##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