SC.UCL
## 1  0.9926952 1.0000000
## 2  0.9925861 1.0000000
## 3  0.9926447 1.0000000
## 4  0.9992587 1.0000000
## 5  0.9974002 1.0000000
## 6  0.9978464 1.0000000
## 7  0.9978581 1.0000000
## 8  0.9993196 1.0000000
## 9  0.9907819 0.9995042
## 10 0.9928966 1.0000000
## 11 0.9927725 1.0000000
## 12 0.9927831 1.0000000
## 13 0.9931705 1.0000000
## 14 0.9904564 1.0000000
## 15 0.9904814 1.0000000
## 16 0.9905062 1.0000000
## 17 0.9939012 1.0000000
## 18 0.9714268 1.0000000
## 19 0.9705837 1.0000000
## 20 0.9710770 1.0000000
## 21 0.9993056 1.0000000
## 22 0.9820935 0.9993880
## 23 0.9815431 1.0000000
## 24 0.9816488 1.0000000
## 25 0.9967567 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 1.0000000 213      Observed       0  6.000000  4.219876  7.780124
## 2   Quadrat_2 1.0000000 396      Observed       0  7.000000  6.034693  7.965307
## 3   Quadrat_3 0.9951430 617      Observed       0 10.000000  4.839030 15.160970
## 4   Quadrat_4 0.9965338 576   Rarefaction       0 14.995943 12.092942 17.898944
## 5   Quadrat_4 0.9965398 577      Observed       0 15.000000 12.095115 17.904885
## 6   Quadrat_4 0.9965458 578 Extrapolation       0 15.003460 12.096942 17.909978
## 7   Quadrat_4 0.9967717 617 Extrapolation       0 15.133831 12.156933 18.110730
## 8   Quadrat_5 0.9953811 431   Rarefaction       0 17.993045 14.145026 21.841064
## 9   Quadrat_5 0.9954023 433      Observed       0 18.000000 14.145372 21.854628
## 10  Quadrat_5 0.9954235 434 Extrapolation       0 18.004598 14.142945 21.866250
## 11  Quadrat_5 0.9980347 617 Extrapolation       0 18.571214 13.786646 23.355782
## 12  Quadrat_6 0.9905660 104   Rarefaction       0  6.981784  3.668141 10.295427
## 13  Quadrat_6 0.9909122 106      Observed       0  7.000000  3.662178 10.337822
## 14  Quadrat_6 0.9912457 107 Extrapolation       0  7.009088  3.646381 10.371794
## 15  Quadrat_6 1.0000000 617 Extrapolation       0  7.247642  3.188554 11.306729
## 16  Quadrat_7 0.9907407 215   Rarefaction       0 13.988843 11.350211 16.627476
## 17  Quadrat_7 0.9908261 216      Observed       0 14.000000 11.349198 16.650802
## 18  Quadrat_7 0.9909106 217 Extrapolation       0 14.009174 11.346424 16.671923
## 19  Quadrat_7 0.9997761 617 Extrapolation       0 14.971079 10.914911 19.027247
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 0.95652503  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.13760557  2.112068
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.09862329  1.641715
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.44503214  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.17983508  3.219015
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.17589500  2.405929
## 7   Quadrat_3  Species richness 10.000000 14.492707 4.76783310 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.15039183  4.049335
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.12667648  3.256237
## 10  Quadrat_4  Species richness 15.000000 16.996534 2.37347817 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.30475856  6.751038
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.25455439  5.315498
## 13  Quadrat_5  Species richness 18.000000 18.997691 3.10552692 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.43751330 10.480664
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.42599218  8.873188
## 16  Quadrat_6  Species richness  7.000000  7.247642 1.65526750  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.31742928  2.140829
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.19150918  1.427954
## 19  Quadrat_7  Species richness 14.000000 14.995370 2.40086923 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.42005045  8.855642
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.45694645  7.309348
##          UCL
## 1   7.874755
## 2   2.651471
## 3   2.028311
## 4   7.872247
## 5   3.923955
## 6   3.095425
## 7  23.837488
## 8   4.638860
## 9   3.752799
## 10 21.648466
## 11  7.945670
## 12  6.313333
## 13 25.084411
## 14 12.195685
## 15 10.543046
## 16 10.491906
## 17  3.385129
## 18  2.178656
## 19 19.700988
## 20 10.502209
## 21  9.100546
p <- c(577)

Hodbarrow_Datap <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance", size = p)

Hodbarrow_Datap
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 212   Rarefaction       0  6.000000  4.803211  7.196789 1.0000000
## 2   Quadrat_1 213      Observed       0  6.000000  4.801570  7.198430 1.0000000
## 3   Quadrat_1 214 Extrapolation       0  6.000000  4.798874  7.201126 1.0000000
## 4   Quadrat_1 577 Extrapolation       0  6.000000  3.828079  8.171921 1.0000000
## 5   Quadrat_2 395   Rarefaction       0  7.000000  6.313607  7.686393 1.0000000
## 6   Quadrat_2 396      Observed       0  7.000000  6.313013  7.686987 1.0000000
## 7   Quadrat_2 397 Extrapolation       0  7.000000  6.312688  7.687312 1.0000000
## 8   Quadrat_2 577 Extrapolation       0  7.000000  6.225748  7.774252 1.0000000
## 9   Quadrat_3 577   Rarefaction       0  9.801391  7.591412 12.011370 0.9949310
## 10  Quadrat_3 616   Rarefaction       0  9.995138  7.716685 12.273591 0.9951378
## 11  Quadrat_3 617      Observed       0 10.000000  7.719803 12.280197 0.9951430
## 12  Quadrat_3 618 Extrapolation       0 10.004857  7.722630 12.287084 0.9951483
## 13  Quadrat_4 577      Observed       0 15.000000 12.785030 17.214970 0.9965398
## 14  Quadrat_5 432   Rarefaction       0 17.995381 16.270904 19.719859 0.9953811
## 15  Quadrat_5 433      Observed       0 18.000000 16.273996 19.726004 0.9954023
## 16  Quadrat_5 434 Extrapolation       0 18.004598 16.276729 19.732467 0.9954235
## 17  Quadrat_5 577 Extrapolation       0 18.484670 16.457770 20.511570 0.9976359
## 18  Quadrat_6 105   Rarefaction       0  6.990566  5.019400  8.961732 0.9905660
## 19  Quadrat_6 106      Observed       0  7.000000  5.020137  8.979863 0.9909122
## 20  Quadrat_6 107 Extrapolation       0  7.009088  5.018418  8.999757 0.9912457
## 21  Quadrat_6 577 Extrapolation       0  7.247642  3.751261 10.744022 1.0000000
## 22  Quadrat_7 215   Rarefaction       0 13.990741 12.190096 15.791385 0.9907407
## 23  Quadrat_7 216      Observed       0 14.000000 12.193653 15.806347 0.9908261
## 24  Quadrat_7 217 Extrapolation       0 14.009174 12.196958 15.821390 0.9909106
## 25  Quadrat_7 577 Extrapolation       0 14.960190 11.477589 18.442790 0.9996758
##       SC.LCL    SC.UCL
## 1  0.9913821 1.0000000
## 2  0.9904793 1.0000000
## 3  0.9905387 1.0000000
## 4  0.9984773 1.0000000
## 5  0.9971436 1.0000000
## 6  0.9976967 1.0000000
## 7  0.9977083 1.0000000
## 8  0.9990767 1.0000000
## 9  0.9919303 0.9979317
## 10 0.9919833 0.9982922
## 11 0.9917311 0.9985550
## 12 0.9917349 0.9985617
## 13 0.9923703 1.0000000
## 14 0.9910058 0.9997563
## 15 0.9907292 1.0000000
## 16 0.9907544 1.0000000
## 17 0.9935711 1.0000000
## 18 0.9746251 1.0000000
## 19 0.9727511 1.0000000
## 20 0.9732551 1.0000000
## 21 0.9995607 1.0000000
## 22 0.9811993 1.0000000
## 23 0.9807818 1.0000000
## 24 0.9809026 1.0000000
## 25 0.9963061 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 1.0000000 213      Observed       0  6.000000  3.560591  8.439409
## 2   Quadrat_2 1.0000000 396      Observed       0  7.000000  6.123314  7.876686
## 3   Quadrat_3 0.9949310 577   Rarefaction       0  9.801391  5.827012 13.775770
## 4   Quadrat_3 0.9951378 616   Rarefaction       0  9.992800  6.117355 13.868245
## 5   Quadrat_3 0.9951430 617      Observed       0 10.000000  6.158787 13.841213
## 6   Quadrat_3 0.9951483 618 Extrapolation       0 10.004857  6.189215 13.820499
## 7   Quadrat_4 0.9965398 577      Observed       0 15.000000 10.708358 19.291642
## 8   Quadrat_5 0.9953811 431   Rarefaction       0 17.993045 14.678062 21.308027
## 9   Quadrat_5 0.9954023 433      Observed       0 18.000000 14.679410 21.320590
## 10  Quadrat_5 0.9954235 434 Extrapolation       0 18.004598 14.677880 21.331315
## 11  Quadrat_5 0.9976359 577 Extrapolation       0 18.484670 14.494270 22.475071
## 12  Quadrat_6 0.9905660 104   Rarefaction       0  6.981784  4.030062  9.933506
## 13  Quadrat_6 0.9909122 106      Observed       0  7.000000  4.029911  9.970089
## 14  Quadrat_6 0.9912457 107 Extrapolation       0  7.009088  4.019263  9.998912
## 15  Quadrat_6 1.0000000 577 Extrapolation       0  7.247642  3.705763 10.789520
## 16  Quadrat_7 0.9907407 215   Rarefaction       0 13.988843 10.979270 16.998416
## 17  Quadrat_7 0.9908261 216      Observed       0 14.000000 10.979755 17.020245
## 18  Quadrat_7 0.9909106 217 Extrapolation       0 14.009174 10.977496 17.040852
## 19  Quadrat_7 0.9996758 577 Extrapolation       0 14.960190 10.604497 19.315883
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 1.0440260  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.1546568  2.078648
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.1053282  1.628573
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.5086523  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.1547126  3.268254
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.1476888  2.461212
## 7   Quadrat_3  Species richness 10.000000 14.492707 4.6848298 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.1449525  4.059996
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.1262217  3.257128
## 10  Quadrat_4  Species richness 15.000000 16.996534 3.1796409 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.2650080  6.828948
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.2143436  5.394310
## 13  Quadrat_5  Species richness 18.000000 18.997691 3.0905770 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.3591500 10.634254
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.3423677  9.037089
## 16  Quadrat_6  Species richness  7.000000  7.247642 1.9665536  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.3141790  2.147200
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.1857355  1.439270
## 19  Quadrat_7  Species richness 14.000000 14.995370 2.1216552 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.4665899  8.764426
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.4822010  7.259850
##          UCL
## 1   8.046253
## 2   2.684891
## 3   2.041453
## 4   7.996940
## 5   3.874716
## 6   3.040142
## 7  23.674804
## 8   4.628200
## 9   3.751908
## 10 23.228515
## 11  7.867760
## 12  6.234521
## 13 25.055110
## 14 12.042096
## 15 10.379145
## 16 11.102016
## 17  3.378759
## 18  2.167340
## 19 19.153738
## 20 10.593425
## 21  9.150044
q <- c(433)

Hodbarrow_Dataq <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance", size = q)

Hodbarrow_Dataq
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 212   Rarefaction       0  6.000000  5.012123  6.987877 1.0000000
## 2   Quadrat_1 213      Observed       0  6.000000  5.010069  6.989931 1.0000000
## 3   Quadrat_1 214 Extrapolation       0  6.000000  5.007527  6.992473 1.0000000
## 4   Quadrat_1 433 Extrapolation       0  6.000000  4.363843  7.636157 1.0000000
## 5   Quadrat_2 395   Rarefaction       0  7.000000  6.406370  7.593630 1.0000000
## 6   Quadrat_2 396      Observed       0  7.000000  6.406041  7.593959 1.0000000
## 7   Quadrat_2 397 Extrapolation       0  7.000000  6.405807  7.594193 1.0000000
## 8   Quadrat_2 433 Extrapolation       0  7.000000  6.395574  7.604426 1.0000000
## 9   Quadrat_3 433   Rarefaction       0  9.009026  6.794413 11.223639 0.9940068
## 10  Quadrat_3 616   Rarefaction       0  9.995138  7.392751 12.597524 0.9951378
## 11  Quadrat_3 617      Observed       0 10.000000  7.395897 12.604103 0.9951430
## 12  Quadrat_3 618 Extrapolation       0 10.004857  7.398814 12.610900 0.9951483
## 13  Quadrat_4 433   Rarefaction       0 14.418875 12.613490 16.224261 0.9952155
## 14  Quadrat_4 576   Rarefaction       0 14.996534 12.931183 17.061884 0.9965338
## 15  Quadrat_4 577      Observed       0 15.000000 12.932963 17.067037 0.9965398
## 16  Quadrat_4 578 Extrapolation       0 15.003460 12.934367 17.072554 0.9965458
## 17  Quadrat_5 433      Observed       0 18.000000 16.090690 19.909310 0.9954023
## 18  Quadrat_6 105   Rarefaction       0  6.990566  4.978812  9.002320 0.9905660
## 19  Quadrat_6 106      Observed       0  7.000000  4.977437  9.022563 0.9909122
## 20  Quadrat_6 107 Extrapolation       0  7.009088  4.973479  9.044696 0.9912457
## 21  Quadrat_6 433 Extrapolation       0  7.247640  3.378815 11.116465 1.0000000
## 22  Quadrat_7 215   Rarefaction       0 13.990741 12.187327 15.794154 0.9907407
## 23  Quadrat_7 216      Observed       0 14.000000 12.192352 15.807648 0.9908261
## 24  Quadrat_7 217 Extrapolation       0 14.009174 12.196577 15.821771 0.9909106
## 25  Quadrat_7 433 Extrapolation       0 14.861905 12.145277 17.578533 0.9987699
##       SC.LCL    SC.UCL
## 1  0.9922543 1.0000000
## 2  0.9919379 1.0000000
## 3  0.9919872 1.0000000
## 4  0.9973829 1.0000000
## 5  0.9975507 1.0000000
## 6  0.9982752 1.0000000
## 7  0.9982851 1.0000000
## 8  0.9986005 1.0000000
## 9  0.9907442 0.9972693
## 10 0.9921249 0.9981507
## 11 0.9918440 0.9984420
## 12 0.9918503 0.9984463
## 13 0.9916092 0.9988219
## 14 0.9928375 1.0000000
## 15 0.9924604 1.0000000
## 16 0.9924707 1.0000000
## 17 0.9886627 1.0000000
## 18 0.9717244 1.0000000
## 19 0.9699879 1.0000000
## 20 0.9705283 1.0000000
## 21 0.9980685 1.0000000
## 22 0.9824995 0.9989820
## 23 0.9814473 1.0000000
## 24 0.9815789 1.0000000
## 25 0.9948498 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 1.0000000 213      Observed       0  6.000000  3.902095  8.097905
## 2   Quadrat_2 1.0000000 396      Observed       0  7.000000  6.286546  7.713454
## 3   Quadrat_3 0.9940068 433   Rarefaction       0  9.009026  4.956119 13.061932
## 4   Quadrat_3 0.9951378 616   Rarefaction       0  9.992800  5.729723 14.255877
## 5   Quadrat_3 0.9951430 617      Observed       0 10.000000  5.734937 14.265063
## 6   Quadrat_3 0.9951483 618 Extrapolation       0 10.004857  5.739024 14.270690
## 7   Quadrat_4 0.9952155 433   Rarefaction       0 14.418876 11.336832 17.500919
## 8   Quadrat_4 0.9965338 576   Rarefaction       0 14.995943 11.543497 18.448390
## 9   Quadrat_4 0.9965398 577      Observed       0 15.000000 11.545569 18.454431
## 10  Quadrat_4 0.9965458 578 Extrapolation       0 15.003460 11.547424 18.459496
## 11  Quadrat_5 0.9954023 433      Observed       0 18.000000 11.869886 24.130114
## 12  Quadrat_6 0.9905660 104   Rarefaction       0  6.981784  3.592323 10.371245
## 13  Quadrat_6 0.9909122 106      Observed       0  7.000000  3.587344 10.412656
## 14  Quadrat_6 0.9912457 107 Extrapolation       0  7.009088  3.573100 10.445076
## 15  Quadrat_6 1.0000000 433 Extrapolation       0  7.247640  3.151650 11.343631
## 16  Quadrat_7 0.9907407 215   Rarefaction       0 13.988843 11.474165 16.503522
## 17  Quadrat_7 0.9908261 216      Observed       0 14.000000 11.476363 16.523637
## 18  Quadrat_7 0.9909106 217 Extrapolation       0 14.009174 11.476518 16.541830
## 19  Quadrat_7 0.9987699 433 Extrapolation       0 14.861905 11.425826 18.297984
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 0.9769866  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.1328149  2.121457
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.1017171  1.635651
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.5115245  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.1530086  3.271594
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.1517189  2.453313
## 7   Quadrat_3  Species richness 10.000000 14.492707 4.4901200 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.1431000  4.063627
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.1321810  3.245448
## 10  Quadrat_4  Species richness 15.000000 16.996534 2.7152753 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.2617237  6.835385
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.2386790  5.346613
## 13  Quadrat_5  Species richness 18.000000 18.997691 2.6977336 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.3808862 10.591651
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.3586529  9.005170
## 16  Quadrat_6  Species richness  7.000000  7.247642 1.9140816  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.3081261  2.159063
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.1761968  1.457966
## 19  Quadrat_7  Species richness 14.000000 14.995370 1.7430406 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.3904727  8.913613
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.4140122  7.393498
##          UCL
## 1   7.914859
## 2   2.642082
## 3   2.034375
## 4   8.002570
## 5   3.871377
## 6   3.048041
## 7  23.293180
## 8   4.624569
## 9   3.763588
## 10 22.318376
## 11  7.861323
## 12  6.282218
## 13 24.285151
## 14 12.084698
## 15 10.411064
## 16 10.999172
## 17  3.366895
## 18  2.148645
## 19 18.411667
## 20 10.444238
## 21  9.016396
r <- c(106)

Hodbarrow_Datar <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance", size = r)

Hodbarrow_Datar
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 106   Rarefaction       0  5.245657  4.158392  6.332921 0.9858387
## 2   Quadrat_1 212   Rarefaction       0  6.000000  4.736939  7.263061 1.0000000
## 3   Quadrat_1 213      Observed       0  6.000000  4.734745  7.265255 1.0000000
## 4   Quadrat_1 214 Extrapolation       0  6.000000  4.731719  7.268281 1.0000000
## 5   Quadrat_2 106   Rarefaction       0  5.969452  5.291008  6.647896 0.9887561
## 6   Quadrat_2 395   Rarefaction       0  7.000000  6.313654  7.686346 1.0000000
## 7   Quadrat_2 396      Observed       0  7.000000  6.313013  7.686987 1.0000000
## 8   Quadrat_2 397 Extrapolation       0  7.000000  6.312770  7.687230 1.0000000
## 9   Quadrat_3 106   Rarefaction       0  6.360050  5.560343  7.159756 0.9887665
## 10  Quadrat_3 616   Rarefaction       0  9.995138  6.956560 13.033716 0.9951378
## 11  Quadrat_3 617      Observed       0 10.000000  6.957447 13.042553 0.9951430
## 12  Quadrat_3 618 Extrapolation       0 10.004857  6.958100 13.051614 0.9951483
## 13  Quadrat_4 106   Rarefaction       0 10.959510 10.028811 11.890209 0.9753072
## 14  Quadrat_4 576   Rarefaction       0 14.996534 13.015256 16.977811 0.9965338
## 15  Quadrat_4 577      Observed       0 15.000000 13.016577 16.983423 0.9965398
## 16  Quadrat_4 578 Extrapolation       0 15.003460 13.017349 16.989572 0.9965458
## 17  Quadrat_5 106   Rarefaction       0 14.048474 12.935762 15.161185 0.9726455
## 18  Quadrat_5 432   Rarefaction       0 17.995381 15.829334 20.161428 0.9953811
## 19  Quadrat_5 433      Observed       0 18.000000 15.831169 20.168831 0.9954023
## 20  Quadrat_5 434 Extrapolation       0 18.004598 15.832883 20.176313 0.9954235
## 21  Quadrat_6 106      Observed       0  7.000000  5.266744  8.733256 0.9909122
## 22  Quadrat_7 106   Rarefaction       0 12.438862 11.098111 13.779612 0.9797776
## 23  Quadrat_7 215   Rarefaction       0 13.990741 12.073946 15.907536 0.9907407
## 24  Quadrat_7 216      Observed       0 14.000000 12.078003 15.921997 0.9908261
## 25  Quadrat_7 217 Extrapolation       0 14.009174 12.081035 15.937313 0.9909106
##       SC.LCL    SC.UCL
## 1  0.9804096 0.9912677
## 2  0.9920235 1.0000000
## 3  0.9915478 1.0000000
## 4  0.9916141 1.0000000
## 5  0.9859638 0.9915483
## 6  0.9974625 1.0000000
## 7  0.9981019 1.0000000
## 8  0.9981114 1.0000000
## 9  0.9825577 0.9949753
## 10 0.9900193 1.0000000
## 11 0.9898567 1.0000000
## 12 0.9898636 1.0000000
## 13 0.9698487 0.9807658
## 14 0.9926299 1.0000000
## 15 0.9921807 1.0000000
## 16 0.9921901 1.0000000
## 17 0.9649439 0.9803471
## 18 0.9901269 1.0000000
## 19 0.9900466 1.0000000
## 20 0.9900726 1.0000000
## 21 0.9722794 1.0000000
## 22 0.9698552 0.9897001
## 23 0.9809902 1.0000000
## 24 0.9802966 1.0000000
## 25 0.9804222 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9858387 106   Rarefaction       0  5.245657  3.879417  6.611896
## 2   Quadrat_1 1.0000000 213      Observed       0  6.000000  3.890630  8.109370
## 3   Quadrat_2 0.9887561 106   Rarefaction       0  5.969452  5.066935  6.871970
## 4   Quadrat_2 1.0000000 396      Observed       0  7.000000  6.175621  7.824379
## 5   Quadrat_3 0.9887665 106   Rarefaction       0  6.360050  3.722706  8.997394
## 6   Quadrat_3 0.9951378 616   Rarefaction       0  9.992800  2.818280 17.167319
## 7   Quadrat_3 0.9951430 617      Observed       0 10.000000  2.846977 17.153023
## 8   Quadrat_3 0.9951483 618 Extrapolation       0 10.004857  2.869147 17.140567
## 9   Quadrat_4 0.9753072 106   Rarefaction       0 10.959510  9.650667 12.268353
## 10  Quadrat_4 0.9965338 576   Rarefaction       0 14.995943 10.525810 19.466076
## 11  Quadrat_4 0.9965398 577      Observed       0 15.000000 10.526848 19.473152
## 12  Quadrat_4 0.9965458 578 Extrapolation       0 15.003460 10.527333 19.479587
## 13  Quadrat_5 0.9726455 106   Rarefaction       0 14.048474 12.282791 15.814157
## 14  Quadrat_5 0.9953811 431   Rarefaction       0 17.993045 13.718850 22.267239
## 15  Quadrat_5 0.9954023 433      Observed       0 18.000000 13.720347 22.279653
## 16  Quadrat_5 0.9954235 434 Extrapolation       0 18.004598 13.718590 22.290605
## 17  Quadrat_6 0.9909122 106      Observed       0  7.000000  4.020474  9.979526
## 18  Quadrat_7 0.9797776 106   Rarefaction       0 12.438862 10.513584 14.364140
## 19  Quadrat_7 0.9907407 215   Rarefaction       0 13.988843 10.950225 17.027462
## 20  Quadrat_7 0.9908261 216      Observed       0 14.000000 10.952180 17.047820
## 21  Quadrat_7 0.9909106 217 Extrapolation       0 14.009174 10.949899 17.068449
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 0.7278409  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.1801538  2.028675
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.1215012  1.596875
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.4450321  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.1451033  3.287088
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.1539280  2.448984
## 7   Quadrat_3  Species richness 10.000000 14.492707 5.7948719 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.1650870  4.020533
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.1349337  3.240053
## 10  Quadrat_4  Species richness 15.000000 16.996534 2.6297984 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.2660480  6.826909
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.2203457  5.382546
## 13  Quadrat_5  Species richness 18.000000 18.997691 3.4871294 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.3967454 10.560568
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.3545853  9.013143
## 16  Quadrat_6  Species richness  7.000000  7.247642 1.8102340  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.3575316  2.062230
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.2125926  1.386631
## 19  Quadrat_7  Species richness 14.000000 14.995370 2.0555085 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.4999837  8.698975
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.5410486  7.144511
##          UCL
## 1   7.426542
## 2   2.734864
## 3   2.073151
## 4   7.872247
## 5   3.855882
## 6   3.052370
## 7  25.850447
## 8   4.667662
## 9   3.768983
## 10 22.150844
## 11  7.869798
## 12  6.246285
## 13 25.832338
## 14 12.115781
## 15 10.403091
## 16 10.795635
## 17  3.463728
## 18  2.219979
## 19 19.024093
## 20 10.658875
## 21  9.265383
s <- c(216)

Hodbarrow_Datas <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance", size = s)

Hodbarrow_Datas
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 212   Rarefaction       0  6.000000  4.808748  7.191252 1.0000000
## 2   Quadrat_1 213      Observed       0  6.000000  4.806158  7.193842 1.0000000
## 3   Quadrat_1 214 Extrapolation       0  6.000000  4.803540  7.196460 1.0000000
## 4   Quadrat_1 216 Extrapolation       0  6.000000  4.798178  7.201822 1.0000000
## 5   Quadrat_2 216   Rarefaction       0  6.733287  6.176855  7.289718 0.9962572
## 6   Quadrat_2 395   Rarefaction       0  7.000000  6.463343  7.536657 1.0000000
## 7   Quadrat_2 396      Observed       0  7.000000  6.462877  7.537123 1.0000000
## 8   Quadrat_2 397 Extrapolation       0  7.000000  6.462787  7.537213 1.0000000
## 9   Quadrat_3 216   Rarefaction       0  7.450737  6.200506  8.700968 0.9912625
## 10  Quadrat_3 616   Rarefaction       0  9.995138  7.205881 12.784395 0.9951378
## 11  Quadrat_3 617      Observed       0 10.000000  7.206779 12.793221 0.9951430
## 12  Quadrat_3 618 Extrapolation       0 10.004857  7.207401 12.802312 0.9951483
## 13  Quadrat_4 216   Rarefaction       0 12.820735 11.682690 13.958781 0.9883736
## 14  Quadrat_4 576   Rarefaction       0 14.996534 13.093504 16.899564 0.9965338
## 15  Quadrat_4 577      Observed       0 15.000000 13.094389 16.905611 0.9965398
## 16  Quadrat_4 578 Extrapolation       0 15.003460 13.095003 16.911917 0.9965458
## 17  Quadrat_5 216   Rarefaction       0 16.200342 14.728017 17.672666 0.9861703
## 18  Quadrat_5 432   Rarefaction       0 17.995381 16.008495 19.982267 0.9953811
## 19  Quadrat_5 433      Observed       0 18.000000 16.010263 19.989737 0.9954023
## 20  Quadrat_5 434 Extrapolation       0 18.004598 16.011506 19.997689 0.9954235
## 21  Quadrat_6 105   Rarefaction       0  6.990566  5.214705  8.766427 0.9905660
## 22  Quadrat_6 106      Observed       0  7.000000  5.216365  8.783635 0.9909122
## 23  Quadrat_6 107 Extrapolation       0  7.009088  5.214137  8.804039 0.9912457
## 24  Quadrat_6 216 Extrapolation       0  7.243589  4.340460 10.146718 0.9998513
## 25  Quadrat_7 216      Observed       0 14.000000 12.157983 15.842017 0.9908261
##       SC.LCL    SC.UCL
## 1  0.9919738 1.0000000
## 2  0.9913768 1.0000000
## 3  0.9914252 1.0000000
## 4  0.9915209 1.0000000
## 5  0.9934802 0.9990342
## 6  0.9974625 1.0000000
## 7  0.9984570 1.0000000
## 8  0.9984663 1.0000000
## 9  0.9867499 0.9957752
## 10 0.9902972 0.9999783
## 11 0.9900432 1.0000000
## 12 0.9900489 1.0000000
## 13 0.9849717 0.9917755
## 14 0.9924831 1.0000000
## 15 0.9922546 1.0000000
## 16 0.9922616 1.0000000
## 17 0.9808596 0.9914811
## 18 0.9896965 1.0000000
## 19 0.9892544 1.0000000
## 20 0.9892820 1.0000000
## 21 0.9712418 1.0000000
## 22 0.9698579 1.0000000
## 23 0.9703609 1.0000000
## 24 0.9901772 1.0000000
## 25 0.9797505 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 1.0000000 213      Observed       0  6.000000  3.617416  8.382584
## 2   Quadrat_2 0.9962572 216   Rarefaction       0  6.733287  6.175444  7.291129
## 3   Quadrat_2 1.0000000 396      Observed       0  7.000000  6.379854  7.620146
## 4   Quadrat_3 0.9912625 216   Rarefaction       0  7.450737  3.031704 11.869770
## 5   Quadrat_3 0.9951378 616   Rarefaction       0  9.992800  2.293057 17.692542
## 6   Quadrat_3 0.9951430 617      Observed       0 10.000000  2.301730 17.698270
## 7   Quadrat_3 0.9951483 618 Extrapolation       0 10.004857  2.320868 17.688846
## 8   Quadrat_4 0.9883736 216   Rarefaction       0 12.820735 11.230514 14.410956
## 9   Quadrat_4 0.9965338 576   Rarefaction       0 14.995943 10.060331 19.931555
## 10  Quadrat_4 0.9965398 577      Observed       0 15.000000 10.061530 19.938470
## 11  Quadrat_4 0.9965458 578 Extrapolation       0 15.003460 10.062093 19.944827
## 12  Quadrat_5 0.9861703 216   Rarefaction       0 16.200342 14.234253 18.166431
## 13  Quadrat_5 0.9953811 431   Rarefaction       0 17.993045 14.075231 21.910858
## 14  Quadrat_5 0.9954023 433      Observed       0 18.000000 14.073736 21.926264
## 15  Quadrat_5 0.9954235 434 Extrapolation       0 18.004598 14.069814 21.939381
## 16  Quadrat_6 0.9905660 104   Rarefaction       0  6.981784  3.555716 10.407852
## 17  Quadrat_6 0.9909122 106      Observed       0  7.000000  3.547027 10.452973
## 18  Quadrat_6 0.9912457 107 Extrapolation       0  7.009088  3.528528 10.489648
## 19  Quadrat_6 0.9998513 216 Extrapolation       0  7.243589  3.025248 11.461929
## 20  Quadrat_7 0.9908261 216      Observed       0 14.000000 10.621125 17.378875
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 0.7801449  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.1659044  2.056603
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.1185225  1.602713
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.4201727  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.1634873  3.251056
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.1641785  2.428893
## 7   Quadrat_3  Species richness 10.000000 14.492707 5.2166470 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.1511047  4.047938
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.1346296  3.240649
## 10  Quadrat_4  Species richness 15.000000 16.996534 2.8826071 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.2584740  6.841754
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.2325133  5.358698
## 13  Quadrat_5  Species richness 18.000000 18.997691 2.7772286 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.3946785 10.564619
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.3715540  8.979885
## 16  Quadrat_6  Species richness  7.000000  7.247642 1.9030247  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.2930494  2.188613
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.1741539  1.461970
## 19  Quadrat_7  Species richness 14.000000 14.995370 2.4047452 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.4632092  8.771052
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.5248719  7.176217
##          UCL
## 1   7.529056
## 2   2.706936
## 3   2.067313
## 4   7.823523
## 5   3.891914
## 6   3.072461
## 7  24.717147
## 8   4.640258
## 9   3.768387
## 10 22.646340
## 11  7.854953
## 12  6.270133
## 13 24.440959
## 14 12.111730
## 15 10.436349
## 16 10.977501
## 17  3.337346
## 18  2.144641
## 19 19.708584
## 20 10.586799
## 21  9.233677

#Now to run the analysis again without specificying the size, can do this for #looking at the other diversity indices

Hodbarrow_Data <- iNEXT(Hodbarrow_Nos, q=c(0), datatype= "abundance")

print(Hodbarrow_Data)
## Compare 7 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 213     6 1.0000  0  3  0  0  0  0  0  0  0   1
## 2  Quadrat_2 396     7 1.0000  0  1  0  1  1  0  0  0  0   0
## 3  Quadrat_3 617    10 0.9951  3  1  0  1  0  0  0  0  0   0
## 4  Quadrat_4 577    15 0.9965  2  1  1  1  1  0  1  0  0   1
## 5  Quadrat_5 433    18 0.9954  2  2  2  0  1  1  0  0  0   0
## 6  Quadrat_6 106     7 0.9909  1  2  0  0  0  1  1  0  0   1
## 7  Quadrat_7 216    14 0.9908  2  2  0  0  0  1  1  0  0   2
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage    m        Method Order.q        qD    qD.LCL    qD.UCL
## 1    Quadrat_1    1   Rarefaction       0  1.000000  1.000000  1.000000
## 10   Quadrat_1  106   Rarefaction       0  5.245657  4.097313  6.394001
## 20   Quadrat_1  213      Observed       0  6.000000  4.614096  7.385904
## 30   Quadrat_1  314 Extrapolation       0  6.000000  4.413162  7.586838
## 40   Quadrat_1  426 Extrapolation       0  6.000000  4.260573  7.739427
## 41   Quadrat_2    1   Rarefaction       0  1.000000  1.000000  1.000000
## 50   Quadrat_2  198   Rarefaction       0  6.658619  5.854405  7.462833
## 60   Quadrat_2  396      Observed       0  7.000000  6.313013  7.686987
## 70   Quadrat_2  584 Extrapolation       0  7.000000  6.173414  7.826586
## 80   Quadrat_2  792 Extrapolation       0  7.000000  6.011740  7.988260
## 81   Quadrat_3    1   Rarefaction       0  1.000000  1.000000  1.000000
## 90   Quadrat_3  308   Rarefaction       0  8.184868  6.553318  9.816417
## 100  Quadrat_3  617      Observed       0 10.000000  7.319936 12.680064
## 110  Quadrat_3  909 Extrapolation       0 11.216753  7.548459 14.885048
## 120  Quadrat_3 1234 Extrapolation       0 12.187737  7.506769 16.868705
## 121  Quadrat_4    1   Rarefaction       0  1.000000  1.000000  1.000000
## 130  Quadrat_4  288   Rarefaction       0 13.521031 12.175913 14.866149
## 140  Quadrat_4  577      Observed       0 15.000000 12.994955 17.005045
## 150  Quadrat_4  850 Extrapolation       0 15.753114 13.113436 18.392793
## 160  Quadrat_4 1154 Extrapolation       0 16.262687 13.023511 19.501863
## 161  Quadrat_5    1   Rarefaction       0  1.000000  1.000000  1.000000
## 170  Quadrat_5  216   Rarefaction       0 16.200342 14.643204 17.757479
## 180  Quadrat_5  433      Observed       0 18.000000 15.849683 20.150317
## 190  Quadrat_5  638 Extrapolation       0 18.610638 15.744227 21.477050
## 200  Quadrat_5  866 Extrapolation       0 18.862668 15.368989 22.356347
## 201  Quadrat_6    1   Rarefaction       0  1.000000  1.000000  1.000000
## 210  Quadrat_6   53   Rarefaction       0  5.984367  4.815823  7.152911
## 220  Quadrat_6  106      Observed       0  7.000000  5.319564  8.680436
## 230  Quadrat_6  156 Extrapolation       0  7.209450  5.023146  9.395755
## 240  Quadrat_6  212 Extrapolation       0  7.242935  4.664355  9.821515
## 241  Quadrat_7    1   Rarefaction       0  1.000000  1.000000  1.000000
## 250  Quadrat_7  108   Rarefaction       0 12.479137 11.222523 13.735751
## 260  Quadrat_7  216      Observed       0 14.000000 12.130523 15.869477
## 270  Quadrat_7  318 Extrapolation       0 14.608278 12.082160 17.134396
## 280  Quadrat_7  432 Extrapolation       0 14.860664 11.743204 17.978123
##            SC     SC.LCL    SC.UCL
## 1   0.5449553 0.47802610 0.6118844
## 10  0.9858387 0.97916920 0.9925081
## 20  1.0000000 0.99310034 1.0000000
## 30  1.0000000 0.99671181 1.0000000
## 40  1.0000000 0.99831951 1.0000000
## 41  0.3635469 0.31816509 0.4089286
## 50  0.9954684 0.99222626 0.9987106
## 60  1.0000000 0.99729604 1.0000000
## 70  1.0000000 0.99841987 1.0000000
## 80  1.0000000 0.99908007 1.0000000
## 81  0.2853459 0.26461060 0.3060813
## 90  0.9927106 0.98812794 0.9972933
## 100 0.9951430 0.99059804 0.9996880
## 110 0.9964584 0.99234359 1.0000000
## 120 0.9975081 0.99414807 1.0000000
## 121 0.1719863 0.16027676 0.1836959
## 130 0.9918886 0.98792654 0.9958506
## 140 0.9965398 0.99264651 1.0000000
## 150 0.9978450 0.99478267 1.0000000
## 160 0.9987282 0.99643696 1.0000000
## 161 0.1030066 0.09519929 0.1108139
## 170 0.9861703 0.98109590 0.9912448
## 180 0.9954023 0.98954848 1.0000000
## 190 0.9982163 0.99383038 1.0000000
## 200 0.9993778 0.99617323 1.0000000
## 201 0.5545373 0.45654182 0.6525328
## 210 0.9694034 0.95296021 0.9858466
## 220 0.9909122 0.97213707 1.0000000
## 230 0.9985985 0.98667392 1.0000000
## 240 0.9998273 0.99260699 1.0000000
## 241 0.1218777 0.10824460 0.1355108
## 250 0.9801126 0.97004449 0.9901807
## 260 0.9908261 0.97983488 1.0000000
## 270 0.9964323 0.98875660 1.0000000
## 280 0.9987585 0.99337879 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage        SC    m        Method Order.q        qD     qD.LCL
## 1    Quadrat_1 0.5449607    1   Rarefaction       0  1.000008  0.9405084
## 5    Quadrat_1 0.9733952   47   Rarefaction       0  4.102612  2.9415407
## 10   Quadrat_1 0.9858387  106   Rarefaction       0  5.245657  3.8200610
## 15   Quadrat_1 0.9937549  165   Rarefaction       0  5.850119  4.2574097
## 19   Quadrat_1 1.0000000  213      Observed       0  6.000000  4.0584376
## 20   Quadrat_2 0.3635490    1   Rarefaction       0  1.000005  0.9365375
## 24   Quadrat_2 0.9867185   88   Rarefaction       0  5.748195  4.6806658
## 29   Quadrat_2 0.9954684  198   Rarefaction       0  6.658619  5.7499930
## 34   Quadrat_2 0.9987366  307   Rarefaction       0  6.946986  5.8327065
## 38   Quadrat_2 1.0000000  396      Observed       0  7.000000  5.7328149
## 39   Quadrat_3 0.2853459    1   Rarefaction       0  1.000000  0.9568360
## 48   Quadrat_3 0.9927106  308   Rarefaction       0  8.184868  3.6660335
## 58   Quadrat_3 0.9951430  617      Observed       0 10.000000  4.2486374
## 68   Quadrat_3 0.9964584  909 Extrapolation       0 11.216753  4.7176743
## 78   Quadrat_3 0.9975081 1234 Extrapolation       0 12.187737  5.1775682
## 79   Quadrat_4 0.1719914    1   Rarefaction       0  1.000027  0.9673060
## 88   Quadrat_4 0.9918886  288   Rarefaction       0 13.521031 11.4659881
## 98   Quadrat_4 0.9965398  577      Observed       0 15.000000 11.3983294
## 108  Quadrat_4 0.9978450  850 Extrapolation       0 15.753114 11.6308843
## 118  Quadrat_4 0.9987282 1154 Extrapolation       0 16.262687 11.7684926
## 119  Quadrat_5 0.1030066    1   Rarefaction       0  1.000000  0.9711580
## 128  Quadrat_5 0.9861703  216   Rarefaction       0 16.200342 14.2472930
## 138  Quadrat_5 0.9954023  433      Observed       0 18.000000 14.3995654
## 148  Quadrat_5 0.9982163  638 Extrapolation       0 18.610638 13.9595709
## 158  Quadrat_5 0.9993778  866 Extrapolation       0 18.862668 13.7046982
## 159  Quadrat_6 0.5545389    1   Rarefaction       0  1.000003  0.8673709
## 168  Quadrat_6 0.9694034   53   Rarefaction       0  5.984366  4.2346462
## 178  Quadrat_6 0.9909122  106      Observed       0  7.000000  4.3772090
## 188  Quadrat_6 0.9985985  156 Extrapolation       0  7.209450  4.1147379
## 198  Quadrat_6 0.9998273  212 Extrapolation       0  7.242935  4.0667827
## 199  Quadrat_7 0.1218798    1   Rarefaction       0  1.000017  0.9586527
## 208  Quadrat_7 0.9801126  108   Rarefaction       0 12.479137 10.7047911
## 218  Quadrat_7 0.9908261  216      Observed       0 14.000000 10.7981401
## 228  Quadrat_7 0.9964323  318 Extrapolation       0 14.608278 10.6364429
## 238  Quadrat_7 0.9987585  432 Extrapolation       0 14.860664 10.5096435
##        qD.UCL
## 1    1.059508
## 5    5.263684
## 10   6.671253
## 15   7.442829
## 19   7.941562
## 20   1.063473
## 24   6.815725
## 29   7.567245
## 34   8.061265
## 38   8.267185
## 39   1.043164
## 48  12.703702
## 58  15.751363
## 68  17.715832
## 78  19.197906
## 79   1.032749
## 88  15.576074
## 98  18.601671
## 108 19.875344
## 118 20.756881
## 119  1.028842
## 128 18.153391
## 138 21.600435
## 148 23.261706
## 158 24.020638
## 159  1.132634
## 168  7.734086
## 178  9.622791
## 188 10.304163
## 198 10.419088
## 199  1.041381
## 208 14.253484
## 218 17.201860
## 228 18.580113
## 238 19.211684
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  6.000000  6.000000 0.9380784  6.000000
## 2   Quadrat_1 Shannon diversity  2.352515  2.381769 0.1372054  2.112852
## 3   Quadrat_1 Simpson diversity  1.827847  1.835013 0.1034720  1.632212
## 4   Quadrat_2  Species richness  7.000000  7.000000 0.4817908  7.000000
## 5   Quadrat_2 Shannon diversity  3.543784  3.571485 0.1545620  3.268549
## 6   Quadrat_2 Simpson diversity  2.738570  2.750677 0.1530121  2.450779
## 7   Quadrat_3  Species richness 10.000000 14.492707 4.4601401 10.000000
## 8   Quadrat_3 Shannon diversity  4.294224  4.344098 0.1597099  4.031072
## 9   Quadrat_3 Simpson diversity  3.490350  3.504518 0.1305885  3.248569
## 10  Quadrat_4  Species richness 15.000000 16.996534 2.6034294 15.000000
## 11  Quadrat_4 Shannon diversity  7.241096  7.348354 0.2842600  6.791214
## 12  Quadrat_4 Simpson diversity  5.766302  5.814416 0.2456333  5.332983
## 13  Quadrat_5  Species richness 18.000000 18.997691 3.1254242 18.000000
## 14  Quadrat_5 Shannon diversity 11.090385 11.338175 0.3933559 10.567211
## 15  Quadrat_5 Simpson diversity  9.516725  9.708117 0.3781118  8.967032
## 16  Quadrat_6  Species richness  7.000000  7.247642 1.7702430  7.000000
## 17  Quadrat_6 Shannon diversity  2.675814  2.762979 0.3136038  2.148327
## 18  Quadrat_6 Simpson diversity  1.789742  1.803305 0.1883640  1.434119
## 19  Quadrat_7  Species richness 14.000000 14.995370 2.1557966 14.000000
## 20  Quadrat_7 Shannon diversity  9.347900  9.678925 0.5154802  8.668603
## 21  Quadrat_7 Simpson diversity  7.940095  8.204947 0.4968130  7.231211
##          UCL
## 1   7.838600
## 2   2.650687
## 3   2.037814
## 4   7.944293
## 5   3.874421
## 6   3.050575
## 7  23.234421
## 8   4.657123
## 9   3.760467
## 10 22.099162
## 11  7.905493
## 12  6.295848
## 13 25.123409
## 14 12.109138
## 15 10.449203
## 16 10.717254
## 17  3.377631
## 18  2.172492
## 19 19.220654
## 20 10.689248
## 21  9.178683

#Running further analyses to obtain additional biodiversity indices, including sample coverage#

Hodbarrow2 <- estimateD(Hodbarrow_Nos, q = c(0,1,2), datatype = "abundance", base="coverage")
Hodbarrow2
##    Assemblage         m        Method Order.q        SC        qD    qD.LCL
## 1   Quadrat_1  193.2463   Rarefaction       0 0.9975081  5.975376  4.385207
## 2   Quadrat_1  193.2463   Rarefaction       1 0.9975081  2.349177  2.062580
## 3   Quadrat_1  193.2463   Rarefaction       2 0.9975081  1.827118  1.613516
## 4   Quadrat_2  252.7154   Rarefaction       0 0.9975081  6.847050  6.016434
## 5   Quadrat_2  252.7154   Rarefaction       1 0.9975081  3.526803  3.210834
## 6   Quadrat_2  252.7154   Rarefaction       2 0.9975081  2.731753  2.425556
## 7   Quadrat_3 1234.0000 Extrapolation       0 0.9975081 12.187737  4.339551
## 8   Quadrat_3 1234.0000 Extrapolation       1 0.9975081  4.323037  4.053776
## 9   Quadrat_3 1234.0000 Extrapolation       2 0.9975081  3.497420  3.255940
## 10  Quadrat_4  766.2629 Extrapolation       0 0.9975081 15.558731 11.496982
## 11  Quadrat_4  766.2629 Extrapolation       1 0.9975081  7.270478  6.717240
## 12  Quadrat_4  766.2629 Extrapolation       2 0.9975081  5.778112  5.324217
## 13  Quadrat_5  565.6096 Extrapolation       0 0.9975081 18.456957 11.918367
## 14  Quadrat_5  565.6096 Extrapolation       1 0.9975081 11.157573 10.407259
## 15  Quadrat_5  565.6096 Extrapolation       2 0.9975081  9.560917  8.844314
## 16  Quadrat_6  140.6078 Extrapolation       0 0.9975081  7.179738  3.930310
## 17  Quadrat_6  140.6078 Extrapolation       1 0.9975081  2.702222  2.071842
## 18  Quadrat_6  140.6078 Extrapolation       2 0.9975081  1.793061  1.447792
## 19  Quadrat_7  356.7592 Extrapolation       0 0.9975081 14.725004 10.953915
## 20  Quadrat_7  356.7592 Extrapolation       1 0.9975081  9.509648  8.466486
## 21  Quadrat_7  356.7592 Extrapolation       2 0.9975081  8.042524  7.112466
##       qD.UCL
## 1   7.565544
## 2   2.635773
## 3   2.040720
## 4   7.677665
## 5   3.842771
## 6   3.037950
## 7  20.035923
## 8   4.592299
## 9   3.738900
## 10 19.620480
## 11  7.823717
## 12  6.232007
## 13 24.995547
## 14 11.907887
## 15 10.277521
## 16 10.429166
## 17  3.332603
## 18  2.138331
## 19 18.496092
## 20 10.552811
## 21  8.972581

#Running vegan analyses for Hodbarrow, to obtain species evenness indices

R1 <- diversity(Hodbarrow_Nos$Quadrat_1)

Revenness1 <- R1/log(specnumber(Hodbarrow_Nos$Quadrat_1))

summary(Revenness1)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.4775  0.4775  0.4775  0.4775  0.4775  0.4775
R2 <- diversity(Hodbarrow_Nos$Quadrat_2)

Revenness2 <- R2/log(specnumber(Hodbarrow_Nos$Quadrat_2))

summary(Revenness2)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6502  0.6502  0.6502  0.6502  0.6502  0.6502
R3 <- diversity(Hodbarrow_Nos$Quadrat_3)

Revenness3 <- R3/log(specnumber(Hodbarrow_Nos$Quadrat_3))

summary(Revenness3)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6329  0.6329  0.6329  0.6329  0.6329  0.6329
R4 <- diversity(Hodbarrow_Nos$Quadrat_4)

Revenness4 <- R4/log(specnumber(Hodbarrow_Nos$Quadrat_4))

summary(Revenness4)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7311  0.7311  0.7311  0.7311  0.7311  0.7311
R5 <- diversity(Hodbarrow_Nos$Quadrat_5)

Revenness5 <- R5/log(specnumber(Hodbarrow_Nos$Quadrat_5))

summary(Revenness5)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8324  0.8324  0.8324  0.8324  0.8324  0.8324
R6 <- diversity(Hodbarrow_Nos$Quadrat_6)

Revenness6 <- R6/log(specnumber(Hodbarrow_Nos$Quadrat_6))

summary(Revenness6)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.5058  0.5058  0.5058  0.5058  0.5058  0.5058
R7 <- diversity(Hodbarrow_Nos$Quadrat_7)

Revenness7 <- R7/log(specnumber(Hodbarrow_Nos$Quadrat_7))

summary(Revenness7)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.847   0.847   0.847   0.847   0.847   0.847

#Now for some data visualisation for the Hodbarrow data, including species curves graphs#

Hodbarrow_Data_Graph1 <- ggiNEXT(x = Hodbarrow_Data, se=TRUE, 
                                 facet.var= "None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Hodbarrow_Data_Graph1
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.
## Warning: Removed 1 rows containing missing values (`geom_point()`).

Hodbarrow_Data_Graph2 <- ggiNEXT(x = Hodbarrow_Data, se=TRUE, type = 1,
                                 facet.var= "None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Hodbarrow_Data_Graph2
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 1 rows containing missing values (`geom_point()`).

Hodbarrow_Data_Graph3 <- ggiNEXT(x = Hodbarrow_Data, se=TRUE, type = 2,
                                 facet.var= "None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Hodbarrow_Data_Graph3
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 1 rows containing missing values (`geom_point()`).

Hodbarrow_Data_Graph4 <- ggiNEXT(x = Hodbarrow_Data, se=TRUE, type = 3,
                                 facet.var= "None", grey=TRUE)
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
Hodbarrow_Data_Graph4
## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 1 rows containing missing values (`geom_point()`).

#Warton#

#Loading the Warton data

urlfile5 <- 'https://raw.githubusercontent.com/Savannankvm/Biodiversity-analyses-for-six-study-sites/PhD-files/Warton_Abundance_Data.csv'

Warton_Nos <-read.csv(urlfile5)

print(Warton_Nos)
##     Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5 Quadrat_6 Quadrat_7
## 1           0         0         0         0         0         0         0
## 2           0         0         0         0         0         0         0
## 3           0         0         0         0         0         0         0
## 4           0         0         0         0         0        27         0
## 5           0         0         0         0         0         0         0
## 6           0         0         0         0         0         0         0
## 7           0         0         0         0         0         0         0
## 8           0         0         0         0         0         0         0
## 9           1         0         0         0         0         0         0
## 10          0         0         0         0         0         0         0
## 11          0         0         0         0         0        11         0
## 12          0         0        11         0         0        10         0
## 13          0         0         0         0         0         0         0
## 14          0         0         0         0         0         0         0
## 15          0         0         0         0         0         0         0
## 16          0         0         0         0         0         0         0
## 17          0         0         0         0         0         0         0
## 18          0         0         0         0         0         0         0
## 19          0         0         0         0         0         0         0
## 20          0         0         0         0         0         0         0
## 21          0         0         0         0         0         0         0
## 22         60         0         0         0         0         0        50
## 23          0         0         0         0         0         0         0
## 24          0         0         0        20         0         0         0
## 25          0         0         0       120         0        10         0
## 26          0         0         0         0         0         0         0
## 27          0         0         0         0         0         0         0
## 28          0         0        23         0         0         0         0
## 29          0         0         0        24         0         0         0
## 30          0         0         0         0         0         0         0
## 31         11         5         4         0         0         0         3
## 32          0         0         0         0         0         0         0
## 33          0         0         0         0         0         0         0
## 34          0         0         0         0         0         0         0
## 35          0         0         0         0         0         0         0
## 36          1         0         0         0         0         0         0
## 37          0         0         0         0         0         0         0
## 38          0         0         0         0         0         0         0
## 39          0         0         0         0         0         0         0
## 40          0         0         0         0         0         0         0
## 41          0         0         0         0         0         0         0
## 42          0         0         0         0         0         0         0
## 43          0         0         0         0         0         0         0
## 44          0         0         0         0         0         0         0
## 45          0         0         0         0         0         0         0
## 46          0         0         0         0         0         0         0
## 47          0         0         0         0         0         0        50
## 48          0         0         0         0         0         0         0
## 49          0         0         0         0         0         0         0
## 50          0         0         0         0         0         0         0
## 51          0         0         0         0         0         0         0
## 52          0         0         0         0         0         0         0
## 53         16         0         0         0         0         0         0
## 54          0         0        17        55        27         5         0
## 55          0         0         0         0         0         0         0
## 56          0         0         0         0         0         0         0
## 57          0         0         0         0         0         0         0
## 58          0         0         0         0         0         0         0
## 59          0         0         0        20         0         0         0
## 60          0         0         0         0         0         0        60
## 61          0         0         0         0         0         0         0
## 62          0         0         0         0         0         0         0
## 63          0         0         0         0         0         0         0
## 64          0         0         0         0         1         0         0
## 65          0         0         0         0         0         0         0
## 66          0         0         0         0         0         0         0
## 67          0         0         0         0         0         0         0
## 68          0         0         0         0         0         0         0
## 69          0         0         0         0         0         0         0
## 70          0         0         0         0         0         0         0
## 71         42         0        40        58        70        23         0
## 72          0         0         8         3         0         0         0
## 73          0         0         0         0         0         0         0
## 74          0         0         0         0       160        10         0
## 75          0         0         0         0         0         0         0
## 76          0         0         0         0         0         0         0
## 77         60       150        60         0         0         0         0
## 78          0         0         0         0         0         0         0
## 79          0         0         0         0         0         0         0
## 80          0         0         0         0         0         0         0
## 81          0         0         0         0         0         0         0
## 82          0         0         0         0         0         0         0
## 83          0         0         0         0         0         0         0
## 84          0         0         0         0         0         0         0
## 85          0         0         0         0         0         0         0
## 86          5         0         0         0         0         0         0
## 87          0         0         0         0         0         0         0
## 88          0         0         0         0         0         0         0
## 89          0         0       220        19         0         0         0
## 90          0         0         0         0         0         0         0
## 91          0         0         0         0         0         0         0
## 92          0         0         5         0         0         0         0
## 93          0         1         0         0         6         4         0
## 94          0         0         0         0         2        63         0
## 95          0         0         0         0         0         0         0
## 96          0         0         0         0         0         0         0
## 97          0         0         0         0         0         0         0
## 98         33       286         2         0        54         0         1
## 99          0         0         0         1        19         0         0
## 100         1         0         0         0         0         1         0
## 101         0         0         0         0         0         0         0
## 102         0         0         0         0         0         0         0
## 103         0         0         0         0         0         0         0
## 104         0         0         0         0         0         0         0
## 105         0         0         0         0         0         0         0
## 106         0         0         0         0         0         0         0
## 107         0         0         0         0         0         0         0
## 108         0         0         0         0         0         0         0
## 109         0         0         0         0        30         0         0
## 110         0         0         0         0         0         0         0
## 111         0         0         0         0         0         0         0
## 112         0         0         0         0         0         0         0
## 113         0         0         0         0         0         0         0
## 114         0         0         0         0         0         0         0
## 115         0         0         0         0         0         0         0
## 116         0         0         0         0         0         0         0
## 117        60         0         0         0       140        20         0
## 118         0         0         0         0         0         0         0
## 119         0         0         0         0         0         0         0
## 120         0         0         0         0         0         0         0
## 121         0         0         0         0         0         0         0
## 122         0         0         0         0         0         0         0
## 123         0         0         0         0         0         0         0
## 124         0         0         0         0         0         0         0
## 125         0         0         0         0         0         0         0
## 126         0         0         0         0         0         0         0
## 127         0         0         0         0         0         0         0
## 128         0         1         3         2         1         0         0
## 129         0         0         0         0         0         0         0
## 130       283         7       159         0         0        20        45
## 131        60         0         0         0         0         0       110
## 132         0         0         0         0         0         0         0
## 133       162       118         0         0         0         0         0
## 134         0         0         0         0         0         0         0
## 135         0         0         0         0         0         2         0
## 136         0         0         0         0         0         0         0
## 137         0         0         0         0         0         0         0
## 138         0         0         0         0         7         0         0
## 139         0         0         0         0         0         0         0
## 140         0         0         0         0         0         0         0
## 141         0         0         0         0         0         0         0
## 142         0         0         0         0         0         0         0
## 143         0         0         0         0         0         0         0
##     Quadrat_8
## 1           0
## 2           0
## 3           0
## 4           0
## 5           0
## 6           0
## 7           0
## 8           0
## 9           0
## 10          0
## 11          0
## 12          0
## 13          0
## 14          0
## 15          0
## 16          0
## 17         20
## 18          0
## 19          0
## 20          0
## 21          0
## 22          0
## 23          0
## 24          0
## 25          0
## 26          0
## 27          0
## 28         52
## 29          0
## 30          0
## 31          0
## 32          0
## 33          0
## 34          0
## 35          8
## 36          0
## 37          0
## 38          0
## 39          0
## 40          0
## 41          0
## 42          0
## 43          0
## 44          0
## 45          0
## 46          0
## 47          0
## 48          0
## 49          0
## 50          0
## 51          0
## 52          0
## 53          0
## 54         25
## 55          0
## 56          0
## 57          0
## 58          0
## 59          0
## 60          0
## 61          0
## 62          0
## 63          0
## 64          0
## 65          0
## 66          0
## 67          0
## 68          0
## 69          0
## 70          0
## 71         13
## 72          0
## 73          0
## 74          0
## 75          0
## 76          0
## 77          0
## 78          0
## 79          0
## 80          0
## 81          0
## 82          0
## 83          0
## 84          0
## 85          0
## 86          0
## 87          0
## 88          0
## 89          0
## 90          0
## 91         80
## 92          0
## 93          0
## 94          0
## 95          0
## 96          0
## 97          0
## 98          0
## 99        114
## 100         0
## 101         0
## 102         0
## 103         0
## 104         0
## 105         0
## 106         0
## 107         0
## 108         0
## 109        20
## 110         0
## 111         0
## 112         0
## 113         0
## 114         0
## 115         0
## 116         0
## 117         0
## 118         0
## 119         0
## 120         0
## 121         0
## 122         0
## 123         0
## 124         0
## 125         0
## 126         0
## 127         0
## 128         0
## 129         0
## 130         0
## 131         0
## 132        11
## 133         0
## 134         0
## 135         0
## 136         0
## 137         0
## 138         0
## 139         0
## 140         0
## 141         0
## 142         0
## 143         0

#colSums to establish sample size for each of the quadrats.

colSums(Warton_Nos)
## Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5 Quadrat_6 Quadrat_7 Quadrat_8 
##       795       568       552       322       517       206       319       343

#Setting m to sample size for Quadrat 1. This will give me observed #qD value that will be most representative for Quadrat and Community. Will do the same #for the other communities below.

m <- c(795)

Warton_Datam <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = m)

Warton_Datam
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 795      Observed       0 14.000000 12.505237 15.494763 0.9962312
## 2   Quadrat_2 567   Rarefaction       0  6.996479  5.880364  8.112594 0.9964789
## 3   Quadrat_2 568      Observed       0  7.000000  5.882824  8.117176 0.9964912
## 4   Quadrat_2 569 Extrapolation       0  7.003509  5.885297  8.121720 0.9965036
## 5   Quadrat_2 795 Extrapolation       0  7.549386  6.234179  8.864593 0.9984223
## 6   Quadrat_3 551   Rarefaction       0 12.000000 10.877496 13.122504 1.0000000
## 7   Quadrat_3 552      Observed       0 12.000000 10.877224 13.122776 1.0000000
## 8   Quadrat_3 553 Extrapolation       0 12.000000 10.876981 13.123019 1.0000000
## 9   Quadrat_3 795 Extrapolation       0 12.000000 10.810786 13.189214 1.0000000
## 10  Quadrat_4 321   Rarefaction       0  9.996894  8.205114 11.788675 0.9968944
## 11  Quadrat_4 322      Observed       0 10.000000  8.204536 11.795464 0.9969136
## 12  Quadrat_4 323 Extrapolation       0 10.003086  8.203661 11.802512 0.9969328
## 13  Quadrat_4 795 Extrapolation       0 10.472041  7.450021 13.494061 0.9998365
## 14  Quadrat_5 516   Rarefaction       0 11.996132 10.081156 13.911107 0.9961315
## 15  Quadrat_5 517      Observed       0 12.000000 10.082904 13.917096 0.9961390
## 16  Quadrat_5 518 Extrapolation       0 12.003861 10.084165 13.923557 0.9961465
## 17  Quadrat_5 795 Extrapolation       0 12.830838 10.225373 15.436303 0.9977460
## 18  Quadrat_6 205   Rarefaction       0 12.995146 11.437600 14.552691 0.9951456
## 19  Quadrat_6 206      Observed       0 13.000000 11.438040 14.561960 0.9951925
## 20  Quadrat_6 207 Extrapolation       0 13.004807 11.437309 14.572306 0.9952390
## 21  Quadrat_6 795 Extrapolation       0 13.495938 10.543660 16.448217 0.9999842
## 22  Quadrat_7 318   Rarefaction       0  6.996865  5.861832  8.131899 0.9968652
## 23  Quadrat_7 319      Observed       0  7.000000  5.863345  8.136655 1.0000000
## 24  Quadrat_7 320 Extrapolation       0  7.000000  5.862413  8.137587 1.0000000
## 25  Quadrat_7 795 Extrapolation       0  7.000000  5.653777  8.346223 1.0000000
## 26  Quadrat_8 342   Rarefaction       0  9.000000  9.000000  9.000000 1.0000000
## 27  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
## 28  Quadrat_8 344 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
## 29  Quadrat_8 795 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9937135 0.9987488
## 2  0.9944765 0.9984812
## 3  0.9946516 0.9983309
## 4  0.9946688 0.9983384
## 5  0.9973636 0.9994810
## 6  0.9980805 1.0000000
## 7  0.9982445 1.0000000
## 8  0.9982520 1.0000000
## 9  0.9993040 1.0000000
## 10 0.9910938 1.0000000
## 11 0.9906172 1.0000000
## 12 0.9906594 1.0000000
## 13 0.9980370 1.0000000
## 14 0.9923943 0.9998688
## 15 0.9918873 1.0000000
## 16 0.9918998 1.0000000
## 17 0.9947784 1.0000000
## 18 0.9860786 1.0000000
## 19 0.9852238 1.0000000
## 20 0.9853350 1.0000000
## 21 0.9992523 1.0000000
## 22 0.9933020 1.0000000
## 23 0.9970576 1.0000000
## 24 0.9970760 1.0000000
## 25 0.9998512 1.0000000
## 26 1.0000000 1.0000000
## 27 1.0000000 1.0000000
## 28 1.0000000 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9962312 795      Observed       0 14.000000 12.110203 15.889797
## 2   Quadrat_2 0.9964789 563   Rarefaction       0  6.983786  5.863575  8.103997
## 3   Quadrat_2 0.9964912 568      Observed       0  7.000000  5.876835  8.123165
## 4   Quadrat_2 0.9965036 569 Extrapolation       0  7.003509  5.878845  8.128173
## 5   Quadrat_2 0.9984223 795 Extrapolation       0  7.549386  6.160335  8.938437
## 6   Quadrat_3 1.0000000 552      Observed       0 12.000000 10.734521 13.265479
## 7   Quadrat_4 0.9968944 321   Rarefaction       0  9.995413  6.952751 13.038074
## 8   Quadrat_4 0.9969136 322      Observed       0 10.000000  6.953963 13.046037
## 9   Quadrat_4 0.9969328 323 Extrapolation       0 10.003086  6.953591 13.052582
## 10  Quadrat_4 0.9998365 795 Extrapolation       0 10.472041  6.852933 14.091149
## 11  Quadrat_5 0.9961315 516   Rarefaction       0 11.995720  9.032455 14.958985
## 12  Quadrat_5 0.9961390 517      Observed       0 12.000000  9.034334 14.965666
## 13  Quadrat_5 0.9961465 518 Extrapolation       0 12.003861  9.036472 14.971250
## 14  Quadrat_5 0.9977460 795 Extrapolation       0 12.830838  9.329473 16.332204
## 15  Quadrat_6 0.9951456 204   Rarefaction       0 12.992177 10.505659 15.478695
## 16  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.508291 15.491709
## 17  Quadrat_6 0.9952390 207 Extrapolation       0 13.004807 10.507511 15.502104
## 18  Quadrat_6 0.9999842 795 Extrapolation       0 13.495938 10.397771 16.594106
## 19  Quadrat_7 0.9968652 318   Rarefaction       0  6.995767  5.683771  8.307764
## 20  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.639396  8.360604
## 21  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.73853077 14.000000
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.23430045  6.675868
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.23726976  4.658746
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.74420301  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.08226620  2.992580
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.08253181  2.573835
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.60621118 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.23507388  4.866245
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.17737771  3.483651
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.70166382 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.25685181  5.503060
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.27122954  4.120574
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.07047779 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.25012906  5.763823
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.23365629  4.429767
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.40881917 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.48092250  8.017932
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.63341270  5.474501
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.67871024  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.14331717  4.723582
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.21636292  4.101365
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.00000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.28514080  5.786496
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.30715073  4.382105
##          UCL
## 1  20.403684
## 2   7.594309
## 3   5.588827
## 4   9.456851
## 5   3.315058
## 6   2.897353
## 7  13.188152
## 8   5.787718
## 9   4.178959
## 10 13.833647
## 11  6.509901
## 12  5.183774
## 13 18.054193
## 14  6.744311
## 15  5.345682
## 16 16.258808
## 17  9.903114
## 18  7.957433
## 19  8.330248
## 20  5.285375
## 21  4.949492
## 22  9.000000
## 23  6.904228
## 24  5.586114
n <- c(568)

Warton_Datan <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = n)

Warton_Datan
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 568   Rarefaction       0 13.141557 11.756777 14.526337 0.9961859
## 2   Quadrat_1 794   Rarefaction       0 13.996226 12.297295 15.695158 0.9962264
## 3   Quadrat_1 795      Observed       0 14.000000 12.299622 15.700378 0.9962312
## 4   Quadrat_1 796 Extrapolation       0 14.003769 12.301591 15.705947 0.9962359
## 5   Quadrat_2 568      Observed       0  7.000000  5.780173  8.219827 0.9964912
## 6   Quadrat_3 551   Rarefaction       0 12.000000 11.274332 12.725668 1.0000000
## 7   Quadrat_3 552      Observed       0 12.000000 11.274170 12.725830 1.0000000
## 8   Quadrat_3 553 Extrapolation       0 12.000000 11.273864 12.726136 1.0000000
## 9   Quadrat_3 568 Extrapolation       0 12.000000 11.268831 12.731169 1.0000000
## 10  Quadrat_4 321   Rarefaction       0  9.996894  8.520427 11.473361 0.9968944
## 11  Quadrat_4 322      Observed       0 10.000000  8.520525 11.479475 0.9969136
## 12  Quadrat_4 323 Extrapolation       0 10.003086  8.519749 11.486424 0.9969328
## 13  Quadrat_4 568 Extrapolation       0 10.390295  8.153121 12.627468 0.9993303
## 14  Quadrat_5 516   Rarefaction       0 11.996132 10.018932 13.973331 0.9961315
## 15  Quadrat_5 517      Observed       0 12.000000 10.020137 13.979863 0.9961390
## 16  Quadrat_5 518 Extrapolation       0 12.003861 10.020679 13.987043 0.9961465
## 17  Quadrat_5 568 Extrapolation       0 12.187683 10.042785 14.332580 0.9965020
## 18  Quadrat_6 205   Rarefaction       0 12.995146 11.567969 14.422322 0.9951456
## 19  Quadrat_6 206      Observed       0 13.000000 11.570106 14.429894 0.9951925
## 20  Quadrat_6 207 Extrapolation       0 13.004807 11.570998 14.438617 0.9952390
## 21  Quadrat_6 568 Extrapolation       0 13.482765 11.112728 15.852802 0.9998569
## 22  Quadrat_7 318   Rarefaction       0  6.996865  6.060519  7.933211 0.9968652
## 23  Quadrat_7 319      Observed       0  7.000000  6.062122  7.937878 1.0000000
## 24  Quadrat_7 320 Extrapolation       0  7.000000  6.060520  7.939480 1.0000000
## 25  Quadrat_7 568 Extrapolation       0  7.000000  5.757632  8.242368 1.0000000
## 26  Quadrat_8 342   Rarefaction       0  9.000000  9.000000  9.000000 1.0000000
## 27  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
## 28  Quadrat_8 344 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
## 29  Quadrat_8 568 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9941885 0.9981833
## 2  0.9939218 0.9985311
## 3  0.9937136 0.9987487
## 4  0.9937229 0.9987489
## 5  0.9940789 0.9989036
## 6  0.9979408 1.0000000
## 7  0.9980503 1.0000000
## 8  0.9980572 1.0000000
## 9  0.9981566 1.0000000
## 10 0.9915894 1.0000000
## 11 0.9910940 1.0000000
## 12 0.9911342 1.0000000
## 13 0.9966359 1.0000000
## 14 0.9923630 0.9999001
## 15 0.9918116 1.0000000
## 16 0.9918269 1.0000000
## 17 0.9925473 1.0000000
## 18 0.9873400 1.0000000
## 19 0.9865772 1.0000000
## 20 0.9866810 1.0000000
## 21 0.9979832 1.0000000
## 22 0.9926085 1.0000000
## 23 0.9957699 1.0000000
## 24 0.9957963 1.0000000
## 25 0.9991121 1.0000000
## 26 1.0000000 1.0000000
## 27 1.0000000 1.0000000
## 28 1.0000000 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9961859 568   Rarefaction       0 13.141557 11.386768 14.896345
## 2   Quadrat_1 0.9962264 791   Rarefaction       0 13.984626 12.045823 15.923429
## 3   Quadrat_1 0.9962312 795      Observed       0 14.000000 12.057032 15.942968
## 4   Quadrat_1 0.9962359 796 Extrapolation       0 14.003769 12.059082 15.948455
## 5   Quadrat_2 0.9964912 568      Observed       0  7.000000  5.415454  8.584546
## 6   Quadrat_3 1.0000000 552      Observed       0 12.000000 10.930342 13.069658
## 7   Quadrat_4 0.9968944 321   Rarefaction       0  9.995413  7.585344 12.405482
## 8   Quadrat_4 0.9969136 322      Observed       0 10.000000  7.587148 12.412852
## 9   Quadrat_4 0.9969328 323 Extrapolation       0 10.003086  7.586961 12.419212
## 10  Quadrat_4 0.9993303 568 Extrapolation       0 10.390295  7.533348 13.247241
## 11  Quadrat_5 0.9961315 516   Rarefaction       0 11.995720  8.825671 15.165769
## 12  Quadrat_5 0.9961390 517      Observed       0 12.000000  8.827617 15.172383
## 13  Quadrat_5 0.9961465 518 Extrapolation       0 12.003861  8.829205 15.178516
## 14  Quadrat_5 0.9965020 568 Extrapolation       0 12.187683  8.911188 15.464178
## 15  Quadrat_6 0.9951456 204   Rarefaction       0 12.992177 10.840696 15.143657
## 16  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.842830 15.157170
## 17  Quadrat_6 0.9952390 207 Extrapolation       0 13.004807 10.842175 15.167440
## 18  Quadrat_6 0.9998569 568 Extrapolation       0 13.482765 10.740652 16.224878
## 19  Quadrat_7 0.9968652 318   Rarefaction       0  6.995767  5.730225  8.261310
## 20  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.652413  8.347587
## 21  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.78477977 14.000000
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.26136187  6.622829
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.27198352  4.590709
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.83021288  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.09543044  2.966779
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.10006367  2.539473
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.63096113 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.22243529  4.891017
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.17449649  3.489298
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.60479035 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.25879050  5.499260
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.29511265  4.073764
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.18004811 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.22162644  5.819687
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.21093959  4.474290
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.83864710 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.55262575  7.877396
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.64889614  5.444154
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.67071568  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.15618130  4.698368
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.21910847  4.095984
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.00000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.24078852  5.873425
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.25576416  4.482821
##          UCL
## 1  20.494330
## 2   7.647348
## 3   5.656864
## 4   9.625427
## 5   3.340860
## 6   2.931715
## 7  13.236661
## 8   5.762947
## 9   4.173312
## 10 13.643778
## 11  6.513701
## 12  5.230584
## 13 18.268947
## 14  6.688446
## 15  5.301158
## 16 17.101255
## 17 10.043649
## 18  7.987780
## 19  8.314579
## 20  5.310588
## 21  4.954873
## 22  9.000000
## 23  6.817299
## 24  5.485398
o <- c(552)

Warton_Datao <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = o)

Warton_Datao
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 552   Rarefaction       0 13.080425 11.751979 14.408871 0.9961730
## 2   Quadrat_1 794   Rarefaction       0 13.996226 12.382204 15.610249 0.9962264
## 3   Quadrat_1 795      Observed       0 14.000000 12.384743 15.615257 0.9962312
## 4   Quadrat_1 796 Extrapolation       0 14.003769 12.386748 15.620789 0.9962359
## 5   Quadrat_2 552   Rarefaction       0  6.943662  6.244967  7.642357 0.9964789
## 6   Quadrat_2 567   Rarefaction       0  6.996479  6.283613  7.709345 0.9964789
## 7   Quadrat_2 568      Observed       0  7.000000  6.286150  7.713850 0.9964912
## 8   Quadrat_2 569 Extrapolation       0  7.003509  6.288943  7.718074 0.9965036
## 9   Quadrat_3 552      Observed       0 12.000000 11.066311 12.933689 1.0000000
## 10  Quadrat_4 321   Rarefaction       0  9.996894  8.441497 11.552292 0.9968944
## 11  Quadrat_4 322      Observed       0 10.000000  8.441558 11.558442 0.9969136
## 12  Quadrat_4 323 Extrapolation       0 10.003086  8.440646 11.565526 0.9969328
## 13  Quadrat_4 552 Extrapolation       0 10.378994  8.102587 12.655402 0.9992604
## 14  Quadrat_5 516   Rarefaction       0 11.996132  9.989115 14.003148 0.9961315
## 15  Quadrat_5 517      Observed       0 12.000000  9.990269 14.009731 0.9961390
## 16  Quadrat_5 518 Extrapolation       0 12.003861  9.990998 14.016724 0.9961465
## 17  Quadrat_5 552 Extrapolation       0 12.130784 10.013080 14.248488 0.9963920
## 18  Quadrat_6 205   Rarefaction       0 12.995146 11.155809 14.834483 0.9951456
## 19  Quadrat_6 206      Observed       0 13.000000 11.155856 14.844144 0.9951925
## 20  Quadrat_6 207 Extrapolation       0 13.004807 11.154976 14.854639 0.9952390
## 21  Quadrat_6 552 Extrapolation       0 13.480277 10.589069 16.371484 0.9998329
## 22  Quadrat_7 318   Rarefaction       0  6.996865  6.048098  7.945632 0.9968652
## 23  Quadrat_7 319      Observed       0  7.000000  6.049666  7.950334 1.0000000
## 24  Quadrat_7 320 Extrapolation       0  7.000000  6.049015  7.950985 1.0000000
## 25  Quadrat_7 552 Extrapolation       0  7.000000  5.918579  8.081421 1.0000000
## 26  Quadrat_8 342   Rarefaction       0  9.000000  9.000000  9.000000 1.0000000
## 27  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
## 28  Quadrat_8 344 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
## 29  Quadrat_8 552 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9942862 0.9980597
## 2  0.9940576 0.9983952
## 3  0.9938110 0.9986513
## 4  0.9938199 0.9986519
## 5  0.9943008 0.9986569
## 6  0.9942644 0.9986933
## 7  0.9946500 0.9983325
## 8  0.9946668 0.9983403
## 9  0.9979718 1.0000000
## 10 0.9920937 1.0000000
## 11 0.9912182 1.0000000
## 12 0.9912583 1.0000000
## 13 0.9964132 1.0000000
## 14 0.9922829 0.9999801
## 15 0.9920141 1.0000000
## 16 0.9920276 1.0000000
## 17 0.9924671 1.0000000
## 18 0.9875026 1.0000000
## 19 0.9862653 1.0000000
## 20 0.9863668 1.0000000
## 21 0.9979696 1.0000000
## 22 0.9933194 1.0000000
## 23 0.9972390 1.0000000
## 24 0.9972562 1.0000000
## 25 0.9993593 1.0000000
## 26 1.0000000 1.0000000
## 27 1.0000000 1.0000000
## 28 1.0000000 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9961730 552   Rarefaction       0 13.080425 11.330183 14.830667
## 2   Quadrat_1 0.9962264 791   Rarefaction       0 13.984626 12.147452 15.821800
## 3   Quadrat_1 0.9962312 795      Observed       0 14.000000 12.160446 15.839554
## 4   Quadrat_1 0.9962359 796 Extrapolation       0 14.003769 12.162749 15.844789
## 5   Quadrat_2 0.9964789 552   Rarefaction       0  6.943662  5.992533  7.894791
## 6   Quadrat_2 0.9964789 563   Rarefaction       0  6.983786  6.027319  7.940253
## 7   Quadrat_2 0.9964912 568      Observed       0  7.000000  6.041478  7.958522
## 8   Quadrat_2 0.9965036 569 Extrapolation       0  7.003509  6.043869  7.963149
## 9   Quadrat_3 1.0000000 552      Observed       0 12.000000 10.621499 13.378501
## 10  Quadrat_4 0.9968944 321   Rarefaction       0  9.995413  7.458990 12.531835
## 11  Quadrat_4 0.9969136 322      Observed       0 10.000000  7.459417 12.540583
## 12  Quadrat_4 0.9969328 323 Extrapolation       0 10.003086  7.459099 12.547074
## 13  Quadrat_4 0.9992604 552 Extrapolation       0 10.378994  7.387230 13.370758
## 14  Quadrat_5 0.9961315 516   Rarefaction       0 11.995720  8.747491 15.243949
## 15  Quadrat_5 0.9961390 517      Observed       0 12.000000  8.749505 15.250495
## 16  Quadrat_5 0.9961465 518 Extrapolation       0 12.003861  8.752939 15.254783
## 17  Quadrat_5 0.9963920 552 Extrapolation       0 12.130784  8.805063 15.456505
## 18  Quadrat_6 0.9951456 204   Rarefaction       0 12.992177 10.350456 15.633898
## 19  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.353016 15.646984
## 20  Quadrat_6 0.9952390 207 Extrapolation       0 13.004807 10.352426 15.657189
## 21  Quadrat_6 0.9998329 552 Extrapolation       0 13.480277 10.270479 16.690074
## 22  Quadrat_7 0.9968652 318   Rarefaction       0  6.995767  5.809147  8.182387
## 23  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.861918  8.138082
## 24  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.75091705 14.000000
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.21060770  6.722305
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.22573714  4.681350
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.55237801  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.09880344  2.960168
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.09961551  2.540351
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.68151038 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.22851841  4.879094
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.15864293  3.520371
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.37419216 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.28982351  5.438437
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.33236489  4.000751
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.44119113 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.24510909  5.773662
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.21339427  4.469479
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.44275989 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.47968051  8.020366
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.62210089  5.496672
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.62162919  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.15629777  4.698140
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.19181770  4.149472
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.00000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.27946697  5.797617
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.31222474  4.372160
##          UCL
## 1  20.427961
## 2   7.547872
## 3   5.566223
## 4   9.080880
## 5   3.347470
## 6   2.930837
## 7  13.335736
## 8   5.774870
## 9   4.142240
## 10 13.191814
## 11  6.574524
## 12  5.303597
## 13 18.780778
## 14  6.734472
## 15  5.305970
## 16 16.325330
## 17  9.900679
## 18  7.935262
## 19  8.218371
## 20  5.310816
## 21  4.901384
## 22  9.000000
## 23  6.893107
## 24  5.596059
p <- c(322)

Warton_Datap <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = p)

Warton_Datap
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 322   Rarefaction       0 12.137804 11.194321 13.081288 0.9953642
## 2   Quadrat_1 794   Rarefaction       0 13.996226 12.278849 15.713604 0.9962264
## 3   Quadrat_1 795      Observed       0 14.000000 12.281279 15.718721 0.9962312
## 4   Quadrat_1 796 Extrapolation       0 14.003769 12.283296 15.724242 0.9962359
## 5   Quadrat_2 322   Rarefaction       0  6.116193  5.278281  6.954105 0.9960988
## 6   Quadrat_2 567   Rarefaction       0  6.996479  5.809838  8.183120 0.9964789
## 7   Quadrat_2 568      Observed       0  7.000000  5.812082  8.187918 0.9964912
## 8   Quadrat_2 569 Extrapolation       0  7.003509  5.814317  8.192701 0.9965036
## 9   Quadrat_3 322   Rarefaction       0 11.712217 10.844748 12.579686 0.9967434
## 10  Quadrat_3 551   Rarefaction       0 12.000000 11.089894 12.910106 1.0000000
## 11  Quadrat_3 552      Observed       0 12.000000 11.089263 12.910737 1.0000000
## 12  Quadrat_3 553 Extrapolation       0 12.000000 11.089006 12.910994 1.0000000
## 13  Quadrat_4 322      Observed       0 10.000000  8.414131 11.585869 0.9969136
## 14  Quadrat_5 322   Rarefaction       0 11.100084  9.597018 12.603150 0.9945563
## 15  Quadrat_5 516   Rarefaction       0 11.996132 10.106773 13.885490 0.9961315
## 16  Quadrat_5 517      Observed       0 12.000000 10.108843 13.891157 0.9961390
## 17  Quadrat_5 518 Extrapolation       0 12.003861 10.110748 13.896974 0.9961465
## 18  Quadrat_6 205   Rarefaction       0 12.995146 11.453167 14.537124 0.9951456
## 19  Quadrat_6 206      Observed       0 13.000000 11.453678 14.546322 0.9951925
## 20  Quadrat_6 207 Extrapolation       0 13.004807 11.453410 14.556205 0.9952390
## 21  Quadrat_6 322 Extrapolation       0 13.336232 11.280858 15.391606 0.9984412
## 22  Quadrat_7 318   Rarefaction       0  6.996865  6.015472  7.978258 0.9968652
## 23  Quadrat_7 319      Observed       0  7.000000  6.017222  7.982778 1.0000000
## 24  Quadrat_7 320 Extrapolation       0  7.000000  6.016234  7.983766 1.0000000
## 25  Quadrat_7 322 Extrapolation       0  7.000000  6.014254  7.985746 1.0000000
## 26  Quadrat_8 322   Rarefaction       0  9.000000  8.998613  9.001387 1.0000000
## 27  Quadrat_8 342   Rarefaction       0  9.000000  9.000000  9.000000 1.0000000
## 28  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
## 29  Quadrat_8 344 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9926235 0.9981049
## 2  0.9939570 0.9984958
## 3  0.9935524 0.9989099
## 4  0.9935611 0.9989107
## 5  0.9935013 0.9986964
## 6  0.9943690 0.9985888
## 7  0.9945807 0.9984018
## 8  0.9945993 0.9984078
## 9  0.9949369 0.9985498
## 10 0.9979446 1.0000000
## 11 0.9981692 1.0000000
## 12 0.9981757 1.0000000
## 13 0.9907393 1.0000000
## 14 0.9910684 0.9980442
## 15 0.9927851 0.9994779
## 16 0.9925054 0.9997726
## 17 0.9925211 0.9997718
## 18 0.9875317 1.0000000
## 19 0.9863395 1.0000000
## 20 0.9864432 1.0000000
## 21 0.9937984 1.0000000
## 22 0.9933020 1.0000000
## 23 0.9970576 1.0000000
## 24 0.9970760 1.0000000
## 25 0.9971124 1.0000000
## 26 0.9998678 1.0000000
## 27 1.0000000 1.0000000
## 28 1.0000000 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9953642 322   Rarefaction       0 12.137804 10.459363 13.816246
## 2   Quadrat_1 0.9962264 791   Rarefaction       0 13.984626 11.844575 16.124677
## 3   Quadrat_1 0.9962312 795      Observed       0 14.000000 11.856770 16.143230
## 4   Quadrat_1 0.9962359 796 Extrapolation       0 14.003769 11.858324 16.149214
## 5   Quadrat_2 0.9960988 322   Rarefaction       0  6.116193  4.997365  7.235021
## 6   Quadrat_2 0.9964789 563   Rarefaction       0  6.983786  5.744914  8.222658
## 7   Quadrat_2 0.9964912 568      Observed       0  7.000000  5.759062  8.240938
## 8   Quadrat_2 0.9965036 569 Extrapolation       0  7.003509  5.761258  8.245760
## 9   Quadrat_3 0.9967434 322   Rarefaction       0 11.712217 10.769307 12.655127
## 10  Quadrat_3 1.0000000 552      Observed       0 12.000000 10.789373 13.210627
## 11  Quadrat_4 0.9969136 322      Observed       0 10.000000  7.489112 12.510888
## 12  Quadrat_5 0.9945563 322   Rarefaction       0 11.100084  8.783056 13.417113
## 13  Quadrat_5 0.9961315 516   Rarefaction       0 11.995720  9.542666 14.448774
## 14  Quadrat_5 0.9961390 517      Observed       0 12.000000  9.545396 14.454604
## 15  Quadrat_5 0.9961465 518 Extrapolation       0 12.003861  9.548491 14.459231
## 16  Quadrat_6 0.9951456 204   Rarefaction       0 12.992177 10.728836 15.255518
## 17  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.732217 15.267783
## 18  Quadrat_6 0.9952390 207 Extrapolation       0 13.004807 10.732082 15.277533
## 19  Quadrat_6 0.9984412 322 Extrapolation       0 13.336232 10.711347 15.961117
## 20  Quadrat_7 0.9968652 318   Rarefaction       0  6.995767  5.777312  8.214223
## 21  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.776490  8.223510
## 22  Quadrat_8 1.0000000 322   Rarefaction       0  9.000000  8.999995  9.000005
## 23  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.4729969 14.109206
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.2394623  6.665751
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.2318339  4.669400
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.7050369  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.1007283  2.956396
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.0982528  2.543022
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.5973284 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.2445158  4.847740
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.1759888  3.486374
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.8621901 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.2937985  5.430646
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.3237071  4.017720
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.2250031 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.2569270  5.750499
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.2477926  4.402060
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.5233855 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.4989384  7.982621
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.5632622  5.611993
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.7011628  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.1570334  4.696698
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.2075351  4.118667
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.0000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.2927893  5.771505
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.3218921  4.353212
##          UCL
## 1  19.883247
## 2   7.604426
## 3   5.578173
## 4   9.380086
## 5   3.351243
## 6   2.928166
## 7  13.170742
## 8   5.806224
## 9   4.176237
## 10 14.148273
## 11  6.582315
## 12  5.286628
## 13 18.357057
## 14  6.757634
## 15  5.373389
## 16 16.483354
## 17  9.938424
## 18  7.819941
## 19  8.374254
## 20  5.312258
## 21  4.932190
## 22  9.000000
## 23  6.919218
## 24  5.615006
q <- c(517)

Warton_Dataq <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = q)

Warton_Dataq
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 517   Rarefaction       0 12.945828 11.739707 14.151949 0.9961342
## 2   Quadrat_1 794   Rarefaction       0 13.996226 12.389652 15.602800 0.9962264
## 3   Quadrat_1 795      Observed       0 14.000000 12.392039 15.607961 0.9962312
## 4   Quadrat_1 796 Extrapolation       0 14.003769 12.393983 15.613554 0.9962359
## 5   Quadrat_2 517   Rarefaction       0  6.820418  5.973683  7.667152 0.9964784
## 6   Quadrat_2 567   Rarefaction       0  6.996479  6.111836  7.881122 0.9964789
## 7   Quadrat_2 568      Observed       0  7.000000  6.114579  7.885421 0.9964912
## 8   Quadrat_2 569 Extrapolation       0  7.003509  6.117620  7.889397 0.9965036
## 9   Quadrat_3 517   Rarefaction       0 11.995838 10.995429 12.996247 0.9997546
## 10  Quadrat_3 551   Rarefaction       0 12.000000 10.971396 13.028604 1.0000000
## 11  Quadrat_3 552      Observed       0 12.000000 10.970471 13.029529 1.0000000
## 12  Quadrat_3 553 Extrapolation       0 12.000000 10.969766 13.030234 1.0000000
## 13  Quadrat_4 321   Rarefaction       0  9.996894  8.309293 11.684496 0.9968944
## 14  Quadrat_4 322      Observed       0 10.000000  8.308405 11.691595 0.9969136
## 15  Quadrat_4 323 Extrapolation       0 10.003086  8.307312 11.698860 0.9969328
## 16  Quadrat_4 517 Extrapolation       0 10.349987  7.936991 12.762984 0.9990807
## 17  Quadrat_5 517      Observed       0 12.000000  9.703359 14.296641 0.9961390
## 18  Quadrat_6 205   Rarefaction       0 12.995146 11.496708 14.493583 0.9951456
## 19  Quadrat_6 206      Observed       0 13.000000 11.496868 14.503132 0.9951925
## 20  Quadrat_6 207 Extrapolation       0 13.004807 11.495598 14.514017 0.9952390
## 21  Quadrat_6 517 Extrapolation       0 13.473277 10.883307 16.063247 0.9997653
## 22  Quadrat_7 318   Rarefaction       0  6.996865  5.878110  8.115620 0.9968652
## 23  Quadrat_7 319      Observed       0  7.000000  5.880021  8.119979 1.0000000
## 24  Quadrat_7 320 Extrapolation       0  7.000000  5.879233  8.120767 1.0000000
## 25  Quadrat_7 517 Extrapolation       0  7.000000  5.756315  8.243685 1.0000000
## 26  Quadrat_8 342   Rarefaction       0  9.000000  9.000000  9.000000 1.0000000
## 27  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
## 28  Quadrat_8 344 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
## 29  Quadrat_8 517 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9940337 0.9982347
## 2  0.9941197 0.9983331
## 3  0.9937446 0.9987177
## 4  0.9937531 0.9987187
## 5  0.9947613 0.9981955
## 6  0.9948057 0.9981520
## 7  0.9952179 0.9977646
## 8  0.9952347 0.9977725
## 9  0.9975624 1.0000000
## 10 0.9977079 1.0000000
## 11 0.9977851 1.0000000
## 12 0.9977939 1.0000000
## 13 0.9904621 1.0000000
## 14 0.9900347 1.0000000
## 15 0.9900755 1.0000000
## 16 0.9951071 1.0000000
## 17 0.9912864 1.0000000
## 18 0.9869904 1.0000000
## 19 0.9860385 1.0000000
## 20 0.9861408 1.0000000
## 21 0.9976176 1.0000000
## 22 0.9935252 1.0000000
## 23 0.9973286 1.0000000
## 24 0.9973453 1.0000000
## 25 0.9992280 1.0000000
## 26 1.0000000 1.0000000
## 27 1.0000000 1.0000000
## 28 1.0000000 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9961342 517   Rarefaction       0 12.945828 11.288642 14.603015
## 2   Quadrat_1 0.9962264 791   Rarefaction       0 13.984626 12.038365 15.930887
## 3   Quadrat_1 0.9962312 795      Observed       0 14.000000 12.044388 15.955612
## 4   Quadrat_1 0.9962359 796 Extrapolation       0 14.003769 12.046382 15.961156
## 5   Quadrat_2 0.9964784 517   Rarefaction       0  6.820418  6.042421  7.598414
## 6   Quadrat_2 0.9964789 563   Rarefaction       0  6.983786  6.205773  7.761799
## 7   Quadrat_2 0.9964912 568      Observed       0  7.000000  6.221552  7.778448
## 8   Quadrat_2 0.9965036 569 Extrapolation       0  7.003509  6.224614  7.782404
## 9   Quadrat_3 0.9997546 517   Rarefaction       0 11.995838 10.692031 13.299645
## 10  Quadrat_3 1.0000000 552      Observed       0 12.000000 10.663580 13.336420
## 11  Quadrat_4 0.9968944 321   Rarefaction       0  9.995413  6.968597 13.022228
## 12  Quadrat_4 0.9969136 322      Observed       0 10.000000  6.969874 13.030126
## 13  Quadrat_4 0.9969328 323 Extrapolation       0 10.003086  6.969617 13.036556
## 14  Quadrat_4 0.9990807 517 Extrapolation       0 10.349987  6.907224 13.792751
## 15  Quadrat_5 0.9961390 517      Observed       0 12.000000  7.985382 16.014618
## 16  Quadrat_6 0.9951456 204   Rarefaction       0 12.992177 10.595100 15.389254
## 17  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.596923 15.403077
## 18  Quadrat_6 0.9952390 207 Extrapolation       0 13.004807 10.596499 15.413116
## 19  Quadrat_6 0.9997653 517 Extrapolation       0 13.473277 10.504931 16.441623
## 20  Quadrat_7 0.9968652 318   Rarefaction       0  6.995767  5.720658  8.270877
## 21  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.689127  8.310873
## 22  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.71486231 14.000000
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.25074574  6.643636
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.25391159  4.626129
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.54551953  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.09602115  2.965621
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.09708520  2.545310
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.73118895 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.24756871  4.841756
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.18801809  3.462797
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.49375032 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.29351105  5.431209
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.31885927  4.027221
## 13  Quadrat_5  Species richness 12.000000 13.996132 3.15330214 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.22566775  5.811766
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.19998197  4.495767
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.81897807 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.53670003  7.908610
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.62238532  5.496114
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.66951655  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.15702205  4.696721
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.21841120  4.097350
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.00000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.31125418  5.735315
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.34195306  4.313894
##          UCL
## 1  20.357295
## 2   7.626541
## 3   5.621444
## 4   9.067438
## 5   3.342017
## 6   2.925877
## 7  13.433104
## 8   5.812207
## 9   4.199814
## 10 13.426144
## 11  6.581752
## 12  5.277127
## 13 20.176490
## 14  6.696367
## 15  5.279682
## 16 17.062704
## 17 10.012435
## 18  7.935820
## 19  8.312228
## 20  5.312236
## 21  4.953506
## 22  9.000000
## 23  6.955409
## 24  5.654325
r <- c(206)

Warton_Datar <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = r)

Warton_Datar
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 206   Rarefaction       0 11.511241 10.671910 12.350572 0.9934525
## 2   Quadrat_1 794   Rarefaction       0 13.996226 12.319330 15.673123 0.9962264
## 3   Quadrat_1 795      Observed       0 14.000000 12.321899 15.678101 0.9962312
## 4   Quadrat_1 796 Extrapolation       0 14.003769 12.324010 15.683528 0.9962359
## 5   Quadrat_2 206   Rarefaction       0  5.579448  4.808422  6.350475 0.9942326
## 6   Quadrat_2 567   Rarefaction       0  6.996479  5.988573  8.004385 0.9964789
## 7   Quadrat_2 568      Observed       0  7.000000  5.991241  8.008759 0.9964912
## 8   Quadrat_2 569 Extrapolation       0  7.003509  5.994326  8.012691 0.9965036
## 9   Quadrat_3 206   Rarefaction       0 11.084026 10.256313 11.911740 0.9917208
## 10  Quadrat_3 551   Rarefaction       0 12.000000 11.045816 12.954184 1.0000000
## 11  Quadrat_3 552      Observed       0 12.000000 11.045550 12.954450 1.0000000
## 12  Quadrat_3 553 Extrapolation       0 12.000000 11.045190 12.954810 1.0000000
## 13  Quadrat_4 206   Rarefaction       0  9.464713  8.166814 10.762611 0.9934801
## 14  Quadrat_4 321   Rarefaction       0  9.996894  8.346585 11.647204 0.9968944
## 15  Quadrat_4 322      Observed       0 10.000000  8.346370 11.653630 0.9969136
## 16  Quadrat_4 323 Extrapolation       0 10.003086  8.345719 11.660454 0.9969328
## 17  Quadrat_5 206   Rarefaction       0 10.361249  9.336675 11.385822 0.9922834
## 18  Quadrat_5 516   Rarefaction       0 11.996132 10.089860 13.902403 0.9961315
## 19  Quadrat_5 517      Observed       0 12.000000 10.090690 13.909310 0.9961390
## 20  Quadrat_5 518 Extrapolation       0 12.003861 10.090947 13.916775 0.9961465
## 21  Quadrat_6 206      Observed       0 13.000000 11.468451 14.531549 0.9951925
## 22  Quadrat_7 206   Rarefaction       0  6.602082  5.798207  7.405957 0.9957054
## 23  Quadrat_7 318   Rarefaction       0  6.996865  6.015723  7.978008 0.9968652
## 24  Quadrat_7 319      Observed       0  7.000000  6.017222  7.982778 1.0000000
## 25  Quadrat_7 320 Extrapolation       0  7.000000  6.016453  7.983547 1.0000000
## 26  Quadrat_8 206   Rarefaction       0  8.999392  8.879384  9.119400 0.9999636
## 27  Quadrat_8 342   Rarefaction       0  9.000000  8.999192  9.000808 1.0000000
## 28  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
## 29  Quadrat_8 344 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9905894 0.9963155
## 2  0.9940662 0.9983866
## 3  0.9938140 0.9986483
## 4  0.9938233 0.9986486
## 5  0.9917924 0.9966729
## 6  0.9948351 0.9981227
## 7  0.9952389 0.9977436
## 8  0.9952556 0.9977515
## 9  0.9890035 0.9944381
## 10 0.9979711 1.0000000
## 11 0.9980292 1.0000000
## 12 0.9980372 1.0000000
## 13 0.9879705 0.9989898
## 14 0.9909649 1.0000000
## 15 0.9904006 1.0000000
## 16 0.9904427 1.0000000
## 17 0.9880864 0.9964803
## 18 0.9917391 1.0000000
## 19 0.9913905 1.0000000
## 20 0.9914055 1.0000000
## 21 0.9855662 1.0000000
## 22 0.9924414 0.9989694
## 23 0.9933020 1.0000000
## 24 0.9972390 1.0000000
## 25 0.9972562 1.0000000
## 26 0.9988233 1.0000000
## 27 0.9991919 1.0000000
## 28 1.0000000 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9934525 206   Rarefaction       0 11.511241 10.343549 12.678932
## 2   Quadrat_1 0.9962264 791   Rarefaction       0 13.984626 12.139367 15.829885
## 3   Quadrat_1 0.9962312 795      Observed       0 14.000000 12.152259 15.847741
## 4   Quadrat_1 0.9962359 796 Extrapolation       0 14.003769 12.154523 15.853014
## 5   Quadrat_2 0.9942326 206   Rarefaction       0  5.579448  4.674703  6.484194
## 6   Quadrat_2 0.9964789 563   Rarefaction       0  6.983786  5.982030  7.985542
## 7   Quadrat_2 0.9964912 568      Observed       0  7.000000  5.996154  8.003846
## 8   Quadrat_2 0.9965036 569 Extrapolation       0  7.003509  5.999205  8.007813
## 9   Quadrat_3 0.9917208 206   Rarefaction       0 11.084027 10.098556 12.069497
## 10  Quadrat_3 1.0000000 552      Observed       0 12.000000 10.841486 13.158514
## 11  Quadrat_4 0.9934801 206   Rarefaction       0  9.464713  6.959784 11.969642
## 12  Quadrat_4 0.9968944 321   Rarefaction       0  9.995413  7.057798 12.933027
## 13  Quadrat_4 0.9969136 322      Observed       0 10.000000  7.058274 12.941726
## 14  Quadrat_4 0.9969328 323 Extrapolation       0 10.003086  7.057249 12.948924
## 15  Quadrat_5 0.9922834 206   Rarefaction       0 10.361249  7.804821 12.917677
## 16  Quadrat_5 0.9961315 516   Rarefaction       0 11.995720  7.943921 16.047519
## 17  Quadrat_5 0.9961390 517      Observed       0 12.000000  7.945204 16.054796
## 18  Quadrat_5 0.9961465 518 Extrapolation       0 12.003861  7.946295 16.061427
## 19  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.562970 15.437030
## 20  Quadrat_7 0.9957054 206   Rarefaction       0  6.602082  5.449419  7.754745
## 21  Quadrat_7 0.9968652 318   Rarefaction       0  6.995767  5.788295  8.203239
## 22  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.816060  8.183940
## 23  Quadrat_8 0.9999636 206   Rarefaction       0  8.999392  8.996692  9.002092
## 24  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.41609234 14.220736
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.23384587  6.676759
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.23737221  4.658545
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.63766602  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.09090988  2.975639
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.08423956  2.570487
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.62442824 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.23905730  4.858438
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.18071405  3.477112
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.76269602 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.26594513  5.485238
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.26389062  4.134958
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.55624776 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.23721124  5.789141
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.21118348  4.473812
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.55103877 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.49459527  7.991134
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.59620833  5.547420
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.69750049  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.14307905  4.724048
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.19448193  4.144251
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.00000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.22840004  5.897706
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.25495356  4.484410
##          UCL
## 1  19.771716
## 2   7.593418
## 3   5.589027
## 4   9.248042
## 5   3.331999
## 6   2.900700
## 7  13.223857
## 8   5.795525
## 9   4.185498
## 10 13.953268
## 11  6.527723
## 12  5.169390
## 13 19.006285
## 14  6.718992
## 15  5.301636
## 16 16.537553
## 17  9.929912
## 18  7.884514
## 19  8.367076
## 20  5.284908
## 21  4.906606
## 22  9.000000
## 23  6.793018
## 24  5.483809
s <- c(319)

Warton_Datas <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = s)

Warton_Datas
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 319   Rarefaction       0 12.123846 11.130931 13.116760 0.9953385
## 2   Quadrat_1 794   Rarefaction       0 13.996226 12.233768 15.758685 0.9962264
## 3   Quadrat_1 795      Observed       0 14.000000 12.236255 15.763745 0.9962312
## 4   Quadrat_1 796 Extrapolation       0 14.003769 12.238125 15.769413 0.9962359
## 5   Quadrat_2 319   Rarefaction       0  6.104448  5.512637  6.696258 0.9960777
## 6   Quadrat_2 567   Rarefaction       0  6.996479  6.222027  7.770931 0.9964789
## 7   Quadrat_2 568      Observed       0  7.000000  6.224055  7.775945 0.9964912
## 8   Quadrat_2 569 Extrapolation       0  7.003509  6.226313  7.780704 0.9965036
## 9   Quadrat_3 319   Rarefaction       0 11.702282 10.686108 12.718456 0.9966607
## 10  Quadrat_3 551   Rarefaction       0 12.000000 10.907945 13.092055 1.0000000
## 11  Quadrat_3 552      Observed       0 12.000000 10.907661 13.092339 1.0000000
## 12  Quadrat_3 553 Extrapolation       0 12.000000 10.907167 13.092833 1.0000000
## 13  Quadrat_4 319   Rarefaction       0  9.990625  8.579638 11.401612 0.9968555
## 14  Quadrat_4 321   Rarefaction       0  9.996894  8.580649 11.413140 0.9968944
## 15  Quadrat_4 322      Observed       0 10.000000  8.581114 11.418886 0.9969136
## 16  Quadrat_4 323 Extrapolation       0 10.003086  8.580519 11.425654 0.9969328
## 17  Quadrat_5 319   Rarefaction       0 11.083688  9.419391 12.747984 0.9945234
## 18  Quadrat_5 516   Rarefaction       0 11.996132  9.786564 14.205699 0.9961315
## 19  Quadrat_5 517      Observed       0 12.000000  9.787863 14.212137 0.9961390
## 20  Quadrat_5 518 Extrapolation       0 12.003861  9.788731 14.218991 0.9961465
## 21  Quadrat_6 205   Rarefaction       0 12.995146 11.347844 14.642447 0.9951456
## 22  Quadrat_6 206      Observed       0 13.000000 11.347793 14.652207 0.9951925
## 23  Quadrat_6 207 Extrapolation       0 13.004807 11.347507 14.662108 0.9952390
## 24  Quadrat_6 319 Extrapolation       0 13.331464 11.207315 15.455612 0.9983951
## 25  Quadrat_7 319      Observed       0  7.000000  6.076441  7.923559 1.0000000
## 26  Quadrat_8 319   Rarefaction       0  9.000000  8.998694  9.001306 1.0000000
## 27  Quadrat_8 342   Rarefaction       0  9.000000  9.000000  9.000000 1.0000000
## 28  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
## 29  Quadrat_8 344 Extrapolation       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9927558 0.9979212
## 2  0.9940095 0.9984433
## 3  0.9935998 0.9988625
## 4  0.9936088 0.9988630
## 5  0.9937161 0.9984393
## 6  0.9941667 0.9987910
## 7  0.9943419 0.9986406
## 8  0.9943604 0.9986467
## 9  0.9940745 0.9992468
## 10 0.9977316 1.0000000
## 11 0.9977396 1.0000000
## 12 0.9977476 1.0000000
## 13 0.9912679 1.0000000
## 14 0.9912914 1.0000000
## 15 0.9902428 1.0000000
## 16 0.9902858 1.0000000
## 17 0.9905987 0.9984482
## 18 0.9922829 0.9999801
## 19 0.9918318 1.0000000
## 20 0.9918483 1.0000000
## 21 0.9866270 1.0000000
## 22 0.9864732 1.0000000
## 23 0.9865747 1.0000000
## 24 0.9935903 1.0000000
## 25 0.9959820 1.0000000
## 26 0.9998908 1.0000000
## 27 1.0000000 1.0000000
## 28 1.0000000 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9953385 319   Rarefaction       0 12.123846 10.565792 13.681899
## 2   Quadrat_1 0.9962264 791   Rarefaction       0 13.984626 11.956402 16.012850
## 3   Quadrat_1 0.9962312 795      Observed       0 14.000000 11.962510 16.037490
## 4   Quadrat_1 0.9962359 796 Extrapolation       0 14.003769 11.964409 16.043129
## 5   Quadrat_2 0.9960777 319   Rarefaction       0  6.104448  5.270018  6.938877
## 6   Quadrat_2 0.9964789 563   Rarefaction       0  6.983786  6.019181  7.948391
## 7   Quadrat_2 0.9964912 568      Observed       0  7.000000  6.033335  7.966665
## 8   Quadrat_2 0.9965036 569 Extrapolation       0  7.003509  6.035544  7.971474
## 9   Quadrat_3 0.9966607 319   Rarefaction       0 11.702282 10.470944 12.933620
## 10  Quadrat_3 1.0000000 552      Observed       0 12.000000 10.551973 13.448027
## 11  Quadrat_4 0.9968555 319   Rarefaction       0  9.990625  7.307006 12.674244
## 12  Quadrat_4 0.9968944 321   Rarefaction       0  9.995413  7.335418 12.655408
## 13  Quadrat_4 0.9969136 322      Observed       0 10.000000  7.335846 12.664154
## 14  Quadrat_4 0.9969328 323 Extrapolation       0 10.003086  7.334786 12.671387
## 15  Quadrat_5 0.9945234 319   Rarefaction       0 11.083688  8.324358 13.843018
## 16  Quadrat_5 0.9961315 516   Rarefaction       0 11.995720  8.864664 15.126776
## 17  Quadrat_5 0.9961390 517      Observed       0 12.000000  8.866394 15.133606
## 18  Quadrat_5 0.9961465 518 Extrapolation       0 12.003861  8.868101 15.139621
## 19  Quadrat_6 0.9951456 204   Rarefaction       0 12.992177 10.598032 15.386322
## 20  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.601865 15.398135
## 21  Quadrat_6 0.9952390 207 Extrapolation       0 13.004807 10.601844 15.407771
## 22  Quadrat_6 0.9983951 319 Extrapolation       0 13.331464 10.593437 16.069490
## 23  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.699463  8.300537
## 24  Quadrat_8 1.0000000 319   Rarefaction       0  9.000000  8.999997  9.000003
## 25  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.79501290 14.000000
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.23173673  6.680893
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.24047900  4.652456
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.47127160  7.074564
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.10156314  2.954759
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.09037574  2.558461
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.77102008 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.21246657  4.910555
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.16595048  3.506048
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.80056832 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.27913427  5.459387
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.30955195  4.045463
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.13924337 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.24109948  5.781520
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.21854352  4.459387
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.74020968 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.51658426  7.948036
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.62859561  5.483942
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.65739530  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.13777976  4.734435
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.18169773  4.169307
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.00000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.26394591  5.828037
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.29564854  4.404649
##          UCL
## 1  20.514387
## 2   7.589284
## 3   5.595117
## 4   8.921915
## 5   3.352879
## 6   2.912727
## 7  13.511172
## 8   5.743408
## 9   4.156562
## 10 14.027496
## 11  6.553574
## 12  5.258885
## 13 18.188971
## 14  6.726613
## 15  5.316062
## 16 16.908321
## 17  9.973009
## 18  7.947992
## 19  8.288471
## 20  5.274521
## 21  4.881549
## 22  9.000000
## 23  6.862686
## 24  5.563570
t <- c(343)

Warton_Datat <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance", size = t)

Warton_Datat
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1 343   Rarefaction       0 12.233488 11.317194 13.149783 0.9955254
## 2   Quadrat_1 794   Rarefaction       0 13.996226 12.550147 15.442306 0.9962264
## 3   Quadrat_1 795      Observed       0 14.000000 12.552668 15.447332 0.9962312
## 4   Quadrat_1 796 Extrapolation       0 14.003769 12.554835 15.452702 0.9962359
## 5   Quadrat_2 343   Rarefaction       0  6.196808  5.475577  6.918038 0.9962229
## 6   Quadrat_2 567   Rarefaction       0  6.996479  6.069630  7.923327 0.9964789
## 7   Quadrat_2 568      Observed       0  7.000000  6.072207  7.927793 0.9964912
## 8   Quadrat_2 569 Extrapolation       0  7.003509  6.075107  7.931910 0.9965036
## 9   Quadrat_3 343   Rarefaction       0 11.775135 11.128092 12.422179 0.9972773
## 10  Quadrat_3 551   Rarefaction       0 12.000000 11.313613 12.686387 1.0000000
## 11  Quadrat_3 552      Observed       0 12.000000 11.313013 12.686987 1.0000000
## 12  Quadrat_3 553 Extrapolation       0 12.000000 11.312697 12.687303 1.0000000
## 13  Quadrat_4 321   Rarefaction       0  9.996894  8.492857 11.500931 0.9968944
## 14  Quadrat_4 322      Observed       0 10.000000  8.492702 11.507298 0.9969136
## 15  Quadrat_4 323 Extrapolation       0 10.003086  8.491907 11.514265 0.9969328
## 16  Quadrat_4 343 Extrapolation       0 10.060953  8.473100 11.648807 0.9972911
## 17  Quadrat_5 343   Rarefaction       0 11.212226  9.882234 12.542217 0.9947691
## 18  Quadrat_5 516   Rarefaction       0 11.996132 10.227923 13.764340 0.9961315
## 19  Quadrat_5 517      Observed       0 12.000000 10.229157 13.770843 0.9961390
## 20  Quadrat_5 518 Extrapolation       0 12.003861 10.230231 13.777491 0.9961465
## 21  Quadrat_6 205   Rarefaction       0 12.995146 11.384603 14.605689 0.9951456
## 22  Quadrat_6 206      Observed       0 13.000000 11.384743 14.615257 0.9951925
## 23  Quadrat_6 207 Extrapolation       0 13.004807 11.384067 14.625548 0.9952390
## 24  Quadrat_6 343 Extrapolation       0 13.365990 11.124551 15.607430 0.9987287
## 25  Quadrat_7 318   Rarefaction       0  6.996865  6.129782  7.863948 0.9968652
## 26  Quadrat_7 319      Observed       0  7.000000  6.131564  7.868436 1.0000000
## 27  Quadrat_7 320 Extrapolation       0  7.000000  6.130975  7.869025 1.0000000
## 28  Quadrat_7 343 Extrapolation       0  7.000000  6.116279  7.883721 1.0000000
## 29  Quadrat_8 343      Observed       0  9.000000  9.000000  9.000000 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9934047 0.9976462
## 2  0.9939989 0.9984539
## 3  0.9937744 0.9986879
## 4  0.9937833 0.9986885
## 5  0.9943348 0.9981111
## 6  0.9946663 0.9982914
## 7  0.9952389 0.9977436
## 8  0.9952556 0.9977515
## 9  0.9951677 0.9993868
## 10 0.9977135 1.0000000
## 11 0.9977672 1.0000000
## 12 0.9977753 1.0000000
## 13 0.9919311 1.0000000
## 14 0.9913211 1.0000000
## 15 0.9913612 1.0000000
## 16 0.9921121 1.0000000
## 17 0.9911761 0.9983621
## 18 0.9920348 1.0000000
## 19 0.9918791 1.0000000
## 20 0.9918938 1.0000000
## 21 0.9864023 1.0000000
## 22 0.9857580 1.0000000
## 23 0.9858661 1.0000000
## 24 0.9940009 1.0000000
## 25 0.9933543 1.0000000
## 26 0.9971442 1.0000000
## 27 0.9971620 1.0000000
## 28 0.9975431 1.0000000
## 29 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9955254 343   Rarefaction       0 12.233488 10.921998 13.544979
## 2   Quadrat_1 0.9962264 791   Rarefaction       0 13.984626 12.258312 15.710940
## 3   Quadrat_1 0.9962312 795      Observed       0 14.000000 12.269818 15.730182
## 4   Quadrat_1 0.9962359 796 Extrapolation       0 14.003769 12.272191 15.735347
## 5   Quadrat_2 0.9962229 343   Rarefaction       0  6.196808  5.387975  7.005641
## 6   Quadrat_2 0.9964789 563   Rarefaction       0  6.983786  6.096570  7.871002
## 7   Quadrat_2 0.9964912 568      Observed       0  7.000000  6.111213  7.888787
## 8   Quadrat_2 0.9965036 569 Extrapolation       0  7.003509  6.113941  7.893077
## 9   Quadrat_3 0.9972773 343   Rarefaction       0 11.775135 11.011557 12.538713
## 10  Quadrat_3 1.0000000 552      Observed       0 12.000000 10.922576 13.077424
## 11  Quadrat_4 0.9968944 321   Rarefaction       0  9.995413  7.570254 12.420571
## 12  Quadrat_4 0.9969136 322      Observed       0 10.000000  7.571124 12.428876
## 13  Quadrat_4 0.9969328 323 Extrapolation       0 10.003086  7.570423 12.435749
## 14  Quadrat_4 0.9972911 343 Extrapolation       0 10.060953  7.556275 12.565632
## 15  Quadrat_5 0.9947691 343   Rarefaction       0 11.212226  8.451332 13.973119
## 16  Quadrat_5 0.9961315 516   Rarefaction       0 11.995720  8.906057 15.085383
## 17  Quadrat_5 0.9961390 517      Observed       0 12.000000  8.908567 15.091433
## 18  Quadrat_5 0.9961465 518 Extrapolation       0 12.003861  8.911067 15.096655
## 19  Quadrat_6 0.9951456 204   Rarefaction       0 12.992177 10.446727 15.537627
## 20  Quadrat_6 0.9951925 206      Observed       0 13.000000 10.448842 15.551158
## 21  Quadrat_6 0.9952390 207 Extrapolation       0 13.004807 10.448146 15.561469
## 22  Quadrat_6 0.9987287 343 Extrapolation       0 13.365990 10.361554 16.370426
## 23  Quadrat_7 0.9968652 318   Rarefaction       0  6.995767  5.930380  8.061155
## 24  Quadrat_7 1.0000000 319      Observed       0  7.000000  5.939093  8.060907
## 25  Quadrat_8 1.0000000 343      Observed       0  9.000000  9.000000  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 1.5427864 14.000000
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.2363893  6.671774
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.2540803  4.625798
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.7175030  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.1053582  2.947321
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.1050262  2.529746
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.5456222 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.2492326  4.838495
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.1869799  3.464831
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.4376656 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.2837596  5.450322
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.3045808  4.055206
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.3885963 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.2605075  5.743481
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.2337084  4.429664
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.4873641 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.5229426  7.935574
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.5997639  5.540451
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.7077908  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.1450187  4.720247
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.1947955  4.143636
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.0000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.2715904  5.813055
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.2903496  4.415035
##          UCL
## 1  20.020032
## 2   7.598403
## 3   5.621775
## 4   9.404519
## 5   3.360318
## 6   2.941442
## 7  13.069400
## 8   5.815469
## 9   4.197779
## 10 13.316220
## 11  6.562639
## 12  5.249141
## 13 18.677694
## 14  6.764652
## 15  5.345785
## 16 16.412753
## 17  9.985471
## 18  7.891483
## 19  8.387244
## 20  5.288710
## 21  4.907220
## 22  9.000000
## 23  6.877669
## 24  5.553184

#Now to run the analysis again without specificying the size, can do this for #looking at the other diversity indices

Warton_Data <- iNEXT(Warton_Nos, q=c(0), datatype= "abundance")

print(Warton_Data)
## Compare 8 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1 795    14 0.9962  3  0  0  0  1  0  0  0  0   0
## 2  Quadrat_2 568     7 0.9965  2  0  0  0  1  0  1  0  0   0
## 3  Quadrat_3 552    12 1.0000  0  1  1  1  1  0  0  1  0   0
## 4  Quadrat_4 322    10 0.9969  1  1  1  0  0  0  0  0  0   0
## 5  Quadrat_5 517    12 0.9961  2  1  0  0  0  1  1  0  0   0
## 6  Quadrat_6 206    13 0.9952  1  1  0  1  1  0  0  0  0   3
## 7  Quadrat_7 319     7 1.0000  1  0  1  0  0  0  0  0  0   0
## 8  Quadrat_8 343     9 1.0000  0  0  0  0  0  0  0  1  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage    m        Method Order.q        qD    qD.LCL    qD.UCL
## 1    Quadrat_1    1   Rarefaction       0  1.000000  1.000000  1.000000
## 10   Quadrat_1  397   Rarefaction       0 12.466585 11.454352 13.478819
## 20   Quadrat_1  795      Observed       0 14.000000 12.505237 15.494763
## 30   Quadrat_1 1172 Extrapolation       0 15.132009 13.060982 17.203036
## 40   Quadrat_1 1590 Extrapolation       0 15.894670 13.338101 18.451239
## 41   Quadrat_2    1   Rarefaction       0  1.000000  1.000000  1.000000
## 50   Quadrat_2  284   Rarefaction       0  5.961774  5.342425  6.581123
## 60   Quadrat_2  568      Observed       0  7.000000  6.160949  7.839051
## 70   Quadrat_2  837 Extrapolation       0  7.611091  6.605831  8.616350
## 80   Quadrat_2 1136 Extrapolation       0  7.863143  6.779986  8.946299
## 81   Quadrat_3    1   Rarefaction       0  1.000000  1.000000  1.000000
## 90   Quadrat_3  276   Rarefaction       0 11.529472 10.549943 12.509001
## 100  Quadrat_3  552      Observed       0 12.000000 11.173185 12.826815
## 110  Quadrat_3  814 Extrapolation       0 12.000000 11.054734 12.945266
## 120  Quadrat_3 1104 Extrapolation       0 12.000000 10.935404 13.064596
## 121  Quadrat_4    1   Rarefaction       0  1.000000  1.000000  1.000000
## 130  Quadrat_4  161   Rarefaction       0  9.126945  8.122698 10.131191
## 140  Quadrat_4  322      Observed       0 10.000000  8.556464 11.443536
## 150  Quadrat_4  475 Extrapolation       0 10.305738  8.290416 12.321059
## 160  Quadrat_4  644 Extrapolation       0 10.430990  7.964713 12.897267
## 161  Quadrat_5    1   Rarefaction       0  1.000000  1.000000  1.000000
## 170  Quadrat_5  258   Rarefaction       0 10.724628  9.478003 11.971252
## 180  Quadrat_5  517      Observed       0 12.000000 10.091100 13.908900
## 190  Quadrat_5  762 Extrapolation       0 12.753956 10.277724 15.230188
## 200  Quadrat_5 1034 Extrapolation       0 13.262507 10.327011 16.198002
## 201  Quadrat_6    1   Rarefaction       0  1.000000  1.000000  1.000000
## 210  Quadrat_6  103   Rarefaction       0 12.158108 10.955710 13.360507
## 220  Quadrat_6  206      Observed       0 13.000000 11.395945 14.604055
## 230  Quadrat_6  304 Extrapolation       0 13.305422 11.244708 15.366137
## 240  Quadrat_6  412 Extrapolation       0 13.430235 11.048037 15.812432
## 241  Quadrat_7    1   Rarefaction       0  1.000000  1.000000  1.000000
## 250  Quadrat_7  159   Rarefaction       0  6.373436  5.569413  7.177459
## 260  Quadrat_7  319      Observed       0  7.000000  5.873738  8.126262
## 270  Quadrat_7  470 Extrapolation       0  7.000000  5.809909  8.190091
## 280  Quadrat_7  638 Extrapolation       0  7.000000  5.773206  8.226794
## 281  Quadrat_8    1   Rarefaction       0  1.000000  1.000000  1.000000
## 290  Quadrat_8  171   Rarefaction       0  8.995791  8.932563  9.059019
## 300  Quadrat_8  343      Observed       0  9.000000  9.000000  9.000000
## 310  Quadrat_8  506 Extrapolation       0  9.000000  9.000000  9.000000
## 320  Quadrat_8  686 Extrapolation       0  9.000000  9.000000  9.000000
##            SC    SC.LCL    SC.UCL
## 1   0.1951682 0.1762573 0.2140790
## 10  0.9958230 0.9936272 0.9980188
## 20  0.9962312 0.9937042 0.9987582
## 30  0.9976551 0.9960149 0.9992952
## 40  0.9986144 0.9975240 0.9997048
## 41  0.3655513 0.3454189 0.3856838
## 50  0.9957529 0.9934150 0.9980907
## 60  0.9964912 0.9950591 0.9979234
## 70  0.9986392 0.9980838 0.9991946
## 80  0.9995251 0.9993313 0.9997190
## 81  0.2610077 0.2361697 0.2858456
## 90  0.9952631 0.9927348 0.9977913
## 100 1.0000000 0.9973977 1.0000000
## 110 1.0000000 0.9989002 1.0000000
## 120 1.0000000 0.9995240 1.0000000
## 121 0.2149533 0.1858497 0.2440569
## 130 0.9914908 0.9869203 0.9960613
## 140 0.9969136 0.9903572 1.0000000
## 150 0.9988068 0.9948186 1.0000000
## 160 0.9995823 0.9970581 1.0000000
## 161 0.2045942 0.1896433 0.2195450
## 170 0.9936361 0.9897520 0.9975203
## 180 0.9961390 0.9924917 0.9997863
## 190 0.9975973 0.9951326 1.0000000
## 200 0.9985810 0.9969361 1.0000000
## 201 0.1488989 0.1206601 0.1771377
## 210 0.9862494 0.9774527 0.9950461
## 220 0.9951925 0.9859127 1.0000000
## 230 0.9981435 0.9930517 1.0000000
## 240 0.9993494 0.9964238 1.0000000
## 241 0.2209736 0.1980506 0.2438965
## 250 0.9945215 0.9908177 0.9982254
## 260 1.0000000 0.9977762 1.0000000
## 270 1.0000000 0.9991371 1.0000000
## 280 1.0000000 0.9996990 1.0000000
## 281 0.2006376 0.1793256 0.2219497
## 290 0.9997938 0.9985574 1.0000000
## 300 1.0000000 1.0000000 1.0000000
## 310 1.0000000 1.0000000 1.0000000
## 320 1.0000000 1.0000000 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage        SC    m        Method Order.q        qD     qD.LCL
## 1    Quadrat_1 0.1951698    1   Rarefaction       0  1.000008  0.9485775
## 10   Quadrat_1 0.9958230  397   Rarefaction       0 12.466585 10.6850022
## 20   Quadrat_1 0.9962312  795      Observed       0 14.000000 11.9508457
## 30   Quadrat_1 0.9976551 1172 Extrapolation       0 15.132009 12.5494876
## 40   Quadrat_1 0.9986144 1590 Extrapolation       0 15.894670 12.9404489
## 41   Quadrat_2 0.3655588    1   Rarefaction       0  1.000017  0.9744361
## 50   Quadrat_2 0.9957529  284   Rarefaction       0  5.961774  5.2232241
## 60   Quadrat_2 0.9964912  568      Observed       0  7.000000  6.0971083
## 70   Quadrat_2 0.9986392  837 Extrapolation       0  7.611091  6.5858057
## 80   Quadrat_2 0.9995251 1136 Extrapolation       0  7.863143  6.7770598
## 81   Quadrat_3 0.2610100    1   Rarefaction       0  1.000008  0.9478273
## 85   Quadrat_3 0.9825762  123   Rarefaction       0 10.074595  8.9012456
## 90   Quadrat_3 0.9952631  276   Rarefaction       0 11.529472 10.5900850
## 95   Quadrat_3 0.9988210  428   Rarefaction       0 11.935737 10.9121124
## 99   Quadrat_3 1.0000000  552      Observed       0 12.000000 10.8084102
## 100  Quadrat_4 0.2149550    1   Rarefaction       0  1.000008  0.9253382
## 109  Quadrat_4 0.9914908  161   Rarefaction       0  9.126945  6.8916040
## 119  Quadrat_4 0.9969136  322      Observed       0 10.000000  7.2250067
## 129  Quadrat_4 0.9988068  475 Extrapolation       0 10.305738  7.2104832
## 139  Quadrat_4 0.9995823  644 Extrapolation       0 10.430990  7.1893018
## 140  Quadrat_5 0.2045956    1   Rarefaction       0  1.000006  0.9633615
## 149  Quadrat_5 0.9936361  258   Rarefaction       0 10.724628  8.4800196
## 159  Quadrat_5 0.9961390  517      Observed       0 12.000000  9.1460030
## 169  Quadrat_5 0.9975973  762 Extrapolation       0 12.753956  9.5411699
## 179  Quadrat_5 0.9985810 1034 Extrapolation       0 13.262507  9.8269314
## 180  Quadrat_6 0.1488989    1   Rarefaction       0  1.000000  0.9097059
## 189  Quadrat_6 0.9862494  103   Rarefaction       0 12.158108 10.3457862
## 199  Quadrat_6 0.9951925  206      Observed       0 13.000000 10.6767452
## 209  Quadrat_6 0.9981435  304 Extrapolation       0 13.305422 10.6651054
## 219  Quadrat_6 0.9993494  412 Extrapolation       0 13.430235 10.6497665
## 220  Quadrat_7 0.2209752    1   Rarefaction       0  1.000007  0.9598542
## 224  Quadrat_7 0.9911954   71   Rarefaction       0  5.753959  4.9807454
## 229  Quadrat_7 0.9945215  159   Rarefaction       0  6.373436  5.3275532
## 234  Quadrat_7 0.9964015  247   Rarefaction       0  6.763167  5.6303978
## 239  Quadrat_7 1.0000000  319      Observed       0  7.000000  5.7513283
## 240  Quadrat_8 0.2006376    1   Rarefaction       0  1.000000  0.9424450
## 244  Quadrat_8 0.9908143   76   Rarefaction       0  8.758813  8.5879137
## 249  Quadrat_8 0.9997938  171   Rarefaction       0  8.995791  8.9949069
## 254  Quadrat_8 0.9999995  266   Rarefaction       0  8.999995  8.9999928
## 258  Quadrat_8 1.0000000  343      Observed       0  9.000000  9.0000000
##        qD.UCL
## 1    1.051439
## 10  14.248169
## 20  16.049154
## 30  17.714531
## 40  18.848891
## 41   1.025599
## 50   6.700324
## 60   7.902892
## 70   8.636376
## 80   8.949226
## 81   1.052190
## 85  11.247944
## 90  12.468859
## 95  12.959361
## 99  13.191590
## 100  1.074677
## 109 11.362286
## 119 12.774993
## 129 13.400992
## 139 13.672679
## 140  1.036651
## 149 12.969235
## 159 14.853997
## 169 15.966742
## 179 16.698082
## 180  1.090294
## 189 13.970430
## 199 15.323255
## 209 15.945740
## 219 16.210703
## 220  1.040159
## 224  6.527173
## 229  7.419320
## 234  7.895936
## 239  8.248672
## 240  1.057555
## 244  8.929711
## 249  8.996675
## 254  8.999998
## 258  9.000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator       s.e.       LCL
## 1   Quadrat_1  Species richness 14.000000 16.996226 2.01686289 14.000000
## 2   Quadrat_1 Shannon diversity  7.058677  7.135088 0.22031584  6.703277
## 3   Quadrat_1 Simpson diversity  5.097346  5.123786 0.23902172  4.655313
## 4   Quadrat_2  Species richness  7.000000  7.998239 0.53833955  7.000000
## 5   Quadrat_2 Shannon diversity  3.132205  3.153819 0.08922147  2.978948
## 6   Quadrat_2 Simpson diversity  2.727260  2.735594 0.08672328  2.565619
## 7   Quadrat_3  Species richness 12.000000 12.000000 0.72153690 12.000000
## 8   Quadrat_3 Shannon diversity  5.272867  5.326982 0.22513663  4.885722
## 9   Quadrat_3 Simpson diversity  3.811754  3.831305 0.15286323  3.531699
## 10  Quadrat_4  Species richness 10.000000 10.498447 1.56205342 10.000000
## 11  Quadrat_4 Shannon diversity  5.913462  6.006481 0.26361789  5.489799
## 12  Quadrat_4 Simpson diversity  4.600000  4.652174 0.30980003  4.044977
## 13  Quadrat_5  Species richness 12.000000 13.996132 2.35711356 12.000000
## 14  Quadrat_5 Shannon diversity  6.170838  6.254067 0.21635852  5.830012
## 15  Quadrat_5 Simpson diversity  4.851244  4.887724 0.20245694  4.490916
## 16  Quadrat_6  Species richness 13.000000 13.497573 1.60172458 13.000000
## 17  Quadrat_6 Shannon diversity  8.679505  8.960523 0.49166373  7.996880
## 18  Quadrat_6 Simpson diversity  6.534647  6.715967 0.57232094  5.594238
## 19  Quadrat_7  Species richness  7.000000  7.000000 0.64020455  7.000000
## 20  Quadrat_7 Shannon diversity  4.955898  5.004478 0.13241998  4.744940
## 21  Quadrat_7 Simpson diversity  4.475962  4.525428 0.19309695  4.146965
## 22  Quadrat_8  Species richness  9.000000  9.000000 0.00000000  9.000000
## 23  Quadrat_8 Shannon diversity  6.271077  6.345362 0.26126751  5.833287
## 24  Quadrat_8 Simpson diversity  4.926881  4.984109 0.28444675  4.426604
##          UCL
## 1  20.949205
## 2   7.566899
## 3   5.592260
## 4   9.053366
## 5   3.328690
## 6   2.905568
## 7  13.414186
## 8   5.768241
## 9   4.130912
## 10 13.560016
## 11  6.523162
## 12  5.259371
## 13 18.615989
## 14  6.678122
## 15  5.284533
## 16 16.636895
## 17  9.924166
## 18  7.837695
## 19  8.254778
## 20  5.264016
## 21  4.903891
## 22  9.000000
## 23  6.857437
## 24  5.541615
summary(Warton_Data)
##          Length Class      Mode
## DataInfo 14     data.frame list
## iNextEst  2     -none-     list
## AsyEst    7     data.frame list

#Now to obtain additional biodiversity indices for the Warton data, including sample coverage#

W1 <- diversity(Warton_Nos$Quadrat_1)

Warton2 <- estimateD(Warton_Nos, q = c(0,1,2), datatype = "abundance", base="coverage")
Warton2
##    Assemblage         m        Method Order.q        SC        qD    qD.LCL
## 1   Quadrat_1 1571.0768 Extrapolation       0 0.9985810 15.868118 13.278652
## 2   Quadrat_1 1571.0768 Extrapolation       1 0.9985810  7.104569  6.672982
## 3   Quadrat_1 1571.0768 Extrapolation       2 0.9985810  5.110373  4.695801
## 4   Quadrat_2  825.1063 Extrapolation       0 0.9985810  7.594533  6.474955
## 5   Quadrat_2  825.1063 Extrapolation       1 0.9985810  3.140309  2.948680
## 6   Quadrat_2  825.1063 Extrapolation       2 0.9985810  2.729852  2.539643
## 7   Quadrat_3  411.3288   Rarefaction       0 0.9985810 11.913994 10.383177
## 8   Quadrat_3  411.3288   Rarefaction       1 0.9985810  5.253358  4.852529
## 9   Quadrat_3  411.3288   Rarefaction       2 0.9985810  3.805113  3.513213
## 10  Quadrat_4  447.1026 Extrapolation       0 0.9985810 10.269278  7.388081
## 11  Quadrat_4  447.1026 Extrapolation       1 0.9985810  5.944195  5.422146
## 12  Quadrat_4  447.1026 Extrapolation       2 0.9985810  4.614480  4.018714
## 13  Quadrat_5 1034.0000 Extrapolation       0 0.9985810 13.262507  8.982190
## 14  Quadrat_5 1034.0000 Extrapolation       1 0.9985810  6.222248  5.769358
## 15  Quadrat_5 1034.0000 Extrapolation       2 0.9985810  4.869416  4.463777
## 16  Quadrat_6  331.6812 Extrapolation       0 0.9985810 13.350706 10.553986
## 17  Quadrat_6  331.6812 Extrapolation       1 0.9985810  8.809870  7.842528
## 18  Quadrat_6  331.6812 Extrapolation       2 0.9985810  6.602189  5.403993
## 19  Quadrat_7  317.4628   Rarefaction       0 0.9968652  6.995181  5.624020
## 20  Quadrat_7  317.4628   Rarefaction       1 0.9968652  4.955628  4.636444
## 21  Quadrat_7  317.4628   Rarefaction       2 0.9968652  4.475725  4.075218
## 22  Quadrat_8  124.7522   Rarefaction       0 0.9985810  8.965447  8.947112
## 23  Quadrat_8  124.7522   Rarefaction       1 0.9985810  6.138467  5.684416
## 24  Quadrat_8  124.7522   Rarefaction       2 0.9985810  4.829860  4.312148
##       qD.UCL
## 1  18.457585
## 2   7.536156
## 3   5.524945
## 4   8.714111
## 5   3.331938
## 6   2.920060
## 7  13.444812
## 8   5.654188
## 9   4.097014
## 10 13.150476
## 11  6.466244
## 12  5.210247
## 13 17.542823
## 14  6.675138
## 15  5.275055
## 16 16.147426
## 17  9.777213
## 18  7.800386
## 19  8.366343
## 20  5.274812
## 21  4.876233
## 22  8.983782
## 23  6.592517
## 24  5.347573
Wevenness1 <- W1/log(specnumber(Warton_Nos$Quadrat_1))

summary(Wevenness1)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7405  0.7405  0.7405  0.7405  0.7405  0.7405
W2 <- diversity(Warton_Nos$Quadrat_2)

Wevenness2 <- W2/log(specnumber(Warton_Nos$Quadrat_2))

summary(Wevenness2)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.5867  0.5867  0.5867  0.5867  0.5867  0.5867
W3 <- diversity(Warton_Nos$Quadrat_3)

Wevenness3 <- W3/log(specnumber(Warton_Nos$Quadrat_3))

summary(Wevenness3)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6691  0.6691  0.6691  0.6691  0.6691  0.6691
W4 <- diversity(Warton_Nos$Quadrat_4)

Wevenness4 <- W4/log(specnumber(Warton_Nos$Quadrat_4))

summary(Wevenness4)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7718  0.7718  0.7718  0.7718  0.7718  0.7718
W5 <- diversity(Warton_Nos$Quadrat_5)

Wevenness5 <- W5/log(specnumber(Warton_Nos$Quadrat_5))

summary(Wevenness5)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7324  0.7324  0.7324  0.7324  0.7324  0.7324
W6 <- diversity(Warton_Nos$Quadrat_6)

Wevenness6 <- W6/log(specnumber(Warton_Nos$Quadrat_6))

summary(Wevenness6)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8425  0.8425  0.8425  0.8425  0.8425  0.8425
W7 <- diversity(Warton_Nos$Quadrat_7)

Wevenness7 <- W7/log(specnumber(Warton_Nos$Quadrat_7))

summary(Wevenness7)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8225  0.8225  0.8225  0.8225  0.8225  0.8225
W8 <-diversity(Warton_Nos$Quadrat_8)

Wevenness8 <-W8/log(specnumber(Warton_Nos$Quadrat_8))

summary(Wevenness8)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8356  0.8356  0.8356  0.8356  0.8356  0.8356

#Now for Warton data visualisation, including species curve visualisation#

Warton_Data_Graph1 <- ggiNEXT(x = Warton_Data, se=TRUE, color.var="Order.q")

Warton_Data_Graph1

Warton_Data_Graph2 <- ggiNEXT(x = Warton_Data, se=TRUE, type = 1,
                              facet.var="None", color.var="Order.q") 

Warton_Data_Graph2

Warton_Data_Graph3 <- ggiNEXT(x = Warton_Data, se=TRUE, type = 2,
                              facet.var="None", color.var="Order.q") 

Warton_Data_Graph3

Warton_Data_Graph4 <- ggiNEXT(x = Warton_Data, se=TRUE, type = 3,
                              facet.var="None", color.var="Order.q") 

Warton_Data_Graph4

##Penicuik##

##Loading Penicuik Data#

urlfile5 <- 'https://raw.githubusercontent.com/Savannankvm/Biodiversity-analyses-for-six-study-sites/PhD-files/Penicuik_Abundance_Data.csv'

Penicuik_Nos <-read.csv(urlfile5)

print(Penicuik_Nos)
##     Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5
## 1           5         3        32        39         0
## 2           3         0         0         0         0
## 3           0         1         0         0         0
## 4           0         0         0         0         0
## 5           0         1         1         0         0
## 6           0         0         0         0         0
## 7           0         0         0         0         0
## 8           0         0         0         0         0
## 9           0         4         0         0         0
## 10          0         0         0         0         0
## 11          0         0         0         0         0
## 12          0         0         0         0         0
## 13          0         0         0         0         0
## 14          0         0         0         0         0
## 15          0         0         0         0         0
## 16          0         0         0         0         0
## 17          0         0         0         0         0
## 18          0        10        10         0         0
## 19          0         0         0         0         0
## 20          0         0         0         0         0
## 21          0         0         0         0         0
## 22          0         0         0         0         0
## 23          0         0         0         0         0
## 24          0         0         0         0         0
## 25          0        50       110         0         0
## 26          0         0        60         0         0
## 27          0         0         0         0         0
## 28          0         0         0         0         0
## 29          0         0         0         0         0
## 30          0         0         0         0         0
## 31          0         0         0         0         0
## 32          0         0         0         0         0
## 33          0         0         0         0         0
## 34          0         0         0         0         0
## 35          0         0         0         0         0
## 36          0         0         0         0         0
## 37          0         0         0         0         0
## 38          0         0         0         0         0
## 39          3         4         8         0         0
## 40          0         0         0         0         0
## 41          0         0         0         0         0
## 42          0         0         0         0         0
## 43          1         0         4        54         0
## 44          0         0         0         0         0
## 45          0         0         0         0         0
## 46          0         0         0         0         0
## 47          0         0         0         0         0
## 48          0         0         0         0         0
## 49          3         0         0         0         0
## 50          0        49         4         0         0
## 51          0         0         0         0         0
## 52          0         0         0         0         0
## 53          0         0         0         0         0
## 54          0         0         0         0         0
## 55          0         0         0         0         0
## 56          0         0         0         0         0
## 57          3         3         0         0         0
## 58          0         0         0         0         0
## 59          0         0         0         0         0
## 60          0         0         0         0         0
## 61          0         0         0        11         0
## 62          0         0         0         0        47
## 63          1         0         0         0         0
## 64          0         0         0         0         0
## 65          0         0         0         0         0
## 66          0         0         0        48         0
## 67          0         0         0         5         0
## 68          0         0         0         0         0
## 69          0         0         0         0         1
## 70          0         0         0         0         0
## 71          0         0         0         0         0
## 72          0         0         0         0         0
## 73         56        17         4         0         0
## 74          0         0         0         0         0
## 75          0         0         0         0         0
## 76          0         0         0         0         0
## 77          0         0         0         0         0
## 78          0         0         0         0         0
## 79          0         0         0         0         0
## 80          0         0         0         0         0
## 81          0         0        50        50         0
## 82          0         0         0         0         0
## 83          0         0         0         0         0
## 84          0         0         0         0         0
## 85          0         0         0         0         0
## 86          0         0         0         0         0
## 87          0         0         0         0         0
## 88          0         0         0         0         0
## 89          0         0        12         0         0
## 90          0         0         0         0         0
## 91          0         0         0         0         0
## 92          0         0         0         0         0
## 93          0         0         0         0         3
## 94          0         0         0         0         0
## 95          0         0         0       113         0
## 96          0         0         0         0         0
## 97          0         0         0         0         4
## 98          0         0         0         0         0
## 99          0         0         0         0         0
## 100         0         0         0         0         0
## 101         0         0         0         0         0
## 102         0         0         0         0         0
## 103         0         0         0         0         0
## 104         0         0         0         0         0
## 105         0         0         0         0         0
## 106         0         0         0         0         0
## 107         0         0         0         0         0
## 108         0         0         0         0         0
## 109         0         0         0         0         0
## 110         0         0         0         4         0
## 111         0         0         0         0         0
## 112         0         0         0         0         0
## 113         0         0         0         0         0
## 114         0         0         0         0         0
## 115         0         0         0         0         0
## 116         0         0         0         0         0
## 117         0       140        20         0         0
## 118         0         0         0         0         0
## 119         0         0         0         0         0
## 120         0         0         0         0         0
## 121         0         0         0         0         0
## 122         0         0         0         0         0
## 123         0         1         0         0         0
## 124         0         0         0         0         0
## 125         0         0         0         0         0
## 126         1         1         0         0         0
## 127         0         0         0         0         0
## 128         0         0         0         0         0
## 129         0         0         0         0         0
## 130         0         0         0         0         0
## 131         0         0         0         0         0
## 132         0         0         0         0         0
## 133         0         0         0         0         0
## 134         0         0         0         0         0
## 135         0         0         0         0         0
## 136         0         0         0         0         0
## 137         0        15         4         0         0
## 138         0         0         0         0        55
## 139         0         0         0         0         0
## 140         0         0         0         0         0
## 141         0         0         0         0         0
## 142         0         0         0         0         0
## 143         0         0         0         0         0

#colSums to establish sample size for each of the quadrats.

colSums(Penicuik_Nos)
## Quadrat_1 Quadrat_2 Quadrat_3 Quadrat_4 Quadrat_5 
##        76       299       319       324       110

#Setting m to sample size for Quadrat 1. This will give me observed #qD value that will be most representative for Quadrat and Community. Will do the same #for the other communities below.

m <- c(76)

Penicuik_Datam <- iNEXT(Penicuik_Nos, q=c(0), datatype= "abundance", size = m)

Penicuik_Datam
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1  76     9 0.9610  3  0  4  0  1  0  0  0  0   0
## 2  Quadrat_2 299    14 0.9867  4  0  2  2  0  0  0  0  0   1
## 3  Quadrat_3 319    13 1.0000  1  0  0  4  0  0  0  1  0   1
## 4  Quadrat_4 324     8 1.0000  0  0  0  1  1  0  0  0  0   0
## 5  Quadrat_5 110     5 1.0000  1  0  1  1  0  0  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1  76      Observed       0  9.000000  6.327259 11.672741 0.9610457
## 2   Quadrat_2  76   Rarefaction       0  9.508103  8.113589 10.902616 0.9610360
## 3   Quadrat_2 298   Rarefaction       0 13.986622 10.383268 17.589976 0.9866221
## 4   Quadrat_2 299      Observed       0 14.000000 10.387958 17.612042 0.9866519
## 5   Quadrat_2 300 Extrapolation       0 14.013348 10.392621 17.634075 0.9866817
## 6   Quadrat_3  76   Rarefaction       0 10.686842  9.877914 11.495770 0.9665386
## 7   Quadrat_3 318   Rarefaction       0 12.996865 12.048066 13.945665 0.9968652
## 8   Quadrat_3 319      Observed       0 13.000000 12.049666 13.950334 1.0000000
## 9   Quadrat_3 320 Extrapolation       0 13.000000 12.048373 13.951627 1.0000000
## 10  Quadrat_4  76   Rarefaction       0  7.348341  6.730364  7.966317 0.9870238
## 11  Quadrat_4 323   Rarefaction       0  8.000000  7.722900  8.277100 1.0000000
## 12  Quadrat_4 324      Observed       0  8.000000  7.722819  8.277181 1.0000000
## 13  Quadrat_4 325 Extrapolation       0  8.000000  7.722819  8.277181 1.0000000
## 14  Quadrat_5  76   Rarefaction       0  4.655149  3.791609  5.518690 0.9875175
## 15  Quadrat_5 109   Rarefaction       0  4.990909  4.012431  5.969387 0.9909091
## 16  Quadrat_5 110      Observed       0  5.000000  4.017222  5.982778 1.0000000
## 17  Quadrat_5 111 Extrapolation       0  5.000000  4.015470  5.984530 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9148208 1.0000000
## 2  0.9464029 0.9756691
## 3  0.9753840 0.9978601
## 4  0.9754183 0.9978855
## 5  0.9754526 0.9979109
## 6  0.9601154 0.9729618
## 7  0.9929320 1.0000000
## 8  0.9958580 1.0000000
## 9  0.9958792 1.0000000
## 10 0.9836608 0.9903869
## 11 0.9981668 1.0000000
## 12 1.0000000 1.0000000
## 13 1.0000000 1.0000000
## 14 0.9776984 0.9973367
## 15 0.9799609 1.0000000
## 16 0.9906476 1.0000000
## 17 0.9908161 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9610457  76      Observed       0  9.000000  3.014145 14.985855
## 2   Quadrat_2 0.9610360  76   Rarefaction       0  9.508102  7.027122 11.989082
## 3   Quadrat_2 0.9866221 297   Rarefaction       0 13.977493  6.844302 21.110683
## 4   Quadrat_2 0.9866519 299      Observed       0 14.000000  6.855122 21.144878
## 5   Quadrat_2 0.9866817 300 Extrapolation       0 14.013348  6.856551 21.170145
## 6   Quadrat_3 0.9665386  76   Rarefaction       0 10.686843  9.754966 11.618720
## 7   Quadrat_3 0.9968652 316   Rarefaction       0 12.991179 11.822044 14.160313
## 8   Quadrat_3 1.0000000 319      Observed       0 13.000000 11.484019 14.515981
## 9   Quadrat_4 0.9870238  76   Rarefaction       0  7.348341  6.726838  7.969844
## 10  Quadrat_4 1.0000000 324      Observed       0  8.000000  7.722819  8.277181
## 11  Quadrat_5 0.9875175  76   Rarefaction       0  4.655149  3.623021  5.687278
## 12  Quadrat_5 0.9909091 108   Rarefaction       0  4.983271  3.887984  6.078557
## 13  Quadrat_5 1.0000000 110      Observed       0  5.000000  3.807642  6.192358
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  9.000000 11.960526 4.0047923  9.000000
## 2   Quadrat_1 Shannon diversity  2.960433  3.209352 0.5416444  2.147749
## 3   Quadrat_1 Simpson diversity  1.805000  1.824584 0.2510782  1.332480
## 4   Quadrat_2  Species richness 14.000000 19.979933 4.5302479 14.000000
## 5   Quadrat_2 Shannon diversity  5.267568  5.447215 0.3573637  4.746795
## 6   Quadrat_2 Simpson diversity  3.552028  3.582710 0.2490581  3.094565
## 7   Quadrat_3  Species richness 13.000000 13.000000 0.9356981 13.000000
## 8   Quadrat_3 Shannon diversity  6.946592  7.082837 0.3564409  6.384225
## 9   Quadrat_3 Simpson diversity  5.088813  5.155097 0.3473167  4.474369
## 10  Quadrat_4  Species richness  8.000000  8.000000 0.1868612  8.000000
## 11  Quadrat_4 Shannon diversity  5.615883  5.677796 0.2186821  5.249187
## 12  Quadrat_4 Simpson diversity  4.734620  4.790004 0.2707086  4.259425
## 13  Quadrat_5  Species richness  5.000000  5.000000 0.7450515  5.000000
## 14  Quadrat_5 Shannon diversity  2.641582  2.693180 0.1982265  2.304663
## 15  Quadrat_5 Simpson diversity  2.300380  2.328155 0.1266140  2.079996
##          UCL
## 1  19.809775
## 2   4.270956
## 3   2.316688
## 4  28.859056
## 5   6.147635
## 6   4.070855
## 7  14.833935
## 8   7.781448
## 9   5.835825
## 10  8.366241
## 11  6.106405
## 12  5.320583
## 13  6.460274
## 14  3.081697
## 15  2.576314
n <- c(299)

Penicuik_Datan <- iNEXT(Penicuik_Nos, q=c(0), datatype= "abundance", size = n)

Penicuik_Datan
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1  76     9 0.9610  3  0  4  0  1  0  0  0  0   0
## 2  Quadrat_2 299    14 0.9867  4  0  2  2  0  0  0  0  0   1
## 3  Quadrat_3 319    13 1.0000  1  0  0  4  0  0  0  1  0   1
## 4  Quadrat_4 324     8 1.0000  0  0  0  1  1  0  0  0  0   0
## 5  Quadrat_5 110     5 1.0000  1  0  1  1  0  0  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1  75   Rarefaction       0  8.960526  7.035257 10.885796 0.9605263
## 2   Quadrat_1  76      Observed       0  9.000000  7.060139 10.939861 0.9610457
## 3   Quadrat_1  77 Extrapolation       0  9.038954  7.083563 10.994345 0.9615583
## 4   Quadrat_1 299 Extrapolation       0 11.806143  6.682322 16.929965 0.9979686
## 5   Quadrat_2 299      Observed       0 14.000000 11.154503 16.845497 0.9866519
## 6   Quadrat_3 299   Rarefaction       0 12.937258 11.840519 14.033998 0.9968560
## 7   Quadrat_3 318   Rarefaction       0 12.996865 11.878064 14.115666 0.9968652
## 8   Quadrat_3 319      Observed       0 13.000000 11.880021 14.119979 1.0000000
## 9   Quadrat_3 320 Extrapolation       0 13.000000 11.879316 14.120684 1.0000000
## 10  Quadrat_4 299   Rarefaction       0  7.999970  7.722184  8.277757 0.9999951
## 11  Quadrat_4 323   Rarefaction       0  8.000000  7.722868  8.277132 1.0000000
## 12  Quadrat_4 324      Observed       0  8.000000  7.722819  8.277181 1.0000000
## 13  Quadrat_4 325 Extrapolation       0  8.000000  7.722819  8.277181 1.0000000
## 14  Quadrat_5 109   Rarefaction       0  4.990909  3.881807  6.100011 0.9909091
## 15  Quadrat_5 110      Observed       0  5.000000  3.887747  6.112253 1.0000000
## 16  Quadrat_5 111 Extrapolation       0  5.000000  3.884870  6.115130 1.0000000
## 17  Quadrat_5 299 Extrapolation       0  5.000000  3.437578  6.562422 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9296322 0.9914204
## 2  0.9293635 0.9927279
## 3  0.9299258 0.9931908
## 4  0.9888909 1.0000000
## 5  0.9774841 0.9958198
## 6  0.9929073 1.0000000
## 7  0.9929320 1.0000000
## 8  0.9958677 1.0000000
## 9  0.9958912 1.0000000
## 10 0.9985574 1.0000000
## 11 0.9985488 1.0000000
## 12 1.0000000 1.0000000
## 13 1.0000000 1.0000000
## 14 0.9783925 1.0000000
## 15 0.9879142 1.0000000
## 16 0.9880905 1.0000000
## 17 0.9984911 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9605263  74   Rarefaction       0  8.931723  4.916014 12.947432
## 2   Quadrat_1 0.9610457  76      Observed       0  9.000000  4.957482 13.042518
## 3   Quadrat_1 0.9615583  77 Extrapolation       0  9.038954  4.967913 13.109996
## 4   Quadrat_1 0.9979686 299 Extrapolation       0 11.806143  5.480842 18.131445
## 5   Quadrat_2 0.9866519 299      Observed       0 14.000000  8.956182 19.043818
## 6   Quadrat_3 0.9968560 299   Rarefaction       0 12.937258 11.633710 14.240807
## 7   Quadrat_3 0.9968652 316   Rarefaction       0 12.991179 11.690831 14.291526
## 8   Quadrat_3 1.0000000 319      Observed       0 13.000000 11.384095 14.615905
## 9   Quadrat_4 0.9999951 299   Rarefaction       0  7.999970  7.722921  8.277019
## 10  Quadrat_4 1.0000000 324      Observed       0  8.000000  7.722819  8.277181
## 11  Quadrat_5 0.9909091 108   Rarefaction       0  4.983271  3.620198  6.346343
## 12  Quadrat_5 1.0000000 110      Observed       0  5.000000  3.330404  6.669596
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  9.000000 11.960526 3.2117360  9.000000
## 2   Quadrat_1 Shannon diversity  2.960433  3.209352 0.4476131  2.332046
## 3   Quadrat_1 Simpson diversity  1.805000  1.824584 0.2280725  1.377570
## 4   Quadrat_2  Species richness 14.000000 19.979933 5.8786558 14.000000
## 5   Quadrat_2 Shannon diversity  5.267568  5.447215 0.3325136  4.795500
## 6   Quadrat_2 Simpson diversity  3.552028  3.582710 0.2388806  3.114513
## 7   Quadrat_3  Species richness 13.000000 13.000000 1.0093272 13.000000
## 8   Quadrat_3 Shannon diversity  6.946592  7.082837 0.3262819  6.443336
## 9   Quadrat_3 Simpson diversity  5.088813  5.155097 0.3269849  4.514218
## 10  Quadrat_4  Species richness  8.000000  8.000000 0.2067964  8.000000
## 11  Quadrat_4 Shannon diversity  5.615883  5.677796 0.1935491  5.298447
## 12  Quadrat_4 Simpson diversity  4.734620  4.790004 0.2437045  4.312352
## 13  Quadrat_5  Species richness  5.000000  5.000000 0.6977193  5.000000
## 14  Quadrat_5 Shannon diversity  2.641582  2.693180 0.1727488  2.354599
## 15  Quadrat_5 Simpson diversity  2.300380  2.328155 0.1070540  2.118333
##          UCL
## 1  18.255413
## 2   4.086658
## 3   2.271598
## 4  31.501887
## 5   6.098929
## 6   4.050907
## 7  14.978245
## 8   7.722337
## 9   5.795976
## 10  8.405313
## 11  6.057145
## 12  5.267656
## 13  6.367505
## 14  3.031762
## 15  2.537977
o <- c(319)

Penicuik_Datao <- iNEXT(Penicuik_Nos, q=c(0), datatype= "abundance", size = o)

Penicuik_Datao
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1  76     9 0.9610  3  0  4  0  1  0  0  0  0   0
## 2  Quadrat_2 299    14 0.9867  4  0  2  2  0  0  0  0  0   1
## 3  Quadrat_3 319    13 1.0000  1  0  0  4  0  0  0  1  0   1
## 4  Quadrat_4 324     8 1.0000  0  0  0  1  1  0  0  0  0   0
## 5  Quadrat_5 110     5 1.0000  1  0  1  1  0  0  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1  75   Rarefaction       0  8.960526  6.445850 11.475203 0.9605263
## 2   Quadrat_1  76      Observed       0  9.000000  6.456820 11.543180 0.9610457
## 3   Quadrat_1  77 Extrapolation       0  9.038954  6.467244 11.610664 0.9615583
## 4   Quadrat_1 319 Extrapolation       0 11.842071  4.804394 18.879748 0.9984414
## 5   Quadrat_2 298   Rarefaction       0 13.986622 10.945007 17.028237 0.9866221
## 6   Quadrat_2 299      Observed       0 14.000000 10.951012 17.048988 0.9866519
## 7   Quadrat_2 300 Extrapolation       0 14.013348 10.956987 17.069709 0.9866817
## 8   Quadrat_2 319 Extrapolation       0 14.261375 11.064950 17.457801 0.9872354
## 9   Quadrat_3 319      Observed       0 13.000000 11.940450 14.059550 1.0000000
## 10  Quadrat_4 319   Rarefaction       0  8.000000  7.723177  8.276823 1.0000000
## 11  Quadrat_4 323   Rarefaction       0  8.000000  7.722917  8.277083 1.0000000
## 12  Quadrat_4 324      Observed       0  8.000000  7.722819  8.277181 1.0000000
## 13  Quadrat_4 325 Extrapolation       0  8.000000  7.722819  8.277181 1.0000000
## 14  Quadrat_5 109   Rarefaction       0  4.990909  3.864235  6.117583 0.9909091
## 15  Quadrat_5 110      Observed       0  5.000000  3.868876  6.131124 1.0000000
## 16  Quadrat_5 111 Extrapolation       0  5.000000  3.864396  6.135604 1.0000000
## 17  Quadrat_5 319 Extrapolation       0  5.000000  3.413684  6.586316 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9247124 0.9963403
## 2  0.9252260 0.9968654
## 3  0.9257422 0.9973743
## 4  0.9880158 1.0000000
## 5  0.9768105 0.9964337
## 6  0.9768422 0.9964617
## 7  0.9768738 0.9964896
## 8  0.9774613 0.9970094
## 9  0.9953351 1.0000000
## 10 0.9980247 1.0000000
## 11 0.9980143 1.0000000
## 12 1.0000000 1.0000000
## 13 1.0000000 1.0000000
## 14 0.9782894 1.0000000
## 15 0.9866616 1.0000000
## 16 0.9868887 1.0000000
## 17 0.9992286 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9605263  74   Rarefaction       0  8.931723  3.622058 14.241389
## 2   Quadrat_1 0.9610457  76      Observed       0  9.000000  3.650109 14.349891
## 3   Quadrat_1 0.9615583  77 Extrapolation       0  9.038954  3.648596 14.429312
## 4   Quadrat_1 0.9984414 319 Extrapolation       0 11.842071  3.251388 20.432755
## 5   Quadrat_2 0.9866221 297   Rarefaction       0 13.977493  5.312547 22.642439
## 6   Quadrat_2 0.9866519 299      Observed       0 14.000000  5.323337 22.676663
## 7   Quadrat_2 0.9866817 300 Extrapolation       0 14.013348  5.324872 22.701824
## 8   Quadrat_2 0.9872354 319 Extrapolation       0 14.261375  5.354489 23.168261
## 9   Quadrat_3 1.0000000 319      Observed       0 13.000000 10.923097 15.076903
## 10  Quadrat_4 1.0000000 319   Rarefaction       0  8.000000  7.723119  8.276881
## 11  Quadrat_4 1.0000000 324      Observed       0  8.000000  7.722819  8.277181
## 12  Quadrat_5 0.9909091 108   Rarefaction       0  4.983271  3.620957  6.345584
## 13  Quadrat_5 1.0000000 110      Observed       0  5.000000  3.374629  6.625371
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  9.000000 11.960526 3.9843015  9.000000
## 2   Quadrat_1 Shannon diversity  2.960433  3.209352 0.5320701  2.166514
## 3   Quadrat_1 Simpson diversity  1.805000  1.824584 0.2369667  1.360138
## 4   Quadrat_2  Species richness 14.000000 19.979933 7.2152028 14.000000
## 5   Quadrat_2 Shannon diversity  5.267568  5.447215 0.4039583  4.655471
## 6   Quadrat_2 Simpson diversity  3.552028  3.582710 0.2600863  3.072950
## 7   Quadrat_3  Species richness 13.000000 13.000000 0.9646878 13.000000
## 8   Quadrat_3 Shannon diversity  6.946592  7.082837 0.3766660  6.344585
## 9   Quadrat_3 Simpson diversity  5.088813  5.155097 0.3505199  4.468091
## 10  Quadrat_4  Species richness  8.000000  8.000000 0.1714466  8.000000
## 11  Quadrat_4 Shannon diversity  5.615883  5.677796 0.2355196  5.216186
## 12  Quadrat_4 Simpson diversity  4.734620  4.790004 0.2873504  4.226807
## 13  Quadrat_5  Species richness  5.000000  5.000000 0.7860973  5.000000
## 14  Quadrat_5 Shannon diversity  2.641582  2.693180 0.2036010  2.294130
## 15  Quadrat_5 Simpson diversity  2.300380  2.328155 0.1275633  2.078136
##          UCL
## 1  19.769614
## 2   4.252190
## 3   2.289030
## 4  34.121471
## 5   6.238959
## 6   4.092470
## 7  14.890753
## 8   7.821088
## 9   5.842103
## 10  8.336029
## 11  6.139406
## 12  5.353200
## 13  6.540722
## 14  3.092231
## 15  2.578175
p <- c(324)

Penicuik_Datap <- iNEXT(Penicuik_Nos, q=c(0), datatype= "abundance", size = p)

Penicuik_Datap
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1  76     9 0.9610  3  0  4  0  1  0  0  0  0   0
## 2  Quadrat_2 299    14 0.9867  4  0  2  2  0  0  0  0  0   1
## 3  Quadrat_3 319    13 1.0000  1  0  0  4  0  0  0  1  0   1
## 4  Quadrat_4 324     8 1.0000  0  0  0  1  1  0  0  0  0   0
## 5  Quadrat_5 110     5 1.0000  1  0  1  1  0  0  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1  75   Rarefaction       0  8.960526  6.439066 11.481987 0.9605263
## 2   Quadrat_1  76      Observed       0  9.000000  6.461757 11.538243 0.9610457
## 3   Quadrat_1  77 Extrapolation       0  9.038954  6.483200 11.594708 0.9615583
## 4   Quadrat_1 324 Extrapolation       0 11.849662  5.430561 18.268763 0.9985413
## 5   Quadrat_2 298   Rarefaction       0 13.986622 10.972597 17.000647 0.9866221
## 6   Quadrat_2 299      Observed       0 14.000000 10.978130 17.021870 0.9866519
## 7   Quadrat_2 300 Extrapolation       0 14.013348 10.983633 17.043063 0.9866817
## 8   Quadrat_2 324 Extrapolation       0 14.324914 11.106635 17.543193 0.9873772
## 9   Quadrat_3 318   Rarefaction       0 12.996865 11.617701 14.376030 0.9968652
## 10  Quadrat_3 319      Observed       0 13.000000 11.619197 14.380803 1.0000000
## 11  Quadrat_3 320 Extrapolation       0 13.000000 11.617640 14.382360 1.0000000
## 12  Quadrat_3 324 Extrapolation       0 13.000000 11.611380 14.388620 1.0000000
## 13  Quadrat_4 324      Observed       0  8.000000  8.000000  8.000000 1.0000000
## 14  Quadrat_5 109   Rarefaction       0  4.990909  4.008756  5.973062 0.9909091
## 15  Quadrat_5 110      Observed       0  5.000000  4.010861  5.989139 1.0000000
## 16  Quadrat_5 111 Extrapolation       0  5.000000  4.006094  5.993906 1.0000000
## 17  Quadrat_5 324 Extrapolation       0  5.000000  3.549093  6.450907 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9270634 0.9939892
## 2  0.9267229 0.9953685
## 3  0.9272551 0.9958615
## 4  0.9881088 1.0000000
## 5  0.9766905 0.9965536
## 6  0.9767239 0.9965800
## 7  0.9767571 0.9966064
## 8  0.9775258 0.9972285
## 9  0.9925491 1.0000000
## 10 0.9957080 1.0000000
## 11 0.9957320 1.0000000
## 12 0.9958260 1.0000000
## 13 0.9982995 1.0000000
## 14 0.9790736 1.0000000
## 15 0.9878624 1.0000000
## 16 0.9880657 1.0000000
## 17 0.9992710 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9605263  74   Rarefaction       0  8.931723  3.964515 13.898932
## 2   Quadrat_1 0.9610457  76      Observed       0  9.000000  3.996176 14.003824
## 3   Quadrat_1 0.9615583  77 Extrapolation       0  9.038954  4.000210 14.077699
## 4   Quadrat_1 0.9985413 324 Extrapolation       0 11.849662  3.791508 19.907817
## 5   Quadrat_2 0.9866221 297   Rarefaction       0 13.977493  8.211383 19.743603
## 6   Quadrat_2 0.9866519 299      Observed       0 14.000000  8.222467 19.777533
## 7   Quadrat_2 0.9866817 300 Extrapolation       0 14.013348  8.225739 19.800957
## 8   Quadrat_2 0.9873772 324 Extrapolation       0 14.324914  8.281019 20.368810
## 9   Quadrat_3 0.9968652 316   Rarefaction       0 12.991179 11.363496 14.618861
## 10  Quadrat_3 1.0000000 319      Observed       0 13.000000 11.090755 14.909245
## 11  Quadrat_4 1.0000000 324      Observed       0  8.000000  7.723675  8.276325
## 12  Quadrat_5 0.9909091 108   Rarefaction       0  4.983271  3.720725  6.245816
## 13  Quadrat_5 1.0000000 110      Observed       0  5.000000  3.508990  6.491010
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  9.000000 11.960526 3.2693929  9.000000
## 2   Quadrat_1 Shannon diversity  2.960433  3.209352 0.5062872  2.217047
## 3   Quadrat_1 Simpson diversity  1.805000  1.824584 0.2607795  1.313466
## 4   Quadrat_2  Species richness 14.000000 19.979933 6.4501915 14.000000
## 5   Quadrat_2 Shannon diversity  5.267568  5.447215 0.3633918  4.734980
## 6   Quadrat_2 Simpson diversity  3.552028  3.582710 0.2715495  3.050483
## 7   Quadrat_3  Species richness 13.000000 13.000000 1.0538896 13.000000
## 8   Quadrat_3 Shannon diversity  6.946592  7.082837 0.3848126  6.328618
## 9   Quadrat_3 Simpson diversity  5.088813  5.155097 0.3593567  4.450771
## 10  Quadrat_4  Species richness  8.000000  8.000000 0.1121842  8.000000
## 11  Quadrat_4 Shannon diversity  5.615883  5.677796 0.2410314  5.205383
## 12  Quadrat_4 Simpson diversity  4.734620  4.790004 0.3260058  4.151044
## 13  Quadrat_5  Species richness  5.000000  5.000000 0.6614070  5.000000
## 14  Quadrat_5 Shannon diversity  2.641582  2.693180 0.1810478  2.338333
## 15  Quadrat_5 Simpson diversity  2.300380  2.328155 0.1189751  2.094968
##          UCL
## 1  18.368419
## 2   4.201657
## 3   2.335702
## 4  32.622076
## 5   6.159450
## 6   4.114937
## 7  15.065586
## 8   7.837055
## 9   5.859423
## 10  8.219877
## 11  6.150209
## 12  5.428963
## 13  6.296334
## 14  3.048027
## 15  2.561342
q <- c(110)

Penicuik_Dataq <- iNEXT(Penicuik_Nos, q=c(0), datatype= "abundance", size = q)

Penicuik_Dataq
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1  76     9 0.9610  3  0  4  0  1  0  0  0  0   0
## 2  Quadrat_2 299    14 0.9867  4  0  2  2  0  0  0  0  0   1
## 3  Quadrat_3 319    13 1.0000  1  0  0  4  0  0  0  1  0   1
## 4  Quadrat_4 324     8 1.0000  0  0  0  1  1  0  0  0  0   0
## 5  Quadrat_5 110     5 1.0000  1  0  1  1  0  0  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##    Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL        SC
## 1   Quadrat_1  75   Rarefaction       0  8.960526  6.630605 11.290447 0.9605263
## 2   Quadrat_1  76      Observed       0  9.000000  6.650378 11.349622 0.9610457
## 3   Quadrat_1  77 Extrapolation       0  9.038954  6.669579 11.408329 0.9615583
## 4   Quadrat_1 110 Extrapolation       0 10.073449  7.048980 13.097918 0.9751700
## 5   Quadrat_2 110   Rarefaction       0 10.643408  9.072026 12.214790 0.9713866
## 6   Quadrat_2 298   Rarefaction       0 13.986622 10.928107 17.045137 0.9866221
## 7   Quadrat_2 299      Observed       0 14.000000 10.932810 17.067190 0.9866519
## 8   Quadrat_2 300 Extrapolation       0 14.013348 10.937476 17.089220 0.9866817
## 9   Quadrat_3 110   Rarefaction       0 11.563494 10.622581 12.504407 0.9806781
## 10  Quadrat_3 318   Rarefaction       0 12.996865 11.863613 14.130118 0.9968652
## 11  Quadrat_3 319      Observed       0 13.000000 11.865416 14.134584 1.0000000
## 12  Quadrat_3 320 Extrapolation       0 13.000000 11.863896 14.136104 1.0000000
## 13  Quadrat_4 110   Rarefaction       0  7.678262  7.060651  8.295872 0.9930961
## 14  Quadrat_4 323   Rarefaction       0  8.000000  7.722964  8.277036 1.0000000
## 15  Quadrat_4 324      Observed       0  8.000000  7.722819  8.277181 1.0000000
## 16  Quadrat_4 325 Extrapolation       0  8.000000  7.722761  8.277239 1.0000000
## 17  Quadrat_5 110      Observed       0  5.000000  3.936757  6.063243 1.0000000
##       SC.LCL    SC.UCL
## 1  0.9279888 0.9930638
## 2  0.9285695 0.9935219
## 3  0.9291491 0.9939674
## 4  0.9477908 1.0000000
## 5  0.9600966 0.9826766
## 6  0.9747592 0.9984849
## 7  0.9747889 0.9985150
## 8  0.9748185 0.9985449
## 9  0.9750131 0.9863432
## 10 0.9926357 1.0000000
## 11 0.9956833 1.0000000
## 12 0.9957091 1.0000000
## 13 0.9898275 0.9963646
## 14 0.9973533 1.0000000
## 15 0.9981144 1.0000000
## 16 0.9981260 1.0000000
## 17 0.9871600 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##    Assemblage        SC   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1   Quadrat_1 0.9605263  74   Rarefaction       0  8.931723  5.101546 12.761901
## 2   Quadrat_1 0.9610457  76      Observed       0  9.000000  5.148930 12.851070
## 3   Quadrat_1 0.9615583  77 Extrapolation       0  9.038954  5.157336 12.920573
## 4   Quadrat_1 0.9751700 110 Extrapolation       0 10.073449  5.484528 14.662370
## 5   Quadrat_2 0.9713866 110   Rarefaction       0 10.643407  6.984624 14.302191
## 6   Quadrat_2 0.9866221 297   Rarefaction       0 13.977493  4.917018 23.037968
## 7   Quadrat_2 0.9866519 299      Observed       0 14.000000  4.927335 23.072665
## 8   Quadrat_2 0.9866817 300 Extrapolation       0 14.013348  4.927724 23.098972
## 9   Quadrat_3 0.9806781 110   Rarefaction       0 11.563494 10.457333 12.669655
## 10  Quadrat_3 0.9968652 316   Rarefaction       0 12.991179 11.665104 14.317253
## 11  Quadrat_3 1.0000000 319      Observed       0 13.000000 11.382287 14.617713
## 12  Quadrat_4 0.9930961 110   Rarefaction       0  7.678262  7.081834  8.274690
## 13  Quadrat_4 1.0000000 324      Observed       0  8.000000  7.581186  8.418814
## 14  Quadrat_5 1.0000000 110      Observed       0  5.000000  3.449453  6.550547
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  9.000000 11.960526 4.2333416  9.000000
## 2   Quadrat_1 Shannon diversity  2.960433  3.209352 0.5507038  2.129992
## 3   Quadrat_1 Simpson diversity  1.805000  1.824584 0.2481527  1.338214
## 4   Quadrat_2  Species richness 14.000000 19.979933 6.0324017 14.000000
## 5   Quadrat_2 Shannon diversity  5.267568  5.447215 0.4234405  4.617287
## 6   Quadrat_2 Simpson diversity  3.552028  3.582710 0.2836481  3.026770
## 7   Quadrat_3  Species richness 13.000000 13.000000 0.8641431 13.000000
## 8   Quadrat_3 Shannon diversity  6.946592  7.082837 0.3729614  6.351846
## 9   Quadrat_3 Simpson diversity  5.088813  5.155097 0.3362419  4.496075
## 10  Quadrat_4  Species richness  8.000000  8.000000 0.1000000  8.000000
## 11  Quadrat_4 Shannon diversity  5.615883  5.677796 0.2113324  5.263592
## 12  Quadrat_4 Simpson diversity  4.734620  4.790004 0.2800563  4.241103
## 13  Quadrat_5  Species richness  5.000000  5.000000 0.7321027  5.000000
## 14  Quadrat_5 Shannon diversity  2.641582  2.693180 0.1858170  2.328986
## 15  Quadrat_5 Simpson diversity  2.300380  2.328155 0.1241125  2.084899
##          UCL
## 1  20.257723
## 2   4.288712
## 3   2.310954
## 4  31.803223
## 5   6.277143
## 6   4.138650
## 7  14.693689
## 8   7.813828
## 9   5.814119
## 10  8.195996
## 11  6.092000
## 12  5.338904
## 13  6.434895
## 14  3.057375
## 15  2.571411

#Now to run the analysis again without specificying the size, can do this for #looking at the other diversity indices

Penicuik_Data <- iNEXT(Penicuik_Nos, q=c(0), datatype= "abundance")

print(Penicuik_Data)
## Compare 5 assemblages with Hill number order q = 0.
## $class: iNEXT
## 
## $DataInfo: basic data information
##   Assemblage   n S.obs     SC f1 f2 f3 f4 f5 f6 f7 f8 f9 f10
## 1  Quadrat_1  76     9 0.9610  3  0  4  0  1  0  0  0  0   0
## 2  Quadrat_2 299    14 0.9867  4  0  2  2  0  0  0  0  0   1
## 3  Quadrat_3 319    13 1.0000  1  0  0  4  0  0  0  1  0   1
## 4  Quadrat_4 324     8 1.0000  0  0  0  1  1  0  0  0  0   0
## 5  Quadrat_5 110     5 1.0000  1  0  1  1  0  0  0  0  0   0
## 
## $iNextEst: diversity estimates with rarefied and extrapolated samples.
## $size_based (LCL and UCL are obtained for fixed size.)
## 
##     Assemblage   m        Method Order.q        qD    qD.LCL    qD.UCL
## 1    Quadrat_1   1   Rarefaction       0  1.000000  1.000000  1.000000
## 10   Quadrat_1  38   Rarefaction       0  6.992831  5.320762  8.664900
## 20   Quadrat_1  76      Observed       0  9.000000  6.642716 11.357284
## 30   Quadrat_1 112 Extrapolation       0 10.122782  6.860988 13.384576
## 40   Quadrat_1 152 Extrapolation       0 10.878614  6.500425 15.256803
## 41   Quadrat_2   1   Rarefaction       0  1.000000  1.000000  1.000000
## 50   Quadrat_2 149   Rarefaction       0 11.618276  9.666120 13.570432
## 60   Quadrat_2 299      Observed       0 14.000000 11.031262 16.968738
## 70   Quadrat_2 441 Extrapolation       0 15.625951 11.748966 19.502936
## 80   Quadrat_2 598 Extrapolation       0 16.914304 12.029545 21.799064
## 81   Quadrat_3   1   Rarefaction       0  1.000000  1.000000  1.000000
## 90   Quadrat_3 159   Rarefaction       0 12.245282 11.391553 13.099010
## 100  Quadrat_3 319      Observed       0 13.000000 11.862656 14.137344
## 110  Quadrat_3 470 Extrapolation       0 13.000000 11.654982 14.345018
## 120  Quadrat_3 638 Extrapolation       0 13.000000 11.541963 14.458037
## 121  Quadrat_4   1   Rarefaction       0  1.000000  1.000000  1.000000
## 130  Quadrat_4 162   Rarefaction       0  7.907962  7.486002  8.329923
## 140  Quadrat_4 324      Observed       0  8.000000  7.722819  8.277181
## 150  Quadrat_4 478 Extrapolation       0  8.000000  7.695331  8.304669
## 160  Quadrat_4 648 Extrapolation       0  8.000000  7.672138  8.327862
## 161  Quadrat_5   1   Rarefaction       0  1.000000  1.000000  1.000000
## 170  Quadrat_5  55   Rarefaction       0  4.319365  3.603163  5.035567
## 180  Quadrat_5 110      Observed       0  5.000000  3.933811  6.066189
## 190  Quadrat_5 162 Extrapolation       0  5.000000  3.643693  6.356307
## 200  Quadrat_5 220 Extrapolation       0  5.000000  3.458348  6.541652
##            SC    SC.LCL    SC.UCL
## 1   0.5480702 0.4135846 0.6825557
## 10  0.9190567 0.8831778 0.9549356
## 20  0.9610457 0.9195601 1.0000000
## 30  0.9758192 0.9374980 1.0000000
## 40  0.9857643 0.9538953 1.0000000
## 41  0.2791183 0.2377877 0.3204489
## 50  0.9782511 0.9682365 0.9882656
## 60  0.9866519 0.9776629 0.9956409
## 70  0.9902813 0.9813572 0.9992054
## 80  0.9931571 0.9852499 1.0000000
## 81  0.1939828 0.1696749 0.2182906
## 90  0.9904019 0.9854764 0.9953273
## 100 1.0000000 0.9964924 1.0000000
## 110 1.0000000 0.9984652 1.0000000
## 120 1.0000000 0.9992701 1.0000000
## 121 0.2087681 0.1863941 0.2311421
## 130 0.9975228 0.9945335 1.0000000
## 140 1.0000000 0.9988099 1.0000000
## 150 1.0000000 0.9995400 1.0000000
## 160 1.0000000 0.9998389 1.0000000
## 161 0.4295246 0.3891947 0.4698545
## 170 0.9799822 0.9669134 0.9930509
## 180 1.0000000 0.9876000 1.0000000
## 190 1.0000000 0.9938888 1.0000000
## 200 1.0000000 0.9967878 1.0000000
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$size_based to view complete output.
## 
## $coverage_based (LCL and UCL are obtained for fixed coverage; interval length is wider due to varying size in bootstraps.)
## 
##     Assemblage        SC   m        Method Order.q        qD     qD.LCL
## 1    Quadrat_1 0.5480721   1   Rarefaction       0  1.000003  0.6793304
## 10   Quadrat_1 0.9190567  38   Rarefaction       0  6.992831  3.4965104
## 20   Quadrat_1 0.9610457  76      Observed       0  9.000000  2.1815387
## 30   Quadrat_1 0.9758192 112 Extrapolation       0 10.122782  1.9617205
## 40   Quadrat_1 0.9857643 152 Extrapolation       0 10.878614  1.7330241
## 41   Quadrat_2 0.2791183   1   Rarefaction       0  1.000000  0.9138201
## 50   Quadrat_2 0.9782511 149   Rarefaction       0 11.618276  7.9591070
## 60   Quadrat_2 0.9866519 299      Observed       0 14.000000  8.0890121
## 70   Quadrat_2 0.9902813 441 Extrapolation       0 15.625951  8.4941955
## 80   Quadrat_2 0.9931571 598 Extrapolation       0 16.914304  8.7252161
## 81   Quadrat_3 0.1939836   1   Rarefaction       0  1.000004  0.9418689
## 85   Quadrat_3 0.9634258  71   Rarefaction       0 10.510346  9.5701506
## 90   Quadrat_3 0.9904019 159   Rarefaction       0 12.245282 11.2486097
## 95   Quadrat_3 0.9963247 247   Rarefaction       0 12.764570 11.5365567
## 100  Quadrat_3 1.0000000 319      Observed       0 13.000000 11.4291116
## 101  Quadrat_4 0.2087689   1   Rarefaction       0  1.000004  0.9537393
## 105  Quadrat_4 0.9860031  72   Rarefaction       0  7.293911  6.6776295
## 110  Quadrat_4 0.9975228 162   Rarefaction       0  7.907962  7.6080027
## 115  Quadrat_4 0.9998320 251   Rarefaction       0  7.997064  7.6598559
## 119  Quadrat_4 1.0000000 324      Observed       0  8.000000  7.6574302
## 120  Quadrat_5 0.4295246   1   Rarefaction       0  1.000000  0.9657141
## 124  Quadrat_5 0.9582521  25   Rarefaction       0  3.418900  2.4959522
## 129  Quadrat_5 0.9799821  55   Rarefaction       0  4.319364  3.2354612
## 134  Quadrat_5 0.9892797  85   Rarefaction       0  4.759879  3.3645293
## 139  Quadrat_5 1.0000000 110      Observed       0  5.000000  3.2277526
##        qD.UCL
## 1    1.320676
## 10  10.489152
## 20  15.818461
## 30  18.283844
## 40  20.024205
## 41   1.086180
## 50  15.277444
## 60  19.910988
## 70  22.757707
## 80  25.103393
## 81   1.058139
## 85  11.450542
## 90  13.241954
## 95  13.992584
## 100 14.570888
## 101  1.046268
## 105  7.910192
## 110  8.207922
## 115  8.334273
## 119  8.342570
## 120  1.034286
## 124  4.341848
## 129  5.403267
## 134  6.155229
## 139  6.772247
## 
## NOTE: The above output only shows five estimates for each assemblage; call iNEXT.object$iNextEst$coverage_based to view complete output.
## 
## $AsyEst: asymptotic diversity estimates along with related statistics.
##    Assemblage         Diversity  Observed Estimator      s.e.       LCL
## 1   Quadrat_1  Species richness  9.000000 11.960526 5.1668344  9.000000
## 2   Quadrat_1 Shannon diversity  2.960433  3.209352 0.5252254  2.179929
## 3   Quadrat_1 Simpson diversity  1.805000  1.824584 0.2425628  1.349170
## 4   Quadrat_2  Species richness 14.000000 19.979933 5.6069471 14.000000
## 5   Quadrat_2 Shannon diversity  5.267568  5.447215 0.3823115  4.697898
## 6   Quadrat_2 Simpson diversity  3.552028  3.582710 0.2519629  3.088872
## 7   Quadrat_3  Species richness 13.000000 13.000000 0.9246068 13.000000
## 8   Quadrat_3 Shannon diversity  6.946592  7.082837 0.3228147  6.450131
## 9   Quadrat_3 Simpson diversity  5.088813  5.155097 0.3018412  4.563499
## 10  Quadrat_4  Species richness  8.000000  8.000000 0.2257607  8.000000
## 11  Quadrat_4 Shannon diversity  5.615883  5.677796 0.2162180  5.254017
## 12  Quadrat_4 Simpson diversity  4.734620  4.790004 0.2700599  4.260696
## 13  Quadrat_5  Species richness  5.000000  5.000000 0.7312600  5.000000
## 14  Quadrat_5 Shannon diversity  2.641582  2.693180 0.1892945  2.322170
## 15  Quadrat_5 Simpson diversity  2.300380  2.328155 0.1275328  2.078196
##          UCL
## 1  22.087336
## 2   4.238775
## 3   2.299998
## 4  30.969347
## 5   6.196532
## 6   4.076548
## 7  14.812196
## 8   7.715542
## 9   5.746695
## 10  8.442483
## 11  6.101576
## 12  5.319311
## 13  6.433243
## 14  3.064191
## 15  2.578115
summary(Penicuik_Data)
##          Length Class      Mode
## DataInfo 14     data.frame list
## iNextEst  2     -none-     list
## AsyEst    7     data.frame list

#Now to do obtain additional biodiversity indices, including sample coverage, for Penicuik#

P1 <- diversity(Penicuik_Nos$Quadrat_1)

Penicuik2 <- estimateD(Penicuik_Nos, q = c(0,1,2), datatype = "abundance", base="coverage")
Penicuik2
##    Assemblage         m        Method Order.q        SC        qD    qD.LCL
## 1   Quadrat_1 152.00000 Extrapolation       0 0.9857643 10.878614  2.098538
## 2   Quadrat_1 152.00000 Extrapolation       1 0.9857643  3.109637  2.291375
## 3   Quadrat_1 152.00000 Extrapolation       2 0.9857643  1.814739  1.467261
## 4   Quadrat_2 242.30416   Rarefaction       0 0.9857643 13.226103  6.976844
## 5   Quadrat_2 242.30416   Rarefaction       1 0.9857643  5.232833  4.433015
## 6   Quadrat_2 242.30416   Rarefaction       2 0.9857643  3.544925  2.975373
## 7   Quadrat_3 130.77377   Rarefaction       0 0.9857643 11.911443 10.727849
## 8   Quadrat_3 130.77377   Rarefaction       1 0.9857643  6.737450  6.100970
## 9   Quadrat_3 130.77377   Rarefaction       2 0.9857643  4.996346  4.344544
## 10  Quadrat_4  71.11103   Rarefaction       0 0.9857643  7.281229  6.722664
## 11  Quadrat_4  71.11103   Rarefaction       1 0.9857643  5.383352  4.975928
## 12  Quadrat_4  71.11103   Rarefaction       2 0.9857643  4.547625  4.107702
## 13  Quadrat_5  69.58026   Rarefaction       0 0.9857643  4.568704  3.312696
## 14  Quadrat_5  69.58026   Rarefaction       1 0.9857643  2.606841  2.226482
## 15  Quadrat_5  69.58026   Rarefaction       2 0.9857643  2.284546  2.035960
##       qD.UCL
## 1  19.658691
## 2   3.927899
## 3   2.162217
## 4  19.475361
## 5   6.032651
## 6   4.114476
## 7  13.095038
## 8   7.373929
## 9   5.648148
## 10  7.839794
## 11  5.790777
## 12  4.987547
## 13  5.824711
## 14  2.987200
## 15  2.533131

#Now for vegan analyses to determine species eveness for Penicuik data

Pevenness1 <- P1/log(specnumber(Penicuik_Nos$Quadrat_1))

summary(Pevenness1)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.494   0.494   0.494   0.494   0.494   0.494
P2 <- diversity(Penicuik_Nos$Quadrat_2)

Pevenness2 <- P2/log(specnumber(Penicuik_Nos$Quadrat_2))

summary(Pevenness2)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6296  0.6296  0.6296  0.6296  0.6296  0.6296
P3 <- diversity(Penicuik_Nos$Quadrat_3)

Pevenness3 <- P3/log(specnumber(Penicuik_Nos$Quadrat_3))

summary(Pevenness3)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7557  0.7557  0.7557  0.7557  0.7557  0.7557
P4 <- diversity(Penicuik_Nos$Quadrat_4)

Pevenness4 <- P4/log(specnumber(Penicuik_Nos$Quadrat_4))

summary(Pevenness4)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.8298  0.8298  0.8298  0.8298  0.8298  0.8298
P5 <- diversity(Penicuik_Nos$Quadrat_5)

Pevenness5 <- P5/log(specnumber(Penicuik_Nos$Quadrat_5))

summary(Pevenness5)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6036  0.6036  0.6036  0.6036  0.6036  0.6036

#Now for data visualisation for Penicuik data, including the generation of species curve graphs#

Penicuik_Data_Graph1 <- ggiNEXT(x = Penicuik_Data, se=TRUE, color.var="Order.q")

Penicuik_Data_Graph1

Penicuik_Data_Graph2 <- ggiNEXT(x = Penicuik_Data, se=TRUE, type = 1,
                                facet.var="None", color.var="Order.q") 

Penicuik_Data_Graph2

Penicuik_Data_Graph3 <- ggiNEXT(x = Penicuik_Data, se=TRUE, type = 2,
                                facet.var="None", color.var="Order.q") 

Penicuik_Data_Graph3

Penicuik_Data_Graph4 <- ggiNEXT(x = Penicuik_Data, se=TRUE, type = 3,
                                facet.var="None", color.var="Order.q") 

Penicuik_Data_Graph4