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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 Warton slag bank and the RSPB Hodbarrow ##Nature Reserve..
#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://github.com/cran/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://github.com/cran/labdsv/src/contrib:
## cannot open URL 'https://github.com/cran/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://github.com/cran/labdsv/bin/windows/contrib/4.3:
## cannot open URL 'https://github.com/cran/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 two study sites…
urlfile1 <- 'https://raw.githubusercontent.com/Savannankvm/Indval-Analyses-for-Warton-and-Hodbarrow/PhD-files/Carnforth_and_Hodbarrow_Species_with_site_names.csv'
PlantSpecies <-read.csv(urlfile1 , row.names = 1)
urlfile2 <- 'https://raw.githubusercontent.com/Savannankvm/Indval-Analyses-for-Warton-and-Hodbarrow/PhD-files/Carnforth_and_Hodbarrow_Chemistry_with_site_names.csv'
PlantChemistry <-read.csv(urlfile2 , row.names = 1)
#Turning the datasets into dataframes to make them suitable for the Indval analyses
PlantSpecies1 <- data.frame(PlantSpecies)
PlantChemistry1 <- data.frame(PlantChemistry)
#Doing my first analysis, looking into indicator species for quartz. #Much of the code relates to developing a tidy summary with p values for the most #statistically significant indicator species
clustQuartz <- cut(PlantChemistry1$Quartz, 5, labels=FALSE)
QuartzIndval <- indval(as.matrix(PlantSpecies1), clustQuartz, type= "long")
summary(QuartzIndval)
## cluster indicator_value probability
## Holcus.spp. 1 0.7898 0.013
##
## Sum of probabilities = 44.621
##
## Sum of Indicator Values = 13.99
##
## Sum of Significant Indicator Values = 0.79
##
## Number of Significant Indicators = 1
##
## Significant Indicator Distribution
##
## 1
## 1
gr <- QuartzIndval$maxcls[QuartzIndval$pval<=0.05]
iv <- QuartzIndval$indcls[QuartzIndval$pval<=0.05]
pv <- QuartzIndval$pval[QuartzIndval$pval<=0.05]
fr <- apply(PlantSpecies1[,-1]>0, 2, sum)[QuartzIndval$pval<=0.05]
Quartzindvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
Quartzindvalsummary <- Quartzindvalsummary[order(Quartzindvalsummary$group,
-Quartzindvalsummary$indval),]
print(Quartzindvalsummary)
## group indval pvalue freq
## Holcus.spp. 1 0.7898194 0.013 3
summary(indval(as.matrix(PlantSpecies1), clustQuartz, type= "long"))
## cluster indicator_value probability
## Holcus.spp. 1 0.7898 0.012
##
## Sum of probabilities = 44.675
##
## Sum of Indicator Values = 13.99
##
## Sum of Significant Indicator Values = 0.79
##
## Number of Significant Indicators = 1
##
## Significant Indicator Distribution
##
## 1
## 1
print(indval(as.matrix(PlantSpecies1), clustQuartz, type= "long"))
## $relfrq
## 1 5
## Alopercus.pratensis 0.0 0.07692308
## Anthoxanthum.odoratum 0.0 0.07692308
## Anthyllis.vulneraria 0.0 0.15384615
## Arrhenatherum.elatius 0.0 0.07692308
## Avenula.pratensis 0.0 0.07692308
## Bellis.perennis 0.0 0.23076923
## Brachythecium.mildeanum 0.0 0.07692308
## Bryum.c.f..pallescens 0.0 0.15384615
## Bryum.spp. 0.0 0.15384615
## Calliergonella.cupsidata 0.0 0.15384615
## Campanula.rotundifolia 0.0 0.07692308
## Carex.distans 0.0 0.15384615
## Carex.flacca 0.0 0.23076923
## Carex.panicea 0.0 0.07692308
## Carlina.vulgaris 0.5 0.53846154
## Centaurea.nigra 0.0 0.07692308
## Centaurium.littorale 0.0 0.30769231
## Centaurium.pulchellum 0.0 0.07692308
## Cerastium.fontanum 0.0 0.15384615
## Dactylis.glomerata 0.0 0.07692308
## Dicranella.spp. 0.0 0.07692308
## Equisetum.arvense 0.0 0.07692308
## Equisteum.variegatum 0.0 0.07692308
## Euphrasia.agg 0.0 0.23076923
## Festuca.ovina 0.5 0.30769231
## Festuca.rubra 0.0 0.38461538
## Fissidens.dubius 0.0 0.07692308
## Fissidens.exilis 0.0 0.07692308
## Galium.saxatile 0.5 0.00000000
## Holcus.spp. 1.0 0.61538462
## Holcus.lanatus 0.0 0.23076923
## Homalothecium.lutescens 0.5 0.07692308
## Hypnum.cupressiforme 0.0 0.30769231
## Leontodon.hispidus 0.5 0.15384615
## Leucanthemum.vulgare 0.0 0.30769231
## Linum.catharticum 0.5 0.30769231
## Lotus.corniculatus 0.0 0.30769231
## Lysimachia.maritima 0.0 0.15384615
## Medicago.lupulina 0.0 0.15384615
## Myosotis.arvensis 0.5 0.15384615
## Ononis.repens 0.5 0.38461538
## Pillosella.officinarum 0.5 0.53846154
## Plantago.coronopus 0.5 0.23076923
## Plantago.lanceolata 0.0 0.38461538
## Poa.annua 0.0 0.23076923
## Prunella.vulgaris 0.0 0.07692308
## Pseudoscleropidum.purum 0.5 0.07692308
## Rhytidadelphus.squarrosus 0.5 0.15384615
## Taraxacum.agg. 1.0 0.30769231
## Thymus.polytrichus 0.5 0.53846154
## Trichostomum.crispulum 0.0 0.46153846
## Trifolium.campestre 0.0 0.07692308
## Trifolium.dubium 0.0 0.15384615
## Trifolium.pratense 0.0 0.07692308
## Trifolium.repens 0.0 0.07692308
## Urtica.diocia 0.5 0.00000000
## Zygodon.stirtonii 0.5 0.00000000
##
## $relabu
## 1 5
## Alopercus.pratensis 0.00000000 1.00000000
## Anthoxanthum.odoratum 0.00000000 1.00000000
## Anthyllis.vulneraria 0.00000000 1.00000000
## Arrhenatherum.elatius 0.00000000 1.00000000
## Avenula.pratensis 0.00000000 1.00000000
## Bellis.perennis 0.00000000 1.00000000
## Brachythecium.mildeanum 0.00000000 1.00000000
## Bryum.c.f..pallescens 0.00000000 1.00000000
## Bryum.spp. 0.00000000 1.00000000
## Calliergonella.cupsidata 0.00000000 1.00000000
## Campanula.rotundifolia 0.00000000 1.00000000
## Carex.distans 0.00000000 1.00000000
## Carex.flacca 0.00000000 1.00000000
## Carex.panicea 0.00000000 1.00000000
## Carlina.vulgaris 0.15662651 0.84337349
## Centaurea.nigra 0.00000000 1.00000000
## Centaurium.littorale 0.00000000 1.00000000
## Centaurium.pulchellum 0.00000000 1.00000000
## Cerastium.fontanum 0.00000000 1.00000000
## Dactylis.glomerata 0.00000000 1.00000000
## Dicranella.spp. 0.00000000 1.00000000
## Equisetum.arvense 0.00000000 1.00000000
## Equisteum.variegatum 0.00000000 1.00000000
## Euphrasia.agg 0.00000000 1.00000000
## Festuca.ovina 0.63243243 0.36756757
## Festuca.rubra 0.00000000 1.00000000
## Fissidens.dubius 0.00000000 1.00000000
## Fissidens.exilis 0.00000000 1.00000000
## Galium.saxatile 1.00000000 0.00000000
## Holcus.spp. 0.78981938 0.21018062
## Holcus.lanatus 0.00000000 1.00000000
## Homalothecium.lutescens 0.99047619 0.00952381
## Hypnum.cupressiforme 0.00000000 1.00000000
## Leontodon.hispidus 0.18055556 0.81944444
## Leucanthemum.vulgare 0.00000000 1.00000000
## Linum.catharticum 0.73584906 0.26415094
## Lotus.corniculatus 0.00000000 1.00000000
## Lysimachia.maritima 0.00000000 1.00000000
## Medicago.lupulina 0.00000000 1.00000000
## Myosotis.arvensis 0.88636364 0.11363636
## Ononis.repens 0.06666667 0.93333333
## Pillosella.officinarum 0.43602484 0.56397516
## Plantago.coronopus 0.42807626 0.57192374
## Plantago.lanceolata 0.00000000 1.00000000
## Poa.annua 0.00000000 1.00000000
## Prunella.vulgaris 0.00000000 1.00000000
## Pseudoscleropidum.purum 0.90697674 0.09302326
## Rhytidadelphus.squarrosus 0.91919192 0.08080808
## Taraxacum.agg. 0.73584906 0.26415094
## Thymus.polytrichus 0.04423918 0.95576082
## Trichostomum.crispulum 0.00000000 1.00000000
## Trifolium.campestre 0.00000000 1.00000000
## Trifolium.dubium 0.00000000 1.00000000
## Trifolium.pratense 0.00000000 1.00000000
## Trifolium.repens 0.00000000 1.00000000
## Urtica.diocia 1.00000000 0.00000000
## Zygodon.stirtonii 1.00000000 0.00000000
##
## $indval
## 1 5
## Alopercus.pratensis 0.00000000 0.0769230769
## Anthoxanthum.odoratum 0.00000000 0.0769230769
## Anthyllis.vulneraria 0.00000000 0.1538461538
## Arrhenatherum.elatius 0.00000000 0.0769230769
## Avenula.pratensis 0.00000000 0.0769230769
## Bellis.perennis 0.00000000 0.2307692308
## Brachythecium.mildeanum 0.00000000 0.0769230769
## Bryum.c.f..pallescens 0.00000000 0.1538461538
## Bryum.spp. 0.00000000 0.1538461538
## Calliergonella.cupsidata 0.00000000 0.1538461538
## Campanula.rotundifolia 0.00000000 0.0769230769
## Carex.distans 0.00000000 0.1538461538
## Carex.flacca 0.00000000 0.2307692308
## Carex.panicea 0.00000000 0.0769230769
## Carlina.vulgaris 0.07831325 0.4541241891
## Centaurea.nigra 0.00000000 0.0769230769
## Centaurium.littorale 0.00000000 0.3076923077
## Centaurium.pulchellum 0.00000000 0.0769230769
## Cerastium.fontanum 0.00000000 0.1538461538
## Dactylis.glomerata 0.00000000 0.0769230769
## Dicranella.spp. 0.00000000 0.0769230769
## Equisetum.arvense 0.00000000 0.0769230769
## Equisteum.variegatum 0.00000000 0.0769230769
## Euphrasia.agg 0.00000000 0.2307692308
## Festuca.ovina 0.31621622 0.1130977131
## Festuca.rubra 0.00000000 0.3846153846
## Fissidens.dubius 0.00000000 0.0769230769
## Fissidens.exilis 0.00000000 0.0769230769
## Galium.saxatile 0.50000000 0.0000000000
## Holcus.spp. 0.78981938 0.1293419224
## Holcus.lanatus 0.00000000 0.2307692308
## Homalothecium.lutescens 0.49523810 0.0007326007
## Hypnum.cupressiforme 0.00000000 0.3076923077
## Leontodon.hispidus 0.09027778 0.1260683761
## Leucanthemum.vulgare 0.00000000 0.3076923077
## Linum.catharticum 0.36792453 0.0812772134
## Lotus.corniculatus 0.00000000 0.3076923077
## Lysimachia.maritima 0.00000000 0.1538461538
## Medicago.lupulina 0.00000000 0.1538461538
## Myosotis.arvensis 0.44318182 0.0174825175
## Ononis.repens 0.03333333 0.3589743590
## Pillosella.officinarum 0.21801242 0.3036789298
## Plantago.coronopus 0.21403813 0.1319824023
## Plantago.lanceolata 0.00000000 0.3846153846
## Poa.annua 0.00000000 0.2307692308
## Prunella.vulgaris 0.00000000 0.0769230769
## Pseudoscleropidum.purum 0.45348837 0.0071556351
## Rhytidadelphus.squarrosus 0.45959596 0.0124320124
## Taraxacum.agg. 0.73584906 0.0812772134
## Thymus.polytrichus 0.02211959 0.5146404398
## Trichostomum.crispulum 0.00000000 0.4615384615
## Trifolium.campestre 0.00000000 0.0769230769
## Trifolium.dubium 0.00000000 0.1538461538
## Trifolium.pratense 0.00000000 0.0769230769
## Trifolium.repens 0.00000000 0.0769230769
## Urtica.diocia 0.50000000 0.0000000000
## Zygodon.stirtonii 0.50000000 0.0000000000
##
## $maxcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 2 2 2
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 2 2 2
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 2 2 2
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 2 2 2
## Carex.flacca Carex.panicea Carlina.vulgaris
## 2 2 2
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 2 2 2
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 2 2 2
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 2 2 2
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 1 2 2
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 2 1 1
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 2 1 2
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 2 2 1
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 2 2 2
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 1 2 2
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 1 2 2
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 2 1 1
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 1 2 2
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 2 2 2
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 2 1 1
##
## $indcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 0.07692308 0.07692308 0.15384615
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 0.07692308 0.07692308 0.23076923
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 0.07692308 0.15384615 0.15384615
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.15384615 0.07692308 0.15384615
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.23076923 0.07692308 0.45412419
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 0.07692308 0.30769231 0.07692308
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.15384615 0.07692308 0.07692308
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 0.07692308 0.07692308 0.23076923
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.31621622 0.38461538 0.07692308
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 0.07692308 0.50000000 0.78981938
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.23076923 0.49523810 0.30769231
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.12606838 0.30769231 0.36792453
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.30769231 0.15384615 0.15384615
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.44318182 0.35897436 0.30367893
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 0.21403813 0.38461538 0.23076923
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 0.07692308 0.45348837 0.45959596
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.73584906 0.51464044 0.46153846
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 0.07692308 0.15384615 0.07692308
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 0.07692308 0.50000000 0.50000000
##
## $pval
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1.000 1.000 1.000
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 1.000 1.000 0.895
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1.000 1.000 1.000
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 1.000 1.000 1.000
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.759 1.000 0.507
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 1.000 0.899 1.000
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 1.000 1.000 1.000
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1.000 1.000 1.000
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.692 0.683 1.000
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 1.000 0.110 0.009
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.897 0.142 0.776
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 1.000 0.680 0.710
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.685 0.883 0.872
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.153 0.857 0.932
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 1.000 0.740 1.000
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 1.000 0.140 0.129
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.112 0.550 0.484
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1.000 1.000 1.000
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1.000 0.137 0.132
##
## $error
## [1] 0
##
## attr(,"class")
## [1] "indval"
#From the Quartzindvalsummary and from the automatic summary, Holcus spp. is shown to be the #indicator species for quartz, with an indval value of 0.790 and a low p value of 0.01. #Holcus spp. is the indicator species for Quartz.
#Now to do the same for calcite…
clustCalcite <-cut(PlantChemistry1$Calcite, 5, labels=FALSE)
summary(indval(as.matrix(PlantSpecies1), clustCalcite))
## cluster indicator_value probability
## Holcus.spp. 2 0.7496 0.044
##
## Sum of probabilities = 34.652
##
## Sum of Indicator Values = 13.72
##
## Sum of Significant Indicator Values = 0.75
##
## Number of Significant Indicators = 1
##
## Significant Indicator Distribution
##
## 2
## 1
CalciteIndval <- indval(as.matrix(PlantSpecies1), clustCalcite, type= "long")
gr <- CalciteIndval$maxcls[CalciteIndval$pval<=0.05]
iv <- CalciteIndval$indcls[CalciteIndval$pval<=0.05]
pv <- CalciteIndval$pval[CalciteIndval$pval<=0.05]
fr <- apply(PlantSpecies1[,-1]>0, 2, sum)[CalciteIndval$pval<=0.05]
CalciteIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
CalciteIndvalsummary <- CalciteIndvalsummary[order(CalciteIndvalsummary$group,
-CalciteIndvalsummary$indval),]
print(CalciteIndvalsummary)
## group indval pvalue freq
## Holcus.spp. 2 0.7496405 0.029 3
print(indval(as.matrix(PlantSpecies1), clustCalcite))
## $relfrq
## 1 5
## Alopercus.pratensis 0.00 0.09090909
## Anthoxanthum.odoratum 0.25 0.00000000
## Anthyllis.vulneraria 0.50 0.00000000
## Arrhenatherum.elatius 0.00 0.09090909
## Avenula.pratensis 0.00 0.09090909
## Bellis.perennis 0.25 0.18181818
## Brachythecium.mildeanum 0.25 0.00000000
## Bryum.c.f..pallescens 0.00 0.18181818
## Bryum.spp. 0.25 0.09090909
## Calliergonella.cupsidata 0.00 0.18181818
## Campanula.rotundifolia 0.25 0.00000000
## Carex.distans 0.25 0.09090909
## Carex.flacca 0.00 0.27272727
## Carex.panicea 0.25 0.00000000
## Carlina.vulgaris 0.25 0.63636364
## Centaurea.nigra 0.00 0.09090909
## Centaurium.littorale 0.50 0.18181818
## Centaurium.pulchellum 0.25 0.00000000
## Cerastium.fontanum 0.25 0.09090909
## Dactylis.glomerata 0.00 0.09090909
## Dicranella.spp. 0.00 0.09090909
## Equisetum.arvense 0.25 0.00000000
## Equisteum.variegatum 0.25 0.00000000
## Euphrasia.agg 0.00 0.27272727
## Festuca.ovina 0.25 0.36363636
## Festuca.rubra 0.50 0.27272727
## Fissidens.dubius 0.00 0.09090909
## Fissidens.exilis 0.00 0.09090909
## Galium.saxatile 0.00 0.09090909
## Holcus.spp. 0.25 0.81818182
## Holcus.lanatus 0.25 0.18181818
## Homalothecium.lutescens 0.00 0.18181818
## Hypnum.cupressiforme 0.25 0.27272727
## Leontodon.hispidus 0.00 0.27272727
## Leucanthemum.vulgare 0.50 0.18181818
## Linum.catharticum 0.25 0.36363636
## Lotus.corniculatus 0.00 0.36363636
## Lysimachia.maritima 0.25 0.09090909
## Medicago.lupulina 0.25 0.09090909
## Myosotis.arvensis 0.00 0.27272727
## Ononis.repens 0.75 0.27272727
## Pillosella.officinarum 0.25 0.63636364
## Plantago.coronopus 0.25 0.27272727
## Plantago.lanceolata 0.25 0.36363636
## Poa.annua 0.50 0.09090909
## Prunella.vulgaris 0.00 0.09090909
## Pseudoscleropidum.purum 0.25 0.09090909
## Rhytidadelphus.squarrosus 0.00 0.27272727
## Taraxacum.agg. 0.00 0.54545455
## Thymus.polytrichus 0.50 0.54545455
## Trichostomum.crispulum 0.50 0.36363636
## Trifolium.campestre 0.25 0.00000000
## Trifolium.dubium 0.00 0.18181818
## Trifolium.pratense 0.00 0.09090909
## Trifolium.repens 0.00 0.09090909
## Urtica.diocia 0.00 0.09090909
## Zygodon.stirtonii 0.00 0.09090909
##
## $relabu
## 1 5
## Alopercus.pratensis 0.0000000 1.000000000
## Anthoxanthum.odoratum 1.0000000 0.000000000
## Anthyllis.vulneraria 1.0000000 0.000000000
## Arrhenatherum.elatius 0.0000000 1.000000000
## Avenula.pratensis 0.0000000 1.000000000
## Bellis.perennis 0.1157895 0.884210526
## Brachythecium.mildeanum 1.0000000 0.000000000
## Bryum.c.f..pallescens 0.0000000 1.000000000
## Bryum.spp. 0.8918919 0.108108108
## Calliergonella.cupsidata 0.0000000 1.000000000
## Campanula.rotundifolia 1.0000000 0.000000000
## Carex.distans 0.8614458 0.138554217
## Carex.flacca 0.0000000 1.000000000
## Carex.panicea 1.0000000 0.000000000
## Carlina.vulgaris 0.2000000 0.800000000
## Centaurea.nigra 0.0000000 1.000000000
## Centaurium.littorale 0.7857143 0.214285714
## Centaurium.pulchellum 1.0000000 0.000000000
## Cerastium.fontanum 0.7333333 0.266666667
## Dactylis.glomerata 0.0000000 1.000000000
## Dicranella.spp. 0.0000000 1.000000000
## Equisetum.arvense 1.0000000 0.000000000
## Equisteum.variegatum 1.0000000 0.000000000
## Euphrasia.agg 0.0000000 1.000000000
## Festuca.ovina 0.3979740 0.602026049
## Festuca.rubra 0.1594203 0.840579710
## Fissidens.dubius 0.0000000 1.000000000
## Fissidens.exilis 0.0000000 1.000000000
## Galium.saxatile 0.0000000 1.000000000
## Holcus.spp. 0.0837727 0.916227299
## Holcus.lanatus 0.8181818 0.181818182
## Homalothecium.lutescens 0.0000000 1.000000000
## Hypnum.cupressiforme 0.6197183 0.380281690
## Leontodon.hispidus 0.0000000 1.000000000
## Leucanthemum.vulgare 0.5076923 0.492307692
## Linum.catharticum 0.2340426 0.765957447
## Lotus.corniculatus 0.0000000 1.000000000
## Lysimachia.maritima 0.9909910 0.009009009
## Medicago.lupulina 0.9804114 0.019588639
## Myosotis.arvensis 0.0000000 1.000000000
## Ononis.repens 0.8276527 0.172347267
## Pillosella.officinarum 0.3750468 0.624953166
## Plantago.coronopus 0.8174707 0.182529335
## Plantago.lanceolata 0.2123552 0.787644788
## Poa.annua 0.8518519 0.148148148
## Prunella.vulgaris 0.0000000 1.000000000
## Pseudoscleropidum.purum 0.6470588 0.352941176
## Rhytidadelphus.squarrosus 0.0000000 1.000000000
## Taraxacum.agg. 0.0000000 1.000000000
## Thymus.polytrichus 0.7122739 0.287726080
## Trichostomum.crispulum 0.3882353 0.611764706
## Trifolium.campestre 1.0000000 0.000000000
## Trifolium.dubium 0.0000000 1.000000000
## Trifolium.pratense 0.0000000 1.000000000
## Trifolium.repens 0.0000000 1.000000000
## Urtica.diocia 0.0000000 1.000000000
## Zygodon.stirtonii 0.0000000 1.000000000
##
## $indval
## 1 5
## Alopercus.pratensis 0.00000000 0.0909090909
## Anthoxanthum.odoratum 0.25000000 0.0000000000
## Anthyllis.vulneraria 0.50000000 0.0000000000
## Arrhenatherum.elatius 0.00000000 0.0909090909
## Avenula.pratensis 0.00000000 0.0909090909
## Bellis.perennis 0.02894737 0.1607655502
## Brachythecium.mildeanum 0.25000000 0.0000000000
## Bryum.c.f..pallescens 0.00000000 0.1818181818
## Bryum.spp. 0.22297297 0.0098280098
## Calliergonella.cupsidata 0.00000000 0.1818181818
## Campanula.rotundifolia 0.25000000 0.0000000000
## Carex.distans 0.21536145 0.0125958379
## Carex.flacca 0.00000000 0.2727272727
## Carex.panicea 0.25000000 0.0000000000
## Carlina.vulgaris 0.05000000 0.5090909091
## Centaurea.nigra 0.00000000 0.0909090909
## Centaurium.littorale 0.39285714 0.0389610390
## Centaurium.pulchellum 0.25000000 0.0000000000
## Cerastium.fontanum 0.18333333 0.0242424242
## Dactylis.glomerata 0.00000000 0.0909090909
## Dicranella.spp. 0.00000000 0.0909090909
## Equisetum.arvense 0.25000000 0.0000000000
## Equisteum.variegatum 0.25000000 0.0000000000
## Euphrasia.agg 0.00000000 0.2727272727
## Festuca.ovina 0.09949349 0.2189185633
## Festuca.rubra 0.07971014 0.2292490119
## Fissidens.dubius 0.00000000 0.0909090909
## Fissidens.exilis 0.00000000 0.0909090909
## Galium.saxatile 0.00000000 0.0909090909
## Holcus.spp. 0.02094318 0.7496405177
## Holcus.lanatus 0.20454545 0.0330578512
## Homalothecium.lutescens 0.00000000 0.1818181818
## Hypnum.cupressiforme 0.15492958 0.1037131882
## Leontodon.hispidus 0.00000000 0.2727272727
## Leucanthemum.vulgare 0.25384615 0.0895104895
## Linum.catharticum 0.05851064 0.2785299807
## Lotus.corniculatus 0.00000000 0.3636363636
## Lysimachia.maritima 0.24774775 0.0008190008
## Medicago.lupulina 0.24510284 0.0017807853
## Myosotis.arvensis 0.00000000 0.2727272727
## Ononis.repens 0.62073955 0.0470038001
## Pillosella.officinarum 0.09376171 0.3976974693
## Plantago.coronopus 0.20436767 0.0497807277
## Plantago.lanceolata 0.05308880 0.2864162864
## Poa.annua 0.42592593 0.0134680135
## Prunella.vulgaris 0.00000000 0.0909090909
## Pseudoscleropidum.purum 0.16176471 0.0320855615
## Rhytidadelphus.squarrosus 0.00000000 0.2727272727
## Taraxacum.agg. 0.00000000 0.5454545455
## Thymus.polytrichus 0.35613696 0.1569414984
## Trichostomum.crispulum 0.19411765 0.2224598930
## Trifolium.campestre 0.25000000 0.0000000000
## Trifolium.dubium 0.00000000 0.1818181818
## Trifolium.pratense 0.00000000 0.0909090909
## Trifolium.repens 0.00000000 0.0909090909
## Urtica.diocia 0.00000000 0.0909090909
## Zygodon.stirtonii 0.00000000 0.0909090909
##
## $maxcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 2 1 1
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 2 2 2
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1 2 1
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 2 1 1
## Carex.flacca Carex.panicea Carlina.vulgaris
## 2 1 2
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 2 1 1
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 1 2 2
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1 1 2
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 2 2 2
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 2 2 2
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 1 2 1
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 2 1 2
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 2 1 1
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 2 1 2
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 1 2 1
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 2 1 2
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 2 1 2
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1 2 2
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 2 2 2
##
## $indcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 0.09090909 0.25000000 0.50000000
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 0.09090909 0.09090909 0.16076555
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 0.25000000 0.18181818 0.22297297
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.18181818 0.25000000 0.21536145
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.27272727 0.25000000 0.50909091
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 0.09090909 0.39285714 0.25000000
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.18333333 0.09090909 0.09090909
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 0.25000000 0.25000000 0.27272727
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.21891856 0.22924901 0.09090909
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 0.09090909 0.09090909 0.74964052
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.20454545 0.18181818 0.15492958
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.27272727 0.25384615 0.27852998
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.36363636 0.24774775 0.24510284
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.27272727 0.62073955 0.39769747
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 0.20436767 0.28641629 0.42592593
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 0.09090909 0.16176471 0.27272727
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.54545455 0.35613696 0.22245989
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 0.25000000 0.18181818 0.09090909
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 0.09090909 0.09090909 0.09090909
##
## $pval
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1.000 0.264 0.057
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 1.000 1.000 1.000
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 0.273 0.806 0.265
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.782 0.267 0.272
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.459 0.261 0.279
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 1.000 0.145 0.254
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.469 1.000 1.000
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 0.247 0.265 0.512
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.788 0.749 1.000
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 1.000 1.000 0.041
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.680 0.784 0.870
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.471 0.511 0.688
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.423 0.256 0.257
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.509 0.059 0.651
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 0.861 0.728 0.107
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 1.000 1.000 0.517
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.181 0.592 0.913
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 0.253 0.788 1.000
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1.000 1.000 1.000
##
## $error
## [1] 0
##
## attr(,"class")
## [1] "indval"
#Holcus spp. is also the indicator species for calcite, with an indval value of 0.750 and #a significant p value of 0.043. Anthyllis vulneraria is also reported in the analysis, #but it has a lower indval value and a higher p value, so it is not reported in the text.
#After attempting an indval calculation for Gehlenite, no species came up. From now on, #only successful analyses, in which at least one species was determined as an indicator #species, will be included.
clustPericlase <-cut(PlantChemistry1$Periclase, 5, labels=FALSE)
PericlaseIndval <- indval(as.matrix(PlantSpecies1), clustPericlase, type= "long")
gr <- PericlaseIndval$maxcls[PericlaseIndval$pval<=0.05]
iv <- PericlaseIndval$indcls[PericlaseIndval$pval<=0.05]
pv <- PericlaseIndval$pval[PericlaseIndval$pval<=0.05]
fr <- apply(PlantSpecies1[,-1]>0, 2, sum)[PericlaseIndval$pval<=0.05]
PericlaseIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
PericlaseIndvalsummary <- PericlaseIndvalsummary[order(PericlaseIndvalsummary$group,
-PericlaseIndvalsummary$indval),]
print(PericlaseIndvalsummary)
## group indval pvalue freq
## Pillosella.officinarum 2 0.890921 0.032 4
summary(indval(as.matrix(PlantSpecies1), clustPericlase))
## cluster indicator_value probability
## Pillosella.officinarum 2 0.8909 0.033
##
## Sum of probabilities = 40.696
##
## Sum of Indicator Values = 13.3
##
## Sum of Significant Indicator Values = 0.89
##
## Number of Significant Indicators = 1
##
## Significant Indicator Distribution
##
## 2
## 1
print(indval(as.matrix(PlantSpecies1), clustPericlase))
## $relfrq
## 1 5
## Alopercus.pratensis 0.08333333 0.0000000
## Anthoxanthum.odoratum 0.08333333 0.0000000
## Anthyllis.vulneraria 0.16666667 0.0000000
## Arrhenatherum.elatius 0.08333333 0.0000000
## Avenula.pratensis 0.08333333 0.0000000
## Bellis.perennis 0.25000000 0.0000000
## Brachythecium.mildeanum 0.08333333 0.0000000
## Bryum.c.f..pallescens 0.08333333 0.3333333
## Bryum.spp. 0.16666667 0.0000000
## Calliergonella.cupsidata 0.16666667 0.0000000
## Campanula.rotundifolia 0.08333333 0.0000000
## Carex.distans 0.16666667 0.0000000
## Carex.flacca 0.25000000 0.0000000
## Carex.panicea 0.08333333 0.0000000
## Carlina.vulgaris 0.50000000 0.6666667
## Centaurea.nigra 0.08333333 0.0000000
## Centaurium.littorale 0.33333333 0.0000000
## Centaurium.pulchellum 0.08333333 0.0000000
## Cerastium.fontanum 0.16666667 0.0000000
## Dactylis.glomerata 0.08333333 0.0000000
## Dicranella.spp. 0.00000000 0.3333333
## Equisetum.arvense 0.08333333 0.0000000
## Equisteum.variegatum 0.08333333 0.0000000
## Euphrasia.agg 0.25000000 0.0000000
## Festuca.ovina 0.33333333 0.3333333
## Festuca.rubra 0.41666667 0.0000000
## Fissidens.dubius 0.08333333 0.0000000
## Fissidens.exilis 0.00000000 0.3333333
## Galium.saxatile 0.00000000 0.3333333
## Holcus.spp. 0.75000000 0.3333333
## Holcus.lanatus 0.25000000 0.0000000
## Homalothecium.lutescens 0.08333333 0.3333333
## Hypnum.cupressiforme 0.25000000 0.3333333
## Leontodon.hispidus 0.25000000 0.0000000
## Leucanthemum.vulgare 0.33333333 0.0000000
## Linum.catharticum 0.41666667 0.0000000
## Lotus.corniculatus 0.33333333 0.0000000
## Lysimachia.maritima 0.16666667 0.0000000
## Medicago.lupulina 0.16666667 0.0000000
## Myosotis.arvensis 0.08333333 0.6666667
## Ononis.repens 0.41666667 0.3333333
## Pillosella.officinarum 0.41666667 1.0000000
## Plantago.coronopus 0.25000000 0.3333333
## Plantago.lanceolata 0.41666667 0.0000000
## Poa.annua 0.25000000 0.0000000
## Prunella.vulgaris 0.08333333 0.0000000
## Pseudoscleropidum.purum 0.08333333 0.3333333
## Rhytidadelphus.squarrosus 0.16666667 0.3333333
## Taraxacum.agg. 0.33333333 0.6666667
## Thymus.polytrichus 0.50000000 0.6666667
## Trichostomum.crispulum 0.41666667 0.3333333
## Trifolium.campestre 0.08333333 0.0000000
## Trifolium.dubium 0.08333333 0.3333333
## Trifolium.pratense 0.08333333 0.0000000
## Trifolium.repens 0.08333333 0.0000000
## Urtica.diocia 0.00000000 0.3333333
## Zygodon.stirtonii 0.08333333 0.0000000
##
## $relabu
## 1 5
## Alopercus.pratensis 1.00000000 0.00000000
## Anthoxanthum.odoratum 1.00000000 0.00000000
## Anthyllis.vulneraria 1.00000000 0.00000000
## Arrhenatherum.elatius 1.00000000 0.00000000
## Avenula.pratensis 1.00000000 0.00000000
## Bellis.perennis 1.00000000 0.00000000
## Brachythecium.mildeanum 1.00000000 0.00000000
## Bryum.c.f..pallescens 0.23076923 0.76923077
## Bryum.spp. 1.00000000 0.00000000
## Calliergonella.cupsidata 1.00000000 0.00000000
## Campanula.rotundifolia 1.00000000 0.00000000
## Carex.distans 1.00000000 0.00000000
## Carex.flacca 1.00000000 0.00000000
## Carex.panicea 1.00000000 0.00000000
## Carlina.vulgaris 0.46666667 0.53333333
## Centaurea.nigra 1.00000000 0.00000000
## Centaurium.littorale 1.00000000 0.00000000
## Centaurium.pulchellum 1.00000000 0.00000000
## Cerastium.fontanum 1.00000000 0.00000000
## Dactylis.glomerata 1.00000000 0.00000000
## Dicranella.spp. 0.00000000 1.00000000
## Equisetum.arvense 1.00000000 0.00000000
## Equisteum.variegatum 1.00000000 0.00000000
## Euphrasia.agg 1.00000000 0.00000000
## Festuca.ovina 0.48571429 0.51428571
## Festuca.rubra 1.00000000 0.00000000
## Fissidens.dubius 1.00000000 0.00000000
## Fissidens.exilis 0.00000000 1.00000000
## Galium.saxatile 0.00000000 1.00000000
## Holcus.spp. 0.54397394 0.45602606
## Holcus.lanatus 1.00000000 0.00000000
## Homalothecium.lutescens 0.01538462 0.98461538
## Hypnum.cupressiforme 0.31818182 0.68181818
## Leontodon.hispidus 1.00000000 0.00000000
## Leucanthemum.vulgare 1.00000000 0.00000000
## Linum.catharticum 1.00000000 0.00000000
## Lotus.corniculatus 1.00000000 0.00000000
## Lysimachia.maritima 1.00000000 0.00000000
## Medicago.lupulina 1.00000000 0.00000000
## Myosotis.arvensis 0.12500000 0.87500000
## Ononis.repens 0.95789474 0.04210526
## Pillosella.officinarum 0.10907903 0.89092097
## Plantago.coronopus 0.68464730 0.31535270
## Plantago.lanceolata 1.00000000 0.00000000
## Poa.annua 1.00000000 0.00000000
## Prunella.vulgaris 1.00000000 0.00000000
## Pseudoscleropidum.purum 0.14285714 0.85714286
## Rhytidadelphus.squarrosus 0.12500000 0.87500000
## Taraxacum.agg. 0.50000000 0.50000000
## Thymus.polytrichus 0.81849913 0.18150087
## Trichostomum.crispulum 0.45679012 0.54320988
## Trifolium.campestre 1.00000000 0.00000000
## Trifolium.dubium 0.25552050 0.74447950
## Trifolium.pratense 1.00000000 0.00000000
## Trifolium.repens 1.00000000 0.00000000
## Urtica.diocia 0.00000000 1.00000000
## Zygodon.stirtonii 1.00000000 0.00000000
##
## $indval
## 1 5
## Alopercus.pratensis 0.083333333 0.00000000
## Anthoxanthum.odoratum 0.083333333 0.00000000
## Anthyllis.vulneraria 0.166666667 0.00000000
## Arrhenatherum.elatius 0.083333333 0.00000000
## Avenula.pratensis 0.083333333 0.00000000
## Bellis.perennis 0.250000000 0.00000000
## Brachythecium.mildeanum 0.083333333 0.00000000
## Bryum.c.f..pallescens 0.019230769 0.25641026
## Bryum.spp. 0.166666667 0.00000000
## Calliergonella.cupsidata 0.166666667 0.00000000
## Campanula.rotundifolia 0.083333333 0.00000000
## Carex.distans 0.166666667 0.00000000
## Carex.flacca 0.250000000 0.00000000
## Carex.panicea 0.083333333 0.00000000
## Carlina.vulgaris 0.233333333 0.35555556
## Centaurea.nigra 0.083333333 0.00000000
## Centaurium.littorale 0.333333333 0.00000000
## Centaurium.pulchellum 0.083333333 0.00000000
## Cerastium.fontanum 0.166666667 0.00000000
## Dactylis.glomerata 0.083333333 0.00000000
## Dicranella.spp. 0.000000000 0.33333333
## Equisetum.arvense 0.083333333 0.00000000
## Equisteum.variegatum 0.083333333 0.00000000
## Euphrasia.agg 0.250000000 0.00000000
## Festuca.ovina 0.161904762 0.17142857
## Festuca.rubra 0.416666667 0.00000000
## Fissidens.dubius 0.083333333 0.00000000
## Fissidens.exilis 0.000000000 0.33333333
## Galium.saxatile 0.000000000 0.33333333
## Holcus.spp. 0.407980456 0.15200869
## Holcus.lanatus 0.250000000 0.00000000
## Homalothecium.lutescens 0.001282051 0.32820513
## Hypnum.cupressiforme 0.079545455 0.22727273
## Leontodon.hispidus 0.250000000 0.00000000
## Leucanthemum.vulgare 0.333333333 0.00000000
## Linum.catharticum 0.416666667 0.00000000
## Lotus.corniculatus 0.333333333 0.00000000
## Lysimachia.maritima 0.166666667 0.00000000
## Medicago.lupulina 0.166666667 0.00000000
## Myosotis.arvensis 0.010416667 0.58333333
## Ononis.repens 0.399122807 0.01403509
## Pillosella.officinarum 0.045449597 0.89092097
## Plantago.coronopus 0.171161826 0.10511757
## Plantago.lanceolata 0.416666667 0.00000000
## Poa.annua 0.250000000 0.00000000
## Prunella.vulgaris 0.083333333 0.00000000
## Pseudoscleropidum.purum 0.011904762 0.28571429
## Rhytidadelphus.squarrosus 0.020833333 0.29166667
## Taraxacum.agg. 0.166666667 0.33333333
## Thymus.polytrichus 0.409249564 0.12100058
## Trichostomum.crispulum 0.190329218 0.18106996
## Trifolium.campestre 0.083333333 0.00000000
## Trifolium.dubium 0.021293375 0.24815983
## Trifolium.pratense 0.083333333 0.00000000
## Trifolium.repens 0.083333333 0.00000000
## Urtica.diocia 0.000000000 0.33333333
## Zygodon.stirtonii 0.083333333 0.00000000
##
## $maxcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1 1 1
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 1 1 1
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1 2 1
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 1 1 1
## Carex.flacca Carex.panicea Carlina.vulgaris
## 1 1 2
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 1 1 1
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 1 1 2
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1 1 1
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 2 1 1
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 2 2 1
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 1 2 2
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 1 1 1
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 1 1 1
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 2 1 2
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 1 1 1
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 1 2 2
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 2 1 1
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1 2 1
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1 2 1
##
## $indcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 0.08333333 0.08333333 0.16666667
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 0.08333333 0.08333333 0.25000000
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 0.08333333 0.25641026 0.16666667
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.16666667 0.08333333 0.16666667
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.25000000 0.08333333 0.35555556
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 0.08333333 0.33333333 0.08333333
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.16666667 0.08333333 0.33333333
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 0.08333333 0.08333333 0.25000000
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.17142857 0.41666667 0.08333333
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 0.33333333 0.33333333 0.40798046
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.25000000 0.32820513 0.22727273
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.25000000 0.33333333 0.41666667
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.33333333 0.16666667 0.16666667
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.58333333 0.39912281 0.89092097
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 0.17116183 0.41666667 0.25000000
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 0.08333333 0.28571429 0.29166667
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.33333333 0.40924956 0.19032922
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 0.08333333 0.24815983 0.08333333
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 0.08333333 0.33333333 0.08333333
##
## $pval
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1.000 1.000 1.000
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 1.000 1.000 0.868
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1.000 0.388 1.000
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.842 1.000 1.000
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.682 1.000 0.642
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 1.000 0.511 1.000
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 1.000 1.000 0.194
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1.000 1.000 0.727
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.885 0.452 1.000
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 0.200 0.182 0.678
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.706 0.192 0.747
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.697 0.536 0.466
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.492 0.825 0.836
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.060 0.639 0.026
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 1.000 0.414 0.574
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 1.000 0.203 0.211
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.497 0.635 1.000
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1.000 0.378 1.000
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1.000 0.190 1.000
##
## $error
## [1] 0
##
## attr(,"class")
## [1] "indval"
#In the PericlaseIndvalsummary, Pilosella officinarum is reported as an indicator #species. It has an indval number of 0.891 and a low p value of 0.027. Therefore, Pilosella #officinarum is the indicator species for Periclase.
#Looking at Akermanite….
clustAkermanite <-cut(PlantChemistry1$Akermanite, 5, labels=FALSE)
AkermaniteIndval <- indval(as.matrix(PlantSpecies1), clustAkermanite, type= "long")
gr <- AkermaniteIndval$maxcls[AkermaniteIndval$pval<=0.05]
iv <- AkermaniteIndval$indcls[AkermaniteIndval$pval<=0.05]
pv <- AkermaniteIndval$pval[AkermaniteIndval$pval<=0.05]
fr <- apply(PlantSpecies1[,-1]>0, 2, sum)[AkermaniteIndval$pval<=0.05]
AkermaniteIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
AkermaniteIndvalsummary <- AkermaniteIndvalsummary[order(AkermaniteIndvalsummary$group,
-AkermaniteIndvalsummary$indval),]
print(AkermaniteIndvalsummary)
## group indval pvalue freq
## Rhytidadelphus.squarrosus 2 0.6504065 0.034 6
summary(indval(as.matrix(PlantSpecies1), clustAkermanite))
## cluster indicator_value probability
## Rhytidadelphus.squarrosus 2 0.6504 0.035
##
## Sum of probabilities = 38.121
##
## Sum of Indicator Values = 13.67
##
## Sum of Significant Indicator Values = 0.65
##
## Number of Significant Indicators = 1
##
## Significant Indicator Distribution
##
## 2
## 1
print(indval(as.matrix(PlantSpecies1), clustAkermanite))
## $relfrq
## 1 5
## Alopercus.pratensis 0.08333333 0.0000000
## Anthoxanthum.odoratum 0.08333333 0.0000000
## Anthyllis.vulneraria 0.16666667 0.0000000
## Arrhenatherum.elatius 0.00000000 0.3333333
## Avenula.pratensis 0.08333333 0.0000000
## Bellis.perennis 0.25000000 0.0000000
## Brachythecium.mildeanum 0.08333333 0.0000000
## Bryum.c.f..pallescens 0.08333333 0.3333333
## Bryum.spp. 0.16666667 0.0000000
## Calliergonella.cupsidata 0.16666667 0.0000000
## Campanula.rotundifolia 0.08333333 0.0000000
## Carex.distans 0.16666667 0.0000000
## Carex.flacca 0.16666667 0.3333333
## Carex.panicea 0.08333333 0.0000000
## Carlina.vulgaris 0.50000000 0.6666667
## Centaurea.nigra 0.08333333 0.0000000
## Centaurium.littorale 0.25000000 0.3333333
## Centaurium.pulchellum 0.08333333 0.0000000
## Cerastium.fontanum 0.08333333 0.3333333
## Dactylis.glomerata 0.00000000 0.3333333
## Dicranella.spp. 0.08333333 0.0000000
## Equisetum.arvense 0.08333333 0.0000000
## Equisteum.variegatum 0.08333333 0.0000000
## Euphrasia.agg 0.08333333 0.6666667
## Festuca.ovina 0.33333333 0.3333333
## Festuca.rubra 0.33333333 0.3333333
## Fissidens.dubius 0.08333333 0.0000000
## Fissidens.exilis 0.08333333 0.0000000
## Galium.saxatile 0.00000000 0.3333333
## Holcus.spp. 0.58333333 1.0000000
## Holcus.lanatus 0.25000000 0.0000000
## Homalothecium.lutescens 0.08333333 0.3333333
## Hypnum.cupressiforme 0.25000000 0.3333333
## Leontodon.hispidus 0.16666667 0.3333333
## Leucanthemum.vulgare 0.33333333 0.0000000
## Linum.catharticum 0.25000000 0.6666667
## Lotus.corniculatus 0.25000000 0.3333333
## Lysimachia.maritima 0.16666667 0.0000000
## Medicago.lupulina 0.16666667 0.0000000
## Myosotis.arvensis 0.16666667 0.3333333
## Ononis.repens 0.41666667 0.3333333
## Pillosella.officinarum 0.50000000 0.6666667
## Plantago.coronopus 0.25000000 0.3333333
## Plantago.lanceolata 0.25000000 0.6666667
## Poa.annua 0.25000000 0.0000000
## Prunella.vulgaris 0.00000000 0.3333333
## Pseudoscleropidum.purum 0.08333333 0.3333333
## Rhytidadelphus.squarrosus 0.08333333 0.6666667
## Taraxacum.agg. 0.33333333 0.6666667
## Thymus.polytrichus 0.58333333 0.3333333
## Trichostomum.crispulum 0.41666667 0.3333333
## Trifolium.campestre 0.08333333 0.0000000
## Trifolium.dubium 0.08333333 0.3333333
## Trifolium.pratense 0.00000000 0.3333333
## Trifolium.repens 0.08333333 0.0000000
## Urtica.diocia 0.00000000 0.3333333
## Zygodon.stirtonii 0.08333333 0.0000000
##
## $relabu
## 1 5
## Alopercus.pratensis 1.00000000 0.00000000
## Anthoxanthum.odoratum 1.00000000 0.00000000
## Anthyllis.vulneraria 1.00000000 0.00000000
## Arrhenatherum.elatius 0.00000000 1.00000000
## Avenula.pratensis 1.00000000 0.00000000
## Bellis.perennis 1.00000000 0.00000000
## Brachythecium.mildeanum 1.00000000 0.00000000
## Bryum.c.f..pallescens 0.17241379 0.82758621
## Bryum.spp. 1.00000000 0.00000000
## Calliergonella.cupsidata 1.00000000 0.00000000
## Campanula.rotundifolia 1.00000000 0.00000000
## Carex.distans 1.00000000 0.00000000
## Carex.flacca 0.77142857 0.22857143
## Carex.panicea 1.00000000 0.00000000
## Carlina.vulgaris 0.20000000 0.80000000
## Centaurea.nigra 1.00000000 0.00000000
## Centaurium.littorale 0.76470588 0.23529412
## Centaurium.pulchellum 1.00000000 0.00000000
## Cerastium.fontanum 0.20000000 0.80000000
## Dactylis.glomerata 0.00000000 1.00000000
## Dicranella.spp. 1.00000000 0.00000000
## Equisetum.arvense 1.00000000 0.00000000
## Equisteum.variegatum 1.00000000 0.00000000
## Euphrasia.agg 0.16071429 0.83928571
## Festuca.ovina 0.48571429 0.51428571
## Festuca.rubra 0.31250000 0.68750000
## Fissidens.dubius 1.00000000 0.00000000
## Fissidens.exilis 1.00000000 0.00000000
## Galium.saxatile 0.00000000 1.00000000
## Holcus.spp. 0.36623377 0.63376623
## Holcus.lanatus 1.00000000 0.00000000
## Homalothecium.lutescens 0.01538462 0.98461538
## Hypnum.cupressiforme 0.60655738 0.39344262
## Leontodon.hispidus 0.09473684 0.90526316
## Leucanthemum.vulgare 1.00000000 0.00000000
## Linum.catharticum 0.16981132 0.83018868
## Lotus.corniculatus 0.78723404 0.21276596
## Lysimachia.maritima 1.00000000 0.00000000
## Medicago.lupulina 1.00000000 0.00000000
## Myosotis.arvensis 0.17241379 0.82758621
## Ononis.repens 0.95789474 0.04210526
## Pillosella.officinarum 0.54746424 0.45253576
## Plantago.coronopus 0.68464730 0.31535270
## Plantago.lanceolata 0.17808219 0.82191781
## Poa.annua 1.00000000 0.00000000
## Prunella.vulgaris 0.00000000 1.00000000
## Pseudoscleropidum.purum 0.14285714 0.85714286
## Rhytidadelphus.squarrosus 0.02439024 0.97560976
## Taraxacum.agg. 0.50000000 0.50000000
## Thymus.polytrichus 0.38444807 0.61555193
## Trichostomum.crispulum 0.63636364 0.36363636
## Trifolium.campestre 1.00000000 0.00000000
## Trifolium.dubium 0.15404700 0.84595300
## Trifolium.pratense 0.00000000 1.00000000
## Trifolium.repens 1.00000000 0.00000000
## Urtica.diocia 0.00000000 1.00000000
## Zygodon.stirtonii 1.00000000 0.00000000
##
## $indval
## 1 5
## Alopercus.pratensis 0.083333333 0.00000000
## Anthoxanthum.odoratum 0.083333333 0.00000000
## Anthyllis.vulneraria 0.166666667 0.00000000
## Arrhenatherum.elatius 0.000000000 0.33333333
## Avenula.pratensis 0.083333333 0.00000000
## Bellis.perennis 0.250000000 0.00000000
## Brachythecium.mildeanum 0.083333333 0.00000000
## Bryum.c.f..pallescens 0.014367816 0.27586207
## Bryum.spp. 0.166666667 0.00000000
## Calliergonella.cupsidata 0.166666667 0.00000000
## Campanula.rotundifolia 0.083333333 0.00000000
## Carex.distans 0.166666667 0.00000000
## Carex.flacca 0.128571429 0.07619048
## Carex.panicea 0.083333333 0.00000000
## Carlina.vulgaris 0.100000000 0.53333333
## Centaurea.nigra 0.083333333 0.00000000
## Centaurium.littorale 0.191176471 0.07843137
## Centaurium.pulchellum 0.083333333 0.00000000
## Cerastium.fontanum 0.016666667 0.26666667
## Dactylis.glomerata 0.000000000 0.33333333
## Dicranella.spp. 0.083333333 0.00000000
## Equisetum.arvense 0.083333333 0.00000000
## Equisteum.variegatum 0.083333333 0.00000000
## Euphrasia.agg 0.013392857 0.55952381
## Festuca.ovina 0.161904762 0.17142857
## Festuca.rubra 0.104166667 0.22916667
## Fissidens.dubius 0.083333333 0.00000000
## Fissidens.exilis 0.083333333 0.00000000
## Galium.saxatile 0.000000000 0.33333333
## Holcus.spp. 0.213636364 0.63376623
## Holcus.lanatus 0.250000000 0.00000000
## Homalothecium.lutescens 0.001282051 0.32820513
## Hypnum.cupressiforme 0.151639344 0.13114754
## Leontodon.hispidus 0.015789474 0.30175439
## Leucanthemum.vulgare 0.333333333 0.00000000
## Linum.catharticum 0.042452830 0.55345912
## Lotus.corniculatus 0.196808511 0.07092199
## Lysimachia.maritima 0.166666667 0.00000000
## Medicago.lupulina 0.166666667 0.00000000
## Myosotis.arvensis 0.028735632 0.27586207
## Ononis.repens 0.399122807 0.01403509
## Pillosella.officinarum 0.273732120 0.30169051
## Plantago.coronopus 0.171161826 0.10511757
## Plantago.lanceolata 0.044520548 0.54794521
## Poa.annua 0.250000000 0.00000000
## Prunella.vulgaris 0.000000000 0.33333333
## Pseudoscleropidum.purum 0.011904762 0.28571429
## Rhytidadelphus.squarrosus 0.002032520 0.65040650
## Taraxacum.agg. 0.166666667 0.33333333
## Thymus.polytrichus 0.224261374 0.20518398
## Trichostomum.crispulum 0.265151515 0.12121212
## Trifolium.campestre 0.083333333 0.00000000
## Trifolium.dubium 0.012837250 0.28198433
## Trifolium.pratense 0.000000000 0.33333333
## Trifolium.repens 0.083333333 0.00000000
## Urtica.diocia 0.000000000 0.33333333
## Zygodon.stirtonii 0.083333333 0.00000000
##
## $maxcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1 1 1
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 2 1 1
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1 2 1
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 1 1 1
## Carex.flacca Carex.panicea Carlina.vulgaris
## 1 1 2
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 1 1 1
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 2 2 1
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1 1 2
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 2 2 1
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 1 2 2
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 1 2 1
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 2 1 2
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 1 1 1
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 2 1 2
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 1 2 1
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 2 2 2
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 2 1 1
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1 2 2
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1 2 1
##
## $indcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 0.08333333 0.08333333 0.16666667
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 0.33333333 0.08333333 0.25000000
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 0.08333333 0.27586207 0.16666667
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.16666667 0.08333333 0.16666667
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.12857143 0.08333333 0.53333333
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 0.08333333 0.19117647 0.08333333
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.26666667 0.33333333 0.08333333
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 0.08333333 0.08333333 0.55952381
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.17142857 0.22916667 0.08333333
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 0.08333333 0.33333333 0.63376623
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.25000000 0.32820513 0.15163934
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.30175439 0.33333333 0.55345912
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.19680851 0.16666667 0.16666667
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.27586207 0.39912281 0.30169051
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 0.17116183 0.54794521 0.25000000
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 0.33333333 0.28571429 0.65040650
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.33333333 0.22426137 0.26515152
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 0.08333333 0.28198433 0.33333333
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 0.08333333 0.33333333 0.08333333
##
## $pval
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1.000 1.000 1.000
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 0.207 1.000 0.867
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1.000 0.210 1.000
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.813 1.000 1.000
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.863 1.000 0.182
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 1.000 1.000 1.000
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.364 0.201 1.000
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1.000 1.000 0.090
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.909 0.868 1.000
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 1.000 0.171 0.207
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.713 0.174 1.000
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.210 0.502 0.089
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.897 0.823 0.849
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.224 0.617 0.935
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 1.000 0.100 0.558
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 0.206 0.196 0.034
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.485 1.000 0.733
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1.000 0.188 0.201
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1.000 0.184 1.000
##
## $error
## [1] 0
##
## attr(,"class")
## [1] "indval"
#Rhytidiadelphus squarrosus is reported as the indicator species for Akermanite, with an #indval score of 0.650 and a p value of 0.024.
clustNitratine <-cut(PlantChemistry1$Nitratine, 5, labels=FALSE)
NitratineIndval <- indval(as.matrix(PlantSpecies1), clustNitratine, type= "long")
gr <- NitratineIndval$maxcls[NitratineIndval$pval<=0.05]
iv <- NitratineIndval$indcls[NitratineIndval$pval<=0.05]
pv <- NitratineIndval$pval[NitratineIndval$pval<=0.05]
fr <- apply(PlantSpecies1[,-1]>0, 2, sum)[NitratineIndval$pval<=0.05]
NitratineIndvalsummary <- data.frame(group=gr, indval=iv, pvalue=pv, freq=fr)
NitratineIndvalsummary <- NitratineIndvalsummary [order
(NitratineIndvalsummary$group, -NitratineIndvalsummary$indval),]
print(NitratineIndvalsummary)
## group indval pvalue freq
## Pillosella.officinarum 2 0.8597082 0.008 4
summary(indval(as.matrix(PlantSpecies1), clustNitratine))
## cluster indicator_value probability
## Pillosella.officinarum 2 0.8597 0.007
##
## Sum of probabilities = 43.528
##
## Sum of Indicator Values = 10.94
##
## Sum of Significant Indicator Values = 0.86
##
## Number of Significant Indicators = 1
##
## Significant Indicator Distribution
##
## 2
## 1
print(indval(as.matrix(PlantSpecies1), clustNitratine))
## $relfrq
## 1 5
## Alopercus.pratensis 0.1 0.0
## Anthoxanthum.odoratum 0.1 0.0
## Anthyllis.vulneraria 0.2 0.0
## Arrhenatherum.elatius 0.1 0.0
## Avenula.pratensis 0.1 0.0
## Bellis.perennis 0.2 0.2
## Brachythecium.mildeanum 0.1 0.0
## Bryum.c.f..pallescens 0.2 0.0
## Bryum.spp. 0.2 0.0
## Calliergonella.cupsidata 0.2 0.0
## Campanula.rotundifolia 0.1 0.0
## Carex.distans 0.1 0.2
## Carex.flacca 0.2 0.2
## Carex.panicea 0.1 0.0
## Carlina.vulgaris 0.5 0.6
## Centaurea.nigra 0.0 0.2
## Centaurium.littorale 0.3 0.2
## Centaurium.pulchellum 0.1 0.0
## Cerastium.fontanum 0.2 0.0
## Dactylis.glomerata 0.1 0.0
## Dicranella.spp. 0.1 0.0
## Equisetum.arvense 0.1 0.0
## Equisteum.variegatum 0.1 0.0
## Euphrasia.agg 0.2 0.2
## Festuca.ovina 0.3 0.4
## Festuca.rubra 0.3 0.4
## Fissidens.dubius 0.1 0.0
## Fissidens.exilis 0.1 0.0
## Galium.saxatile 0.0 0.2
## Holcus.spp. 0.6 0.8
## Holcus.lanatus 0.2 0.2
## Homalothecium.lutescens 0.1 0.2
## Hypnum.cupressiforme 0.2 0.4
## Leontodon.hispidus 0.2 0.2
## Leucanthemum.vulgare 0.2 0.4
## Linum.catharticum 0.4 0.2
## Lotus.corniculatus 0.2 0.4
## Lysimachia.maritima 0.1 0.2
## Medicago.lupulina 0.1 0.2
## Myosotis.arvensis 0.1 0.4
## Ononis.repens 0.4 0.4
## Pillosella.officinarum 0.3 1.0
## Plantago.coronopus 0.2 0.4
## Plantago.lanceolata 0.4 0.2
## Poa.annua 0.2 0.2
## Prunella.vulgaris 0.1 0.0
## Pseudoscleropidum.purum 0.1 0.2
## Rhytidadelphus.squarrosus 0.2 0.2
## Taraxacum.agg. 0.3 0.6
## Thymus.polytrichus 0.6 0.4
## Trichostomum.crispulum 0.4 0.4
## Trifolium.campestre 0.1 0.0
## Trifolium.dubium 0.1 0.2
## Trifolium.pratense 0.1 0.0
## Trifolium.repens 0.1 0.0
## Urtica.diocia 0.0 0.2
## Zygodon.stirtonii 0.1 0.0
##
## $relabu
## 1 5
## Alopercus.pratensis 1.00000000 0.00000000
## Anthoxanthum.odoratum 1.00000000 0.00000000
## Anthyllis.vulneraria 1.00000000 0.00000000
## Arrhenatherum.elatius 1.00000000 0.00000000
## Avenula.pratensis 1.00000000 0.00000000
## Bellis.perennis 0.33333333 0.66666667
## Brachythecium.mildeanum 1.00000000 0.00000000
## Bryum.c.f..pallescens 1.00000000 0.00000000
## Bryum.spp. 1.00000000 0.00000000
## Calliergonella.cupsidata 1.00000000 0.00000000
## Campanula.rotundifolia 1.00000000 0.00000000
## Carex.distans 0.53061224 0.46938776
## Carex.flacca 0.81250000 0.18750000
## Carex.panicea 1.00000000 0.00000000
## Carlina.vulgaris 0.53191489 0.46808511
## Centaurea.nigra 0.00000000 1.00000000
## Centaurium.littorale 0.47368421 0.52631579
## Centaurium.pulchellum 1.00000000 0.00000000
## Cerastium.fontanum 1.00000000 0.00000000
## Dactylis.glomerata 1.00000000 0.00000000
## Dicranella.spp. 1.00000000 0.00000000
## Equisetum.arvense 1.00000000 0.00000000
## Equisteum.variegatum 1.00000000 0.00000000
## Euphrasia.agg 0.39495798 0.60504202
## Festuca.ovina 0.49132948 0.50867052
## Festuca.rubra 0.26530612 0.73469388
## Fissidens.dubius 1.00000000 0.00000000
## Fissidens.exilis 1.00000000 0.00000000
## Galium.saxatile 0.00000000 1.00000000
## Holcus.spp. 0.38356164 0.61643836
## Holcus.lanatus 0.56756757 0.43243243
## Homalothecium.lutescens 0.03030303 0.96969697
## Hypnum.cupressiforme 0.34375000 0.65625000
## Leontodon.hispidus 0.58441558 0.41558442
## Leucanthemum.vulgare 0.15789474 0.84210526
## Linum.catharticum 0.90476190 0.09523810
## Lotus.corniculatus 0.06576728 0.93423272
## Lysimachia.maritima 0.95238095 0.04761905
## Medicago.lupulina 0.90099010 0.09900990
## Myosotis.arvensis 0.22222222 0.77777778
## Ononis.repens 0.95744681 0.04255319
## Pillosella.officinarum 0.14029181 0.85970819
## Plantago.coronopus 0.45454545 0.54545455
## Plantago.lanceolata 0.47368421 0.52631579
## Poa.annua 0.51111111 0.48888889
## Prunella.vulgaris 1.00000000 0.00000000
## Pseudoscleropidum.purum 0.25000000 0.75000000
## Rhytidadelphus.squarrosus 0.22222222 0.77777778
## Taraxacum.agg. 0.33333333 0.66666667
## Thymus.polytrichus 0.71280277 0.28719723
## Trichostomum.crispulum 0.37142857 0.62857143
## Trifolium.campestre 1.00000000 0.00000000
## Trifolium.dubium 0.40703518 0.59296482
## Trifolium.pratense 1.00000000 0.00000000
## Trifolium.repens 1.00000000 0.00000000
## Urtica.diocia 0.00000000 1.00000000
## Zygodon.stirtonii 1.00000000 0.00000000
##
## $indval
## 1 5
## Alopercus.pratensis 0.100000000 0.00000000
## Anthoxanthum.odoratum 0.100000000 0.00000000
## Anthyllis.vulneraria 0.200000000 0.00000000
## Arrhenatherum.elatius 0.100000000 0.00000000
## Avenula.pratensis 0.100000000 0.00000000
## Bellis.perennis 0.066666667 0.13333333
## Brachythecium.mildeanum 0.100000000 0.00000000
## Bryum.c.f..pallescens 0.200000000 0.00000000
## Bryum.spp. 0.200000000 0.00000000
## Calliergonella.cupsidata 0.200000000 0.00000000
## Campanula.rotundifolia 0.100000000 0.00000000
## Carex.distans 0.053061224 0.09387755
## Carex.flacca 0.162500000 0.03750000
## Carex.panicea 0.100000000 0.00000000
## Carlina.vulgaris 0.265957447 0.28085106
## Centaurea.nigra 0.000000000 0.20000000
## Centaurium.littorale 0.142105263 0.10526316
## Centaurium.pulchellum 0.100000000 0.00000000
## Cerastium.fontanum 0.200000000 0.00000000
## Dactylis.glomerata 0.100000000 0.00000000
## Dicranella.spp. 0.100000000 0.00000000
## Equisetum.arvense 0.100000000 0.00000000
## Equisteum.variegatum 0.100000000 0.00000000
## Euphrasia.agg 0.078991597 0.12100840
## Festuca.ovina 0.147398844 0.20346821
## Festuca.rubra 0.079591837 0.29387755
## Fissidens.dubius 0.100000000 0.00000000
## Fissidens.exilis 0.100000000 0.00000000
## Galium.saxatile 0.000000000 0.20000000
## Holcus.spp. 0.230136986 0.49315068
## Holcus.lanatus 0.113513514 0.08648649
## Homalothecium.lutescens 0.003030303 0.19393939
## Hypnum.cupressiforme 0.068750000 0.26250000
## Leontodon.hispidus 0.116883117 0.08311688
## Leucanthemum.vulgare 0.031578947 0.33684211
## Linum.catharticum 0.361904762 0.01904762
## Lotus.corniculatus 0.013153457 0.37369309
## Lysimachia.maritima 0.095238095 0.00952381
## Medicago.lupulina 0.090099010 0.01980198
## Myosotis.arvensis 0.022222222 0.31111111
## Ononis.repens 0.382978723 0.01702128
## Pillosella.officinarum 0.042087542 0.85970819
## Plantago.coronopus 0.090909091 0.21818182
## Plantago.lanceolata 0.189473684 0.10526316
## Poa.annua 0.102222222 0.09777778
## Prunella.vulgaris 0.100000000 0.00000000
## Pseudoscleropidum.purum 0.025000000 0.15000000
## Rhytidadelphus.squarrosus 0.044444444 0.15555556
## Taraxacum.agg. 0.100000000 0.40000000
## Thymus.polytrichus 0.427681661 0.11487889
## Trichostomum.crispulum 0.148571429 0.25142857
## Trifolium.campestre 0.100000000 0.00000000
## Trifolium.dubium 0.040703518 0.11859296
## Trifolium.pratense 0.100000000 0.00000000
## Trifolium.repens 0.100000000 0.00000000
## Urtica.diocia 0.000000000 0.20000000
## Zygodon.stirtonii 0.100000000 0.00000000
##
## $maxcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1 1 1
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 1 1 2
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1 1 1
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 1 1 2
## Carex.flacca Carex.panicea Carlina.vulgaris
## 1 1 2
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 2 1 1
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 1 1 1
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1 1 2
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 2 2 1
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 1 2 2
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 1 2 2
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 1 2 1
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 2 1 1
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 2 1 2
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 2 1 1
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 1 2 2
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 2 1 2
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1 2 1
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1 2 1
##
## $indcls
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 0.10000000 0.10000000 0.20000000
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 0.10000000 0.10000000 0.13333333
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 0.10000000 0.20000000 0.20000000
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.20000000 0.10000000 0.09387755
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.16250000 0.10000000 0.28085106
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 0.20000000 0.14210526 0.10000000
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.20000000 0.10000000 0.10000000
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 0.10000000 0.10000000 0.12100840
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.20346821 0.29387755 0.10000000
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 0.10000000 0.20000000 0.49315068
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 0.11351351 0.19393939 0.26250000
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 0.11688312 0.33684211 0.36190476
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.37369309 0.09523810 0.09009901
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.31111111 0.38297872 0.85970819
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 0.21818182 0.18947368 0.10222222
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 0.10000000 0.15000000 0.15555556
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.40000000 0.42768166 0.25142857
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 0.10000000 0.11859296 0.10000000
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 0.10000000 0.20000000 0.10000000
##
## $pval
## Alopercus.pratensis Anthoxanthum.odoratum Anthyllis.vulneraria
## 1.000 1.000 0.536
## Arrhenatherum.elatius Avenula.pratensis Bellis.perennis
## 1.000 1.000 0.833
## Brachythecium.mildeanum Bryum.c.f..pallescens Bryum.spp.
## 1.000 0.505 0.506
## Calliergonella.cupsidata Campanula.rotundifolia Carex.distans
## 0.548 1.000 1.000
## Carex.flacca Carex.panicea Carlina.vulgaris
## 0.917 1.000 0.945
## Centaurea.nigra Centaurium.littorale Centaurium.pulchellum
## 0.341 1.000 1.000
## Cerastium.fontanum Dactylis.glomerata Dicranella.spp.
## 0.527 1.000 1.000
## Equisetum.arvense Equisteum.variegatum Euphrasia.agg
## 1.000 1.000 0.825
## Festuca.ovina Festuca.rubra Fissidens.dubius
## 0.803 0.522 1.000
## Fissidens.exilis Galium.saxatile Holcus.spp.
## 1.000 0.346 0.358
## Holcus.lanatus Homalothecium.lutescens Hypnum.cupressiforme
## 1.000 0.772 0.520
## Leontodon.hispidus Leucanthemum.vulgare Linum.catharticum
## 1.000 0.330 0.300
## Lotus.corniculatus Lysimachia.maritima Medicago.lupulina
## 0.268 1.000 1.000
## Myosotis.arvensis Ononis.repens Pillosella.officinarum
## 0.155 0.490 0.007
## Plantago.coronopus Plantago.lanceolata Poa.annua
## 0.655 0.928 1.000
## Prunella.vulgaris Pseudoscleropidum.purum Rhytidadelphus.squarrosus
## 1.000 0.745 0.830
## Taraxacum.agg. Thymus.polytrichus Trichostomum.crispulum
## 0.372 0.404 0.722
## Trifolium.campestre Trifolium.dubium Trifolium.pratense
## 1.000 1.000 1.000
## Trifolium.repens Urtica.diocia Zygodon.stirtonii
## 1.000 0.355 1.000
##
## $error
## [1] 0
##
## attr(,"class")
## [1] "indval"
#Pilosella officinarum is reported as the indicator species for Nitratine, with a high #indval score of 0.860 and a low p value of 0.009.