R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

##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("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'
install.packages("labdsv", repos = "https://CRAN.R-project.org/package=labdsv")
## 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://CRAN.R-project.org/package=labdsv/src/contrib:
##   cannot open URL 'https://CRAN.R-project.org/package=labdsv/src/contrib/PACKAGES'
## Warning: package 'labdsv' 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://CRAN.R-project.org/package=labdsv/bin/windows/contrib/4.3:
##   cannot open URL 'https://CRAN.R-project.org/package=labdsv/bin/windows/contrib/4.3/PACKAGES'

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

library(vegan)
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.6-4
library(labdsv)
## Warning: package 'labdsv' was built under R version 4.3.1
## Loading required package: mgcv
## Loading required package: nlme
## This is mgcv 1.8-42. For overview type 'help("mgcv-package")'.
## This is labdsv 2.1-0
## convert existing ordinations with as.dsvord()
## 
## Attaching package: 'labdsv'
## The following objects are masked from 'package:vegan':
## 
##     calibrate, scores
## The following objects are masked from 'package:stats':
## 
##     density, loadings

#Loading the datasets for the Barrow plant communities and substrate data…

urlfile1 <- 'https://raw.githubusercontent.com/Savannankvm/Indval-Analyses-for-Barrow-Plant-and-Substrate-Data/PhD-files/BarrowPlantSpecies_with_site_names.csv'

BarrowSpecies <-read.csv(urlfile1 , row.names = 1)

urlfile2 <- 'https://raw.githubusercontent.com/Savannankvm/Indval-Analyses-for-Barrow-Plant-and-Substrate-Data/PhD-files/BarrowPlantChemistry_with_site_names.csv'

BarrowChemistry <-read.csv(urlfile2 , row.names = 1)

#Now to convert the files to dataframes for analyses

BarrowSpecies1 <- data.frame(BarrowSpecies)

BarrowChemistry1 <- data.frame(BarrowChemistry)

##Running an Indval analysis with Quartz as the substrate#

clustQuartz <- cut(BarrowChemistry1$Quartz, 5, labels=FALSE)
BQIndval <- indval(as.matrix(BarrowSpecies1), clustQuartz, type= "long")
gr <- BQIndval$maxcls[BQIndval$pval<=0.05]
iv <- BQIndval$indcls[BQIndval$pval<=0.05]
pv <- BQIndval$pval[BQIndval$pval<=0.05]
fr <- apply(BarrowSpecies1[,-1]>0, 2, sum)[BQIndval$pval<=0.05]
BQIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
BQIndvalsummary <- BQIndvalsummary[order(BQIndvalsummary$group, 
                                         -BQIndvalsummary$indval),]
print(BQIndvalsummary)
##                        group    indval pvalue freq
## Pillosella.officinarum     1 0.9585799  0.024    4
## Taraxacum.agg.             1 0.8780488  0.036    6
summary(indval(as.matrix(BarrowSpecies1), clustQuartz, type= "long"))
##                        cluster indicator_value probability
## Pillosella.officinarum       1          0.9586       0.024
## Taraxacum.agg.               1          0.8780       0.029
## 
## Sum of probabilities                 =  39.41 
## 
## Sum of Indicator Values              =  16.79 
## 
## Sum of Significant Indicator Values  =  1.84 
## 
## Number of Significant Indicators     =  2 
## 
## Significant Indicator Distribution
## 
## 1 
## 2
print(indval(as.matrix(BarrowSpecies1), clustQuartz, type= "long"))
## $relfrq
##                            1         5
## Anthyllis.vulneraria     0.5 0.2222222
## Aphanes.arvensis         0.0 0.2222222
## Arrhenatherum.elatius    0.0 0.2222222
## Bellis.perennis          1.0 0.4444444
## Blackstonia.perfoliata   0.0 0.1111111
## Brachythecium.albicans   0.0 0.1111111
## Brachythecium.rutabulum  0.0 0.1111111
## Briza.media              0.0 0.3333333
## Bromus.hordeaceus        0.0 0.1111111
## Calliergonella.cupsidata 0.0 0.4444444
## Carex.flacca             0.0 0.2222222
## Carlina.vulgaris         0.5 0.1111111
## Centaurium.erythraea     0.0 0.2222222
## Cerastium.fontanum       0.0 0.4444444
## Cynosurus.cristatus      0.0 0.2222222
## Daucus.carrota           0.0 0.2222222
## Erigeron.acer            0.5 0.1111111
## Euphrasia.agg            0.5 0.4444444
## Festuca.ovina            0.5 0.1111111
## Festuca.rubra            0.5 1.0000000
## Galium.verum             0.0 0.4444444
## Helicotrichon.spp.       0.0 0.1111111
## Hieracium.spp.           0.0 0.1111111
## Holcus.spp.              0.5 0.7777778
## Holcus.lanatus           0.0 0.5555556
## Holcus.mollis            0.0 0.1111111
## Hypericum.perforatum     0.5 0.0000000
## Hypochaeris.radicata     0.0 0.1111111
## Lathyrus.pratensis       0.0 0.1111111
## Leontodon.hispidus       0.5 0.1111111
## Leontodon.saxatilis      0.5 0.0000000
## Leucanthemum.vulgare     0.5 0.5555556
## Lolium.perenne           0.0 0.4444444
## Lotus.corniculatus       0.5 0.8888889
## Medicago.lupulina        0.5 0.2222222
## Ononis.repens            0.0 0.1111111
## Pastinaca.sativa         0.0 0.1111111
## Pillosella.officinarum   1.0 0.2222222
## Plantago.lanceolata      0.5 0.3333333
## Poa.spp.                 0.0 0.1111111
## Potentilla.reptans       0.5 0.2222222
## Prunella.vulgaris        0.0 0.2222222
## Pseudoscleropidum.purum  0.0 0.1111111
## Ranunculus.repens        0.0 0.1111111
## Reseda.lutea             0.0 0.1111111
## Sedum.anglicum           0.0 0.1111111
## Senecio.jacobaea         0.0 0.1111111
## Senecio.vulgaris         0.5 0.0000000
## Stellaria.apetala        0.0 0.1111111
## Taraxacum.agg.           1.0 0.2222222
## Trifolium.campestre      0.5 0.5555556
## Trifolium.pratense       0.0 0.1111111
## Trifolium.repens         0.0 0.3333333
## Trisetum.flavescens      0.0 0.3333333
## 
## $relabu
##                                   1           5
## Anthyllis.vulneraria     0.10169492 0.898305085
## Aphanes.arvensis         0.00000000 1.000000000
## Arrhenatherum.elatius    0.00000000 1.000000000
## Bellis.perennis          0.70588235 0.294117647
## Blackstonia.perfoliata   0.00000000 1.000000000
## Brachythecium.albicans   0.00000000 1.000000000
## Brachythecium.rutabulum  0.00000000 1.000000000
## Briza.media              0.00000000 1.000000000
## Bromus.hordeaceus        0.00000000 1.000000000
## Calliergonella.cupsidata 0.00000000 1.000000000
## Carex.flacca             0.00000000 1.000000000
## Carlina.vulgaris         0.91836735 0.081632653
## Centaurium.erythraea     0.00000000 1.000000000
## Cerastium.fontanum       0.00000000 1.000000000
## Cynosurus.cristatus      0.00000000 1.000000000
## Daucus.carrota           0.00000000 1.000000000
## Erigeron.acer            0.51923077 0.480769231
## Euphrasia.agg            0.42857143 0.571428571
## Festuca.ovina            0.99331104 0.006688963
## Festuca.rubra            0.45308924 0.546910755
## Galium.verum             0.00000000 1.000000000
## Helicotrichon.spp.       0.00000000 1.000000000
## Hieracium.spp.           0.00000000 1.000000000
## Holcus.spp.              0.04316547 0.956834532
## Holcus.lanatus           0.00000000 1.000000000
## Holcus.mollis            0.00000000 1.000000000
## Hypericum.perforatum     1.00000000 0.000000000
## Hypochaeris.radicata     0.00000000 1.000000000
## Lathyrus.pratensis       0.00000000 1.000000000
## Leontodon.hispidus       0.72972973 0.270270270
## Leontodon.saxatilis      1.00000000 0.000000000
## Leucanthemum.vulgare     0.84375000 0.156250000
## Lolium.perenne           0.00000000 1.000000000
## Lotus.corniculatus       0.16684842 0.833151581
## Medicago.lupulina        0.69230769 0.307692308
## Ononis.repens            0.00000000 1.000000000
## Pastinaca.sativa         0.00000000 1.000000000
## Pillosella.officinarum   0.95857988 0.041420118
## Plantago.lanceolata      0.65853659 0.341463415
## Poa.spp.                 0.00000000 1.000000000
## Potentilla.reptans       0.19148936 0.808510638
## Prunella.vulgaris        0.00000000 1.000000000
## Pseudoscleropidum.purum  0.00000000 1.000000000
## Ranunculus.repens        0.00000000 1.000000000
## Reseda.lutea             0.00000000 1.000000000
## Sedum.anglicum           0.00000000 1.000000000
## Senecio.jacobaea         0.00000000 1.000000000
## Senecio.vulgaris         1.00000000 0.000000000
## Stellaria.apetala        0.00000000 1.000000000
## Taraxacum.agg.           0.87804878 0.121951220
## Trifolium.campestre      0.26865672 0.731343284
## Trifolium.pratense       0.00000000 1.000000000
## Trifolium.repens         0.00000000 1.000000000
## Trisetum.flavescens      0.00000000 1.000000000
## 
## $indval
##                                   1            5
## Anthyllis.vulneraria     0.05084746 0.1996233522
## Aphanes.arvensis         0.00000000 0.2222222222
## Arrhenatherum.elatius    0.00000000 0.2222222222
## Bellis.perennis          0.70588235 0.1307189542
## Blackstonia.perfoliata   0.00000000 0.1111111111
## Brachythecium.albicans   0.00000000 0.1111111111
## Brachythecium.rutabulum  0.00000000 0.1111111111
## Briza.media              0.00000000 0.3333333333
## Bromus.hordeaceus        0.00000000 0.1111111111
## Calliergonella.cupsidata 0.00000000 0.4444444444
## Carex.flacca             0.00000000 0.2222222222
## Carlina.vulgaris         0.45918367 0.0090702948
## Centaurium.erythraea     0.00000000 0.2222222222
## Cerastium.fontanum       0.00000000 0.4444444444
## Cynosurus.cristatus      0.00000000 0.2222222222
## Daucus.carrota           0.00000000 0.2222222222
## Erigeron.acer            0.25961538 0.0534188034
## Euphrasia.agg            0.21428571 0.2539682540
## Festuca.ovina            0.49665552 0.0007432181
## Festuca.rubra            0.22654462 0.5469107551
## Galium.verum             0.00000000 0.4444444444
## Helicotrichon.spp.       0.00000000 0.1111111111
## Hieracium.spp.           0.00000000 0.1111111111
## Holcus.spp.              0.02158273 0.7442046363
## Holcus.lanatus           0.00000000 0.5555555556
## Holcus.mollis            0.00000000 0.1111111111
## Hypericum.perforatum     0.50000000 0.0000000000
## Hypochaeris.radicata     0.00000000 0.1111111111
## Lathyrus.pratensis       0.00000000 0.1111111111
## Leontodon.hispidus       0.36486486 0.0300300300
## Leontodon.saxatilis      0.50000000 0.0000000000
## Leucanthemum.vulgare     0.42187500 0.0868055556
## Lolium.perenne           0.00000000 0.4444444444
## Lotus.corniculatus       0.08342421 0.7405791833
## Medicago.lupulina        0.34615385 0.0683760684
## Ononis.repens            0.00000000 0.1111111111
## Pastinaca.sativa         0.00000000 0.1111111111
## Pillosella.officinarum   0.95857988 0.0092044707
## Plantago.lanceolata      0.32926829 0.1138211382
## Poa.spp.                 0.00000000 0.1111111111
## Potentilla.reptans       0.09574468 0.1796690307
## Prunella.vulgaris        0.00000000 0.2222222222
## Pseudoscleropidum.purum  0.00000000 0.1111111111
## Ranunculus.repens        0.00000000 0.1111111111
## Reseda.lutea             0.00000000 0.1111111111
## Sedum.anglicum           0.00000000 0.1111111111
## Senecio.jacobaea         0.00000000 0.1111111111
## Senecio.vulgaris         0.50000000 0.0000000000
## Stellaria.apetala        0.00000000 0.1111111111
## Taraxacum.agg.           0.87804878 0.0271002710
## Trifolium.campestre      0.13432836 0.4063018242
## Trifolium.pratense       0.00000000 0.1111111111
## Trifolium.repens         0.00000000 0.3333333333
## Trisetum.flavescens      0.00000000 0.3333333333
## 
## $maxcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                        2                        2                        2 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                        1                        2                        2 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                        2                        2                        2 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                        2                        2                        1 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                        2                        2                        2 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                        2                        1                        2 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                        1                        2                        2 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                        2                        2                        2 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                        2                        2                        1 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                        2                        2                        1 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                        1                        1                        2 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                        2                        1                        2 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                        2                        1                        1 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                        2                        2                        2 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                        2                        2                        2 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                        2                        2                        1 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                        2                        1                        2 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                        2                        2                        2 
## 
## $indcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                0.1996234                0.2222222                0.2222222 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                0.7058824                0.1111111                0.1111111 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                0.1111111                0.3333333                0.1111111 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                0.4444444                0.2222222                0.4591837 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                0.2222222                0.4444444                0.2222222 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                0.2222222                0.2596154                0.2539683 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                0.4966555                0.5469108                0.4444444 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                0.1111111                0.1111111                0.7442046 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                0.5555556                0.1111111                0.5000000 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                0.1111111                0.1111111                0.3648649 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                0.5000000                0.4218750                0.4444444 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                0.7405792                0.3461538                0.1111111 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                0.1111111                0.9585799                0.3292683 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                0.1111111                0.1796690                0.2222222 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                0.1111111                0.1111111                0.1111111 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                0.1111111                0.1111111                0.5000000 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                0.1111111                0.8780488                0.4063018 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                0.1111111                0.3333333                0.3333333 
## 
## $pval
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                    1.000                    1.000                    1.000 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                    0.147                    1.000                    1.000 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                    1.000                    0.724                    1.000 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                    0.636                    1.000                    0.185 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                    0.858                    0.511                    1.000 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                    1.000                    0.346                    1.000 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                    0.186                    0.725                    0.471 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                    1.000                    1.000                    0.271 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                    0.343                    1.000                    0.206 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                    1.000                    1.000                    0.336 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                    0.194                    0.707                    0.573 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                    0.277                    0.492                    1.000 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                    1.000                    0.019                    0.886 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                    1.000                    1.000                    1.000 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                    1.000                    1.000                    1.000 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                    1.000                    1.000                    0.193 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                    1.000                    0.037                    0.833 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                    1.000                    0.705                    0.702 
## 
## $error
## [1] 0
## 
## attr(,"class")
## [1] "indval"

#Pilosella officinarum has a high indval score of 0.959, and a low p value of 0.015. This is #the indicator species for Quartz.

clustCalcite <-cut(BarrowChemistry1$Calcite, 5, labels=FALSE)
BCIndval <- indval(as.matrix(BarrowSpecies1), clustCalcite, type= "long")
gr <- BCIndval$maxcls[BCIndval$pval<=0.05]
iv <- BCIndval$indcls[BCIndval$pval<=0.05]
pv <- BCIndval$pval[BCIndval$pval<=0.05]
fr <- apply(BarrowSpecies1[,-1]>0, 2, sum)[BCIndval$pval<=0.05]
BCIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
BCIndvalsummary <- BCIndvalsummary[order(BCIndvalsummary$group, 
                                         -BCIndvalsummary$indval),]
print(BCIndvalsummary)
##                       group    indval pvalue freq
## Lolium.perenne            1 0.9919137  0.014    9
## Arrhenatherum.elatius     1 0.6666667  0.049    6
summary(indval(as.matrix(BarrowSpecies1), clustCalcite))
##                cluster indicator_value probability
## Lolium.perenne       1          0.9919       0.012
## 
## Sum of probabilities                 =  33.764 
## 
## Sum of Indicator Values              =  17.2 
## 
## Sum of Significant Indicator Values  =  0.99 
## 
## Number of Significant Indicators     =  1 
## 
## Significant Indicator Distribution
## 
## 1 
## 1
print(indval(as.matrix(BarrowSpecies1), clustCalcite))
## $relfrq
##                                  1     5
## Anthyllis.vulneraria     0.0000000 0.375
## Aphanes.arvensis         0.3333333 0.125
## Arrhenatherum.elatius    0.6666667 0.000
## Bellis.perennis          0.0000000 0.750
## Blackstonia.perfoliata   0.0000000 0.125
## Brachythecium.albicans   0.0000000 0.125
## Brachythecium.rutabulum  0.0000000 0.125
## Briza.media              0.0000000 0.375
## Bromus.hordeaceus        0.3333333 0.000
## Calliergonella.cupsidata 0.3333333 0.375
## Carex.flacca             0.3333333 0.125
## Carlina.vulgaris         0.0000000 0.250
## Centaurium.erythraea     0.0000000 0.250
## Cerastium.fontanum       0.3333333 0.375
## Cynosurus.cristatus      0.3333333 0.125
## Daucus.carrota           0.3333333 0.125
## Erigeron.acer            0.0000000 0.250
## Euphrasia.agg            0.3333333 0.500
## Festuca.ovina            0.0000000 0.250
## Festuca.rubra            1.0000000 0.875
## Galium.verum             0.3333333 0.375
## Helicotrichon.spp.       0.3333333 0.000
## Hieracium.spp.           0.0000000 0.125
## Holcus.spp.              1.0000000 0.625
## Holcus.lanatus           0.3333333 0.500
## Holcus.mollis            0.3333333 0.000
## Hypericum.perforatum     0.0000000 0.125
## Hypochaeris.radicata     0.0000000 0.125
## Lathyrus.pratensis       0.3333333 0.000
## Leontodon.hispidus       0.0000000 0.250
## Leontodon.saxatilis      0.0000000 0.125
## Leucanthemum.vulgare     0.3333333 0.625
## Lolium.perenne           1.0000000 0.125
## Lotus.corniculatus       0.6666667 0.875
## Medicago.lupulina        0.0000000 0.375
## Ononis.repens            0.0000000 0.125
## Pastinaca.sativa         0.0000000 0.125
## Pillosella.officinarum   0.0000000 0.500
## Plantago.lanceolata      0.3333333 0.375
## Poa.spp.                 0.3333333 0.000
## Potentilla.reptans       0.3333333 0.250
## Prunella.vulgaris        0.3333333 0.125
## Pseudoscleropidum.purum  0.0000000 0.125
## Ranunculus.repens        0.0000000 0.125
## Reseda.lutea             0.0000000 0.125
## Sedum.anglicum           0.0000000 0.125
## Senecio.jacobaea         0.3333333 0.000
## Senecio.vulgaris         0.0000000 0.125
## Stellaria.apetala        0.3333333 0.000
## Taraxacum.agg.           0.0000000 0.500
## Trifolium.campestre      0.3333333 0.625
## Trifolium.pratense       0.0000000 0.125
## Trifolium.repens         0.3333333 0.250
## Trisetum.flavescens      0.0000000 0.375
## 
## $relabu
##                                   1           5
## Anthyllis.vulneraria     0.00000000 1.000000000
## Aphanes.arvensis         0.34782609 0.652173913
## Arrhenatherum.elatius    1.00000000 0.000000000
## Bellis.perennis          0.00000000 1.000000000
## Blackstonia.perfoliata   0.00000000 1.000000000
## Brachythecium.albicans   0.00000000 1.000000000
## Brachythecium.rutabulum  0.00000000 1.000000000
## Briza.media              0.00000000 1.000000000
## Bromus.hordeaceus        1.00000000 0.000000000
## Calliergonella.cupsidata 0.14285714 0.857142857
## Carex.flacca             0.88888889 0.111111111
## Carlina.vulgaris         0.00000000 1.000000000
## Centaurium.erythraea     0.00000000 1.000000000
## Cerastium.fontanum       0.40000000 0.600000000
## Cynosurus.cristatus      0.90566038 0.094339623
## Daucus.carrota           0.57142857 0.428571429
## Erigeron.acer            0.00000000 1.000000000
## Euphrasia.agg            0.08988764 0.910112360
## Festuca.ovina            0.00000000 1.000000000
## Festuca.rubra            0.71447197 0.285528031
## Galium.verum             0.02941176 0.970588235
## Helicotrichon.spp.       1.00000000 0.000000000
## Hieracium.spp.           0.00000000 1.000000000
## Holcus.spp.              0.83054893 0.169451074
## Holcus.lanatus           0.28776978 0.712230216
## Holcus.mollis            1.00000000 0.000000000
## Hypericum.perforatum     0.00000000 1.000000000
## Hypochaeris.radicata     0.00000000 1.000000000
## Lathyrus.pratensis       1.00000000 0.000000000
## Leontodon.hispidus       0.00000000 1.000000000
## Leontodon.saxatilis      0.00000000 1.000000000
## Leucanthemum.vulgare     0.11267606 0.887323944
## Lolium.perenne           0.99191375 0.008086253
## Lotus.corniculatus       0.79765396 0.202346041
## Medicago.lupulina        0.00000000 1.000000000
## Ononis.repens            0.00000000 1.000000000
## Pastinaca.sativa         0.00000000 1.000000000
## Pillosella.officinarum   0.00000000 1.000000000
## Plantago.lanceolata      0.22857143 0.771428571
## Poa.spp.                 1.00000000 0.000000000
## Potentilla.reptans       0.97049180 0.029508197
## Prunella.vulgaris        0.51612903 0.483870968
## Pseudoscleropidum.purum  0.00000000 1.000000000
## Ranunculus.repens        0.00000000 1.000000000
## Reseda.lutea             0.00000000 1.000000000
## Sedum.anglicum           0.00000000 1.000000000
## Senecio.jacobaea         1.00000000 0.000000000
## Senecio.vulgaris         0.00000000 1.000000000
## Stellaria.apetala        1.00000000 0.000000000
## Taraxacum.agg.           0.00000000 1.000000000
## Trifolium.campestre      0.04878049 0.951219512
## Trifolium.pratense       0.00000000 1.000000000
## Trifolium.repens         0.20253165 0.797468354
## Trisetum.flavescens      0.00000000 1.000000000
## 
## $indval
##                                    1           5
## Anthyllis.vulneraria     0.000000000 0.375000000
## Aphanes.arvensis         0.115942029 0.081521739
## Arrhenatherum.elatius    0.666666667 0.000000000
## Bellis.perennis          0.000000000 0.750000000
## Blackstonia.perfoliata   0.000000000 0.125000000
## Brachythecium.albicans   0.000000000 0.125000000
## Brachythecium.rutabulum  0.000000000 0.125000000
## Briza.media              0.000000000 0.375000000
## Bromus.hordeaceus        0.333333333 0.000000000
## Calliergonella.cupsidata 0.047619048 0.321428571
## Carex.flacca             0.296296296 0.013888889
## Carlina.vulgaris         0.000000000 0.250000000
## Centaurium.erythraea     0.000000000 0.250000000
## Cerastium.fontanum       0.133333333 0.225000000
## Cynosurus.cristatus      0.301886792 0.011792453
## Daucus.carrota           0.190476190 0.053571429
## Erigeron.acer            0.000000000 0.250000000
## Euphrasia.agg            0.029962547 0.455056180
## Festuca.ovina            0.000000000 0.250000000
## Festuca.rubra            0.714471969 0.249837027
## Galium.verum             0.009803922 0.363970588
## Helicotrichon.spp.       0.333333333 0.000000000
## Hieracium.spp.           0.000000000 0.125000000
## Holcus.spp.              0.830548926 0.105906921
## Holcus.lanatus           0.095923261 0.356115108
## Holcus.mollis            0.333333333 0.000000000
## Hypericum.perforatum     0.000000000 0.125000000
## Hypochaeris.radicata     0.000000000 0.125000000
## Lathyrus.pratensis       0.333333333 0.000000000
## Leontodon.hispidus       0.000000000 0.250000000
## Leontodon.saxatilis      0.000000000 0.125000000
## Leucanthemum.vulgare     0.037558685 0.554577465
## Lolium.perenne           0.991913747 0.001010782
## Lotus.corniculatus       0.531769306 0.177052786
## Medicago.lupulina        0.000000000 0.375000000
## Ononis.repens            0.000000000 0.125000000
## Pastinaca.sativa         0.000000000 0.125000000
## Pillosella.officinarum   0.000000000 0.500000000
## Plantago.lanceolata      0.076190476 0.289285714
## Poa.spp.                 0.333333333 0.000000000
## Potentilla.reptans       0.323497268 0.007377049
## Prunella.vulgaris        0.172043011 0.060483871
## Pseudoscleropidum.purum  0.000000000 0.125000000
## Ranunculus.repens        0.000000000 0.125000000
## Reseda.lutea             0.000000000 0.125000000
## Sedum.anglicum           0.000000000 0.125000000
## Senecio.jacobaea         0.333333333 0.000000000
## Senecio.vulgaris         0.000000000 0.125000000
## Stellaria.apetala        0.333333333 0.000000000
## Taraxacum.agg.           0.000000000 0.500000000
## Trifolium.campestre      0.016260163 0.594512195
## Trifolium.pratense       0.000000000 0.125000000
## Trifolium.repens         0.067510549 0.199367089
## Trisetum.flavescens      0.000000000 0.375000000
## 
## $maxcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                        2                        1                        1 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                        2                        2                        2 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                        2                        2                        1 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                        2                        1                        2 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                        2                        2                        1 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                        1                        2                        2 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                        2                        1                        2 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                        1                        2                        1 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                        2                        1                        2 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                        2                        1                        2 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                        2                        2                        1 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                        1                        2                        2 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                        2                        2                        2 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                        1                        1                        1 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                        2                        2                        2 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                        2                        1                        2 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                        1                        2                        2 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                        2                        2                        2 
## 
## $indcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                0.3750000                0.1159420                0.6666667 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                0.7500000                0.1250000                0.1250000 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                0.1250000                0.3750000                0.3333333 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                0.3214286                0.2962963                0.2500000 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                0.2500000                0.2250000                0.3018868 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                0.1904762                0.2500000                0.4550562 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                0.2500000                0.7144720                0.3639706 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                0.3333333                0.1250000                0.8305489 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                0.3561151                0.3333333                0.1250000 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                0.1250000                0.3333333                0.2500000 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                0.1250000                0.5545775                0.9919137 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                0.5317693                0.3750000                0.1250000 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                0.1250000                0.5000000                0.2892857 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                0.3333333                0.3234973                0.1720430 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                0.1250000                0.1250000                0.1250000 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                0.1250000                0.3333333                0.1250000 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                0.3333333                0.5000000                0.5945122 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                0.1250000                0.1993671                0.3750000 
## 
## $pval
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                    0.446                    1.000                    0.050 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                    0.087                    1.000                    1.000 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                    1.000                    0.472                    0.297 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                    0.567                    0.301                    0.782 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                    0.772                    0.881                    0.272 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                    1.000                    0.782                    0.429 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                    0.786                    0.074                    0.688 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                    0.286                    1.000                    0.072 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                    0.677                    0.273                    1.000 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                    1.000                    0.296                    0.795 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                    1.000                    0.393                    0.012 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                    0.627                    0.477                    1.000 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                    1.000                    0.370                    0.572 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                    0.279                    0.614                    1.000 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                    1.000                    1.000                    1.000 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                    1.000                    0.268                    1.000 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                    0.278                    0.355                    0.289 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                    1.000                    0.811                    0.418 
## 
## $error
## [1] 0
## 
## attr(,"class")
## [1] "indval"

#Lolium perenne has a high indval score of 0.992 and a low p value of 0.008. This is reported #as the indicator species for Calcite.

clustKaolinite <-cut(BarrowChemistry1$Kaolinite, 5, labels=FALSE)
BKIndval <- indval(as.matrix(BarrowSpecies1), clustKaolinite, type= "long")
gr <- BKIndval$maxcls[BKIndval$pval<=0.05]
iv <- BKIndval$indcls[BKIndval$pval<=0.05]
pv <- BKIndval$pval[BKIndval$pval<=0.05]
fr <- apply(BarrowSpecies1[,-1]>0, 2, sum)[BKIndval$pval<=0.05]
BKIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
BKIndvalsummary <- BKIndvalsummary[order(BKIndvalsummary$group, 
                                         -BKIndvalsummary$indval),]
print(BKIndvalsummary)
##               group    indval pvalue freq
## Euphrasia.agg     1 0.8333333  0.016    2
summary(indval(as.matrix(BarrowSpecies1), clustKaolinite))
##               cluster indicator_value probability
## Euphrasia.agg       1          0.8333        0.02
## 
## Sum of probabilities                 =  34.245 
## 
## Sum of Indicator Values              =  15.1 
## 
## Sum of Significant Indicator Values  =  0.83 
## 
## Number of Significant Indicators     =  1 
## 
## Significant Indicator Distribution
## 
## 1 
## 1
print(indval(as.matrix(BarrowSpecies1), clustKaolinite))
## $relfrq
##                                  1   5
## Anthyllis.vulneraria     0.3333333 0.2
## Aphanes.arvensis         0.1666667 0.2
## Arrhenatherum.elatius    0.1666667 0.2
## Bellis.perennis          0.6666667 0.4
## Blackstonia.perfoliata   0.1666667 0.0
## Brachythecium.albicans   0.0000000 0.2
## Brachythecium.rutabulum  0.0000000 0.2
## Briza.media              0.1666667 0.4
## Bromus.hordeaceus        0.0000000 0.2
## Calliergonella.cupsidata 0.1666667 0.6
## Carex.flacca             0.1666667 0.2
## Carlina.vulgaris         0.3333333 0.0
## Centaurium.erythraea     0.3333333 0.0
## Cerastium.fontanum       0.1666667 0.6
## Cynosurus.cristatus      0.1666667 0.2
## Daucus.carrota           0.1666667 0.2
## Erigeron.acer            0.3333333 0.0
## Euphrasia.agg            0.8333333 0.0
## Festuca.ovina            0.1666667 0.2
## Festuca.rubra            0.8333333 1.0
## Galium.verum             0.3333333 0.4
## Helicotrichon.spp.       0.0000000 0.2
## Hieracium.spp.           0.0000000 0.2
## Holcus.spp.              0.5000000 1.0
## Holcus.lanatus           0.3333333 0.6
## Holcus.mollis            0.1666667 0.0
## Hypericum.perforatum     0.1666667 0.0
## Hypochaeris.radicata     0.0000000 0.2
## Lathyrus.pratensis       0.0000000 0.2
## Leontodon.hispidus       0.1666667 0.2
## Leontodon.saxatilis      0.1666667 0.0
## Leucanthemum.vulgare     0.3333333 0.8
## Lolium.perenne           0.3333333 0.4
## Lotus.corniculatus       0.8333333 0.8
## Medicago.lupulina        0.3333333 0.2
## Ononis.repens            0.1666667 0.0
## Pastinaca.sativa         0.1666667 0.0
## Pillosella.officinarum   0.5000000 0.2
## Plantago.lanceolata      0.3333333 0.4
## Poa.spp.                 0.0000000 0.2
## Potentilla.reptans       0.3333333 0.2
## Prunella.vulgaris        0.1666667 0.2
## Pseudoscleropidum.purum  0.0000000 0.2
## Ranunculus.repens        0.0000000 0.2
## Reseda.lutea             0.1666667 0.0
## Sedum.anglicum           0.1666667 0.0
## Senecio.jacobaea         0.0000000 0.2
## Senecio.vulgaris         0.1666667 0.0
## Stellaria.apetala        0.0000000 0.2
## Taraxacum.agg.           0.6666667 0.0
## Trifolium.campestre      0.3333333 0.8
## Trifolium.pratense       0.0000000 0.2
## Trifolium.repens         0.1666667 0.4
## Trisetum.flavescens      0.3333333 0.2
## 
## $relabu
##                                   1          5
## Anthyllis.vulneraria     0.77331759 0.22668241
## Aphanes.arvensis         0.80645161 0.19354839
## Arrhenatherum.elatius    0.34246575 0.65753425
## Bellis.perennis          0.43307087 0.56692913
## Blackstonia.perfoliata   1.00000000 0.00000000
## Brachythecium.albicans   0.00000000 1.00000000
## Brachythecium.rutabulum  0.00000000 1.00000000
## Briza.media              0.87121212 0.12878788
## Bromus.hordeaceus        0.00000000 1.00000000
## Calliergonella.cupsidata 0.10000000 0.90000000
## Carex.flacca             0.21739130 0.78260870
## Carlina.vulgaris         1.00000000 0.00000000
## Centaurium.erythraea     1.00000000 0.00000000
## Cerastium.fontanum       0.17241379 0.82758621
## Cynosurus.cristatus      0.18796992 0.81203008
## Daucus.carrota           0.29411765 0.70588235
## Erigeron.acer            1.00000000 0.00000000
## Euphrasia.agg            1.00000000 0.00000000
## Festuca.ovina            0.96491228 0.03508772
## Festuca.rubra            0.40420115 0.59579885
## Galium.verum             0.46012270 0.53987730
## Helicotrichon.spp.       0.00000000 1.00000000
## Hieracium.spp.           0.00000000 1.00000000
## Holcus.spp.              0.25195482 0.74804518
## Holcus.lanatus           0.13513514 0.86486486
## Holcus.mollis            1.00000000 0.00000000
## Hypericum.perforatum     1.00000000 0.00000000
## Hypochaeris.radicata     0.00000000 1.00000000
## Lathyrus.pratensis       0.00000000 1.00000000
## Leontodon.hispidus       0.33333333 0.66666667
## Leontodon.saxatilis      1.00000000 0.00000000
## Leucanthemum.vulgare     0.54621849 0.45378151
## Lolium.perenne           0.06283662 0.93716338
## Lotus.corniculatus       0.33184855 0.66815145
## Medicago.lupulina        0.62500000 0.37500000
## Ononis.repens            1.00000000 0.00000000
## Pastinaca.sativa         1.00000000 0.00000000
## Pillosella.officinarum   0.89041096 0.10958904
## Plantago.lanceolata      0.55555556 0.44444444
## Poa.spp.                 0.00000000 1.00000000
## Potentilla.reptans       0.06329114 0.93670886
## Prunella.vulgaris        0.67567568 0.32432432
## Pseudoscleropidum.purum  0.00000000 1.00000000
## Ranunculus.repens        0.00000000 1.00000000
## Reseda.lutea             1.00000000 0.00000000
## Sedum.anglicum           1.00000000 0.00000000
## Senecio.jacobaea         0.00000000 1.00000000
## Senecio.vulgaris         1.00000000 0.00000000
## Stellaria.apetala        0.00000000 1.00000000
## Taraxacum.agg.           1.00000000 0.00000000
## Trifolium.campestre      0.24752475 0.75247525
## Trifolium.pratense       0.00000000 1.00000000
## Trifolium.repens         0.14925373 0.85074627
## Trisetum.flavescens      0.97178683 0.02821317
## 
## $indval
##                                   1           5
## Anthyllis.vulneraria     0.25777253 0.045336482
## Aphanes.arvensis         0.13440860 0.038709677
## Arrhenatherum.elatius    0.05707763 0.131506849
## Bellis.perennis          0.28871391 0.226771654
## Blackstonia.perfoliata   0.16666667 0.000000000
## Brachythecium.albicans   0.00000000 0.200000000
## Brachythecium.rutabulum  0.00000000 0.200000000
## Briza.media              0.14520202 0.051515152
## Bromus.hordeaceus        0.00000000 0.200000000
## Calliergonella.cupsidata 0.01666667 0.540000000
## Carex.flacca             0.03623188 0.156521739
## Carlina.vulgaris         0.33333333 0.000000000
## Centaurium.erythraea     0.33333333 0.000000000
## Cerastium.fontanum       0.02873563 0.496551724
## Cynosurus.cristatus      0.03132832 0.162406015
## Daucus.carrota           0.04901961 0.141176471
## Erigeron.acer            0.33333333 0.000000000
## Euphrasia.agg            0.83333333 0.000000000
## Festuca.ovina            0.16081871 0.007017544
## Festuca.rubra            0.33683429 0.595798854
## Galium.verum             0.15337423 0.215950920
## Helicotrichon.spp.       0.00000000 0.200000000
## Hieracium.spp.           0.00000000 0.200000000
## Holcus.spp.              0.12597741 0.748045178
## Holcus.lanatus           0.04504505 0.518918919
## Holcus.mollis            0.16666667 0.000000000
## Hypericum.perforatum     0.16666667 0.000000000
## Hypochaeris.radicata     0.00000000 0.200000000
## Lathyrus.pratensis       0.00000000 0.200000000
## Leontodon.hispidus       0.05555556 0.133333333
## Leontodon.saxatilis      0.16666667 0.000000000
## Leucanthemum.vulgare     0.18207283 0.363025210
## Lolium.perenne           0.02094554 0.374865350
## Lotus.corniculatus       0.27654046 0.534521158
## Medicago.lupulina        0.20833333 0.075000000
## Ononis.repens            0.16666667 0.000000000
## Pastinaca.sativa         0.16666667 0.000000000
## Pillosella.officinarum   0.44520548 0.021917808
## Plantago.lanceolata      0.18518519 0.177777778
## Poa.spp.                 0.00000000 0.200000000
## Potentilla.reptans       0.02109705 0.187341772
## Prunella.vulgaris        0.11261261 0.064864865
## Pseudoscleropidum.purum  0.00000000 0.200000000
## Ranunculus.repens        0.00000000 0.200000000
## Reseda.lutea             0.16666667 0.000000000
## Sedum.anglicum           0.16666667 0.000000000
## Senecio.jacobaea         0.00000000 0.200000000
## Senecio.vulgaris         0.16666667 0.000000000
## Stellaria.apetala        0.00000000 0.200000000
## Taraxacum.agg.           0.66666667 0.000000000
## Trifolium.campestre      0.08250825 0.601980198
## Trifolium.pratense       0.00000000 0.200000000
## Trifolium.repens         0.02487562 0.340298507
## Trisetum.flavescens      0.32392894 0.005642633
## 
## $maxcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                        1                        1                        2 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                        1                        1                        2 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                        2                        1                        2 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                        2                        2                        1 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                        1                        2                        2 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                        2                        1                        1 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                        1                        2                        2 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                        2                        2                        2 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                        2                        1                        1 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                        2                        2                        2 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                        1                        2                        2 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                        2                        1                        1 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                        1                        1                        1 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                        2                        2                        1 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                        2                        2                        1 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                        1                        2                        1 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                        2                        1                        2 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                        2                        2                        1 
## 
## $indcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                0.2577725                0.1344086                0.1315068 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                0.2887139                0.1666667                0.2000000 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                0.2000000                0.1452020                0.2000000 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                0.5400000                0.1565217                0.3333333 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                0.3333333                0.4965517                0.1624060 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                0.1411765                0.3333333                0.8333333 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                0.1608187                0.5957989                0.2159509 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                0.2000000                0.2000000                0.7480452 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                0.5189189                0.1666667                0.1666667 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                0.2000000                0.2000000                0.1333333 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                0.1666667                0.3630252                0.3748654 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                0.5345212                0.2083333                0.1666667 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                0.1666667                0.4452055                0.1851852 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                0.2000000                0.1873418                0.1126126 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                0.2000000                0.2000000                0.1666667 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                0.1666667                0.2000000                0.1666667 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                0.2000000                0.6666667                0.6019802 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                0.2000000                0.3402985                0.3239289 
## 
## $pval
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                    0.722                    1.000                    0.741 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                    0.926                    1.000                    0.417 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                    0.470                    1.000                    0.411 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                    0.144                    0.688                    0.454 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                    0.436                    0.174                    0.726 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                    0.715                    0.464                    0.013 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                    1.000                    0.360                    1.000 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                    0.470                    0.464                    0.101 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                    0.299                    1.000                    1.000 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                    0.418                    0.438                    0.729 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                    1.000                    0.699                    0.662 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                    0.546                    1.000                    1.000 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                    1.000                    0.297                    1.000 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                    0.456                    0.874                    1.000 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                    0.431                    0.452                    1.000 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                    1.000                    0.469                    1.000 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                    0.467                    0.061                    0.205 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                    0.442                    0.402                    0.727 
## 
## $error
## [1] 0
## 
## attr(,"class")
## [1] "indval"

#Euphrasia agg. has a high indval score of 0.833 and a low p value of 0.017. This is #reported as the indicator species for Kaolinite.

clustMuscovite <-cut(BarrowChemistry1$Muscovite, 5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustMuscovite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  34.36 
## 
## Sum of Indicator Values              =  15.16 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the previous minerals investigated.

clustPigeonite <-cut(BarrowChemistry1$Pigeonite, 5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustPigeonite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  34.172 
## 
## Sum of Indicator Values              =  15.27 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustAlbite <-cut(BarrowChemistry1$Albite, 5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustAlbite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  44.253 
## 
## Sum of Indicator Values              =  16.89 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustAluminium_oxide_hydroxide <-cut(BarrowChemistry1$Aluminium_oxide_hydroxide,
                                      5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustAluminium_oxide_hydroxide))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  45.739 
## 
## Sum of Indicator Values              =  17.13 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustAragonite <-cut(BarrowChemistry1$Aragonite, 5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustAragonite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  47.66 
## 
## Sum of Indicator Values              =  15.83 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustAugite <-cut(BarrowChemistry1$Augite,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustAugite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  44.239 
## 
## Sum of Indicator Values              =  16.89 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustBiotite <-cut(BarrowChemistry1$Biotite,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustBiotite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  54 
## 
## Sum of Indicator Values              =  13.18 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustBirnessite <-cut(BarrowChemistry1$Birnessite,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustBirnessite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  54 
## 
## Sum of Indicator Values              =  13.18 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustClinochlore <-cut(BarrowChemistry1$Clinochlore,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustClinochlore))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  44.298 
## 
## Sum of Indicator Values              =  16.89 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustDiaspore <-cut(BarrowChemistry1$Diaspore,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustDiaspore))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  42.427 
## 
## Sum of Indicator Values              =  17.98 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustGehlenite <-cut(BarrowChemistry1$Diaspore,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustGehlenite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  42.351 
## 
## Sum of Indicator Values              =  17.98 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustIllite <-cut(BarrowChemistry1$Diaspore,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustIllite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  42.438 
## 
## Sum of Indicator Values              =  17.98 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustMelilite <-cut(BarrowChemistry1$Melilite,5, labels=FALSE)
BMeliliteIndval <- indval(as.matrix(BarrowSpecies1), clustMelilite, type= "long")
gr <- BMeliliteIndval$maxcls[BMeliliteIndval$pval<=0.05]
iv <- BMeliliteIndval$indcls[BMeliliteIndval$pval<=0.05]
pv <- BMeliliteIndval$pval[BMeliliteIndval$pval<=0.05]
fr <- apply(BarrowSpecies1[,-1]>0, 2, sum)[BMeliliteIndval$pval<=0.05]
BMeliliteIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
BMeliliteIndvalsummary <- BMeliliteIndvalsummary[order(BMeliliteIndvalsummary$group, 
                                         -BMeliliteIndvalsummary$indval),]
print(BMeliliteIndvalsummary)
##                        group    indval pvalue freq
## Pillosella.officinarum     2 0.9585799  0.021    4
## Taraxacum.agg.             2 0.8780488  0.043    6
summary(indval(as.matrix(BarrowSpecies1), clustMelilite))
##                        cluster indicator_value probability
## Pillosella.officinarum       2          0.9586       0.022
## Taraxacum.agg.               2          0.8780       0.034
## 
## Sum of probabilities                 =  39.386 
## 
## Sum of Indicator Values              =  16.79 
## 
## Sum of Significant Indicator Values  =  1.84 
## 
## Number of Significant Indicators     =  2 
## 
## Significant Indicator Distribution
## 
## 2 
## 2
print(indval(as.matrix(BarrowSpecies1), clustMelilite))
## $relfrq
##                                  1   5
## Anthyllis.vulneraria     0.2222222 0.5
## Aphanes.arvensis         0.2222222 0.0
## Arrhenatherum.elatius    0.2222222 0.0
## Bellis.perennis          0.4444444 1.0
## Blackstonia.perfoliata   0.1111111 0.0
## Brachythecium.albicans   0.1111111 0.0
## Brachythecium.rutabulum  0.1111111 0.0
## Briza.media              0.3333333 0.0
## Bromus.hordeaceus        0.1111111 0.0
## Calliergonella.cupsidata 0.4444444 0.0
## Carex.flacca             0.2222222 0.0
## Carlina.vulgaris         0.1111111 0.5
## Centaurium.erythraea     0.2222222 0.0
## Cerastium.fontanum       0.4444444 0.0
## Cynosurus.cristatus      0.2222222 0.0
## Daucus.carrota           0.2222222 0.0
## Erigeron.acer            0.1111111 0.5
## Euphrasia.agg            0.4444444 0.5
## Festuca.ovina            0.1111111 0.5
## Festuca.rubra            1.0000000 0.5
## Galium.verum             0.4444444 0.0
## Helicotrichon.spp.       0.1111111 0.0
## Hieracium.spp.           0.1111111 0.0
## Holcus.spp.              0.7777778 0.5
## Holcus.lanatus           0.5555556 0.0
## Holcus.mollis            0.1111111 0.0
## Hypericum.perforatum     0.0000000 0.5
## Hypochaeris.radicata     0.1111111 0.0
## Lathyrus.pratensis       0.1111111 0.0
## Leontodon.hispidus       0.1111111 0.5
## Leontodon.saxatilis      0.0000000 0.5
## Leucanthemum.vulgare     0.5555556 0.5
## Lolium.perenne           0.4444444 0.0
## Lotus.corniculatus       0.8888889 0.5
## Medicago.lupulina        0.2222222 0.5
## Ononis.repens            0.1111111 0.0
## Pastinaca.sativa         0.1111111 0.0
## Pillosella.officinarum   0.2222222 1.0
## Plantago.lanceolata      0.3333333 0.5
## Poa.spp.                 0.1111111 0.0
## Potentilla.reptans       0.2222222 0.5
## Prunella.vulgaris        0.2222222 0.0
## Pseudoscleropidum.purum  0.1111111 0.0
## Ranunculus.repens        0.1111111 0.0
## Reseda.lutea             0.1111111 0.0
## Sedum.anglicum           0.1111111 0.0
## Senecio.jacobaea         0.1111111 0.0
## Senecio.vulgaris         0.0000000 0.5
## Stellaria.apetala        0.1111111 0.0
## Taraxacum.agg.           0.2222222 1.0
## Trifolium.campestre      0.5555556 0.5
## Trifolium.pratense       0.1111111 0.0
## Trifolium.repens         0.3333333 0.0
## Trisetum.flavescens      0.3333333 0.0
## 
## $relabu
##                                    1          5
## Anthyllis.vulneraria     0.898305085 0.10169492
## Aphanes.arvensis         1.000000000 0.00000000
## Arrhenatherum.elatius    1.000000000 0.00000000
## Bellis.perennis          0.294117647 0.70588235
## Blackstonia.perfoliata   1.000000000 0.00000000
## Brachythecium.albicans   1.000000000 0.00000000
## Brachythecium.rutabulum  1.000000000 0.00000000
## Briza.media              1.000000000 0.00000000
## Bromus.hordeaceus        1.000000000 0.00000000
## Calliergonella.cupsidata 1.000000000 0.00000000
## Carex.flacca             1.000000000 0.00000000
## Carlina.vulgaris         0.081632653 0.91836735
## Centaurium.erythraea     1.000000000 0.00000000
## Cerastium.fontanum       1.000000000 0.00000000
## Cynosurus.cristatus      1.000000000 0.00000000
## Daucus.carrota           1.000000000 0.00000000
## Erigeron.acer            0.480769231 0.51923077
## Euphrasia.agg            0.571428571 0.42857143
## Festuca.ovina            0.006688963 0.99331104
## Festuca.rubra            0.546910755 0.45308924
## Galium.verum             1.000000000 0.00000000
## Helicotrichon.spp.       1.000000000 0.00000000
## Hieracium.spp.           1.000000000 0.00000000
## Holcus.spp.              0.956834532 0.04316547
## Holcus.lanatus           1.000000000 0.00000000
## Holcus.mollis            1.000000000 0.00000000
## Hypericum.perforatum     0.000000000 1.00000000
## Hypochaeris.radicata     1.000000000 0.00000000
## Lathyrus.pratensis       1.000000000 0.00000000
## Leontodon.hispidus       0.270270270 0.72972973
## Leontodon.saxatilis      0.000000000 1.00000000
## Leucanthemum.vulgare     0.156250000 0.84375000
## Lolium.perenne           1.000000000 0.00000000
## Lotus.corniculatus       0.833151581 0.16684842
## Medicago.lupulina        0.307692308 0.69230769
## Ononis.repens            1.000000000 0.00000000
## Pastinaca.sativa         1.000000000 0.00000000
## Pillosella.officinarum   0.041420118 0.95857988
## Plantago.lanceolata      0.341463415 0.65853659
## Poa.spp.                 1.000000000 0.00000000
## Potentilla.reptans       0.808510638 0.19148936
## Prunella.vulgaris        1.000000000 0.00000000
## Pseudoscleropidum.purum  1.000000000 0.00000000
## Ranunculus.repens        1.000000000 0.00000000
## Reseda.lutea             1.000000000 0.00000000
## Sedum.anglicum           1.000000000 0.00000000
## Senecio.jacobaea         1.000000000 0.00000000
## Senecio.vulgaris         0.000000000 1.00000000
## Stellaria.apetala        1.000000000 0.00000000
## Taraxacum.agg.           0.121951220 0.87804878
## Trifolium.campestre      0.731343284 0.26865672
## Trifolium.pratense       1.000000000 0.00000000
## Trifolium.repens         1.000000000 0.00000000
## Trisetum.flavescens      1.000000000 0.00000000
## 
## $indval
##                                     1          5
## Anthyllis.vulneraria     0.1996233522 0.05084746
## Aphanes.arvensis         0.2222222222 0.00000000
## Arrhenatherum.elatius    0.2222222222 0.00000000
## Bellis.perennis          0.1307189542 0.70588235
## Blackstonia.perfoliata   0.1111111111 0.00000000
## Brachythecium.albicans   0.1111111111 0.00000000
## Brachythecium.rutabulum  0.1111111111 0.00000000
## Briza.media              0.3333333333 0.00000000
## Bromus.hordeaceus        0.1111111111 0.00000000
## Calliergonella.cupsidata 0.4444444444 0.00000000
## Carex.flacca             0.2222222222 0.00000000
## Carlina.vulgaris         0.0090702948 0.45918367
## Centaurium.erythraea     0.2222222222 0.00000000
## Cerastium.fontanum       0.4444444444 0.00000000
## Cynosurus.cristatus      0.2222222222 0.00000000
## Daucus.carrota           0.2222222222 0.00000000
## Erigeron.acer            0.0534188034 0.25961538
## Euphrasia.agg            0.2539682540 0.21428571
## Festuca.ovina            0.0007432181 0.49665552
## Festuca.rubra            0.5469107551 0.22654462
## Galium.verum             0.4444444444 0.00000000
## Helicotrichon.spp.       0.1111111111 0.00000000
## Hieracium.spp.           0.1111111111 0.00000000
## Holcus.spp.              0.7442046363 0.02158273
## Holcus.lanatus           0.5555555556 0.00000000
## Holcus.mollis            0.1111111111 0.00000000
## Hypericum.perforatum     0.0000000000 0.50000000
## Hypochaeris.radicata     0.1111111111 0.00000000
## Lathyrus.pratensis       0.1111111111 0.00000000
## Leontodon.hispidus       0.0300300300 0.36486486
## Leontodon.saxatilis      0.0000000000 0.50000000
## Leucanthemum.vulgare     0.0868055556 0.42187500
## Lolium.perenne           0.4444444444 0.00000000
## Lotus.corniculatus       0.7405791833 0.08342421
## Medicago.lupulina        0.0683760684 0.34615385
## Ononis.repens            0.1111111111 0.00000000
## Pastinaca.sativa         0.1111111111 0.00000000
## Pillosella.officinarum   0.0092044707 0.95857988
## Plantago.lanceolata      0.1138211382 0.32926829
## Poa.spp.                 0.1111111111 0.00000000
## Potentilla.reptans       0.1796690307 0.09574468
## Prunella.vulgaris        0.2222222222 0.00000000
## Pseudoscleropidum.purum  0.1111111111 0.00000000
## Ranunculus.repens        0.1111111111 0.00000000
## Reseda.lutea             0.1111111111 0.00000000
## Sedum.anglicum           0.1111111111 0.00000000
## Senecio.jacobaea         0.1111111111 0.00000000
## Senecio.vulgaris         0.0000000000 0.50000000
## Stellaria.apetala        0.1111111111 0.00000000
## Taraxacum.agg.           0.0271002710 0.87804878
## Trifolium.campestre      0.4063018242 0.13432836
## Trifolium.pratense       0.1111111111 0.00000000
## Trifolium.repens         0.3333333333 0.00000000
## Trisetum.flavescens      0.3333333333 0.00000000
## 
## $maxcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                        1                        1                        1 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                        2                        1                        1 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                        1                        1                        1 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                        1                        1                        2 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                        1                        1                        1 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                        1                        2                        1 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                        2                        1                        1 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                        1                        1                        1 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                        1                        1                        2 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                        1                        1                        2 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                        2                        2                        1 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                        1                        2                        1 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                        1                        2                        2 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                        1                        1                        1 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                        1                        1                        1 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                        1                        1                        2 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                        1                        2                        1 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                        1                        1                        1 
## 
## $indcls
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                0.1996234                0.2222222                0.2222222 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                0.7058824                0.1111111                0.1111111 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                0.1111111                0.3333333                0.1111111 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                0.4444444                0.2222222                0.4591837 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                0.2222222                0.4444444                0.2222222 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                0.2222222                0.2596154                0.2539683 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                0.4966555                0.5469108                0.4444444 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                0.1111111                0.1111111                0.7442046 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                0.5555556                0.1111111                0.5000000 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                0.1111111                0.1111111                0.3648649 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                0.5000000                0.4218750                0.4444444 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                0.7405792                0.3461538                0.1111111 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                0.1111111                0.9585799                0.3292683 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                0.1111111                0.1796690                0.2222222 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                0.1111111                0.1111111                0.1111111 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                0.1111111                0.1111111                0.5000000 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                0.1111111                0.8780488                0.4063018 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                0.1111111                0.3333333                0.3333333 
## 
## $pval
##     Anthyllis.vulneraria         Aphanes.arvensis    Arrhenatherum.elatius 
##                    1.000                    1.000                    1.000 
##          Bellis.perennis   Blackstonia.perfoliata   Brachythecium.albicans 
##                    0.146                    1.000                    1.000 
##  Brachythecium.rutabulum              Briza.media        Bromus.hordeaceus 
##                    1.000                    0.706                    1.000 
## Calliergonella.cupsidata             Carex.flacca         Carlina.vulgaris 
##                    0.601                    1.000                    0.197 
##     Centaurium.erythraea       Cerastium.fontanum      Cynosurus.cristatus 
##                    0.836                    0.500                    1.000 
##           Daucus.carrota            Erigeron.acer            Euphrasia.agg 
##                    1.000                    0.348                    1.000 
##            Festuca.ovina            Festuca.rubra             Galium.verum 
##                    0.184                    0.695                    0.473 
##       Helicotrichon.spp.           Hieracium.spp.              Holcus.spp. 
##                    1.000                    1.000                    0.314 
##           Holcus.lanatus            Holcus.mollis     Hypericum.perforatum 
##                    0.361                    1.000                    0.211 
##     Hypochaeris.radicata       Lathyrus.pratensis       Leontodon.hispidus 
##                    1.000                    1.000                    0.353 
##      Leontodon.saxatilis     Leucanthemum.vulgare           Lolium.perenne 
##                    0.186                    0.705                    0.564 
##       Lotus.corniculatus        Medicago.lupulina            Ononis.repens 
##                    0.284                    0.458                    1.000 
##         Pastinaca.sativa   Pillosella.officinarum      Plantago.lanceolata 
##                    1.000                    0.013                    0.886 
##                 Poa.spp.       Potentilla.reptans        Prunella.vulgaris 
##                    1.000                    1.000                    1.000 
##  Pseudoscleropidum.purum        Ranunculus.repens             Reseda.lutea 
##                    1.000                    1.000                    1.000 
##           Sedum.anglicum         Senecio.jacobaea         Senecio.vulgaris 
##                    1.000                    1.000                    0.203 
##        Stellaria.apetala           Taraxacum.agg.      Trifolium.campestre 
##                    1.000                    0.032                    0.802 
##       Trifolium.pratense         Trifolium.repens      Trisetum.flavescens 
##                    1.000                    0.728                    0.697 
## 
## $error
## [1] 0
## 
## attr(,"class")
## [1] "indval"

#Pilosella officinarum has a high indval score of 0.959 and a low p value of 0.011. This is #the indicator species for Melilite.

clustMicrocline <-cut(BarrowChemistry1$Microcline,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustMicrocline))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  43.188 
## 
## Sum of Indicator Values              =  19.27 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustNitratine <-cut(BarrowChemistry1$Nitratine,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustNitratine))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  40.246 
## 
## Sum of Indicator Values              =  16.04 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustPericlase <-cut(BarrowChemistry1$Periclase,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustPericlase))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  45.683 
## 
## Sum of Indicator Values              =  17.13 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.

clustPhengite <-cut(BarrowChemistry1$Phengite,5, labels=FALSE)
summary(indval(as.matrix(BarrowSpecies1), clustPhengite))
## [1] cluster         indicator_value probability    
## <0 rows> (or 0-length row.names)
## 
## Sum of probabilities                 =  44.34 
## 
## Sum of Indicator Values              =  19 
## 
## Sum of Significant Indicator Values  =  0 
## 
## Number of Significant Indicators     =  0 
## 
## Significant Indicator Distribution
## < table of extent 0 >

#This analysis was not successful, possibly because this mineral was recorded on fewer #communities than the first three minerals investigated.