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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.