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##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.