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##The following is written by Savanna van Mesdag, going through the relevant coding and #analyses for CCAs and ANOSIMs for the plant and substrate data for the Barrow- #in-Furness slag bank.

#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/4.4'
## (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/4.4:
##   cannot open URL 'https://github.com/vegandevs/vegan/bin/windows/contrib/4.4/PACKAGES'
install.packages("ggplot2", repos = "https://github.com/tidyverse/ggplot2")
## Installing package into 'C:/Users/Savanna/AppData/Local/R/win-library/4.4'
## (as 'lib' is unspecified)
## Warning: unable to access index for repository https://github.com/tidyverse/ggplot2/src/contrib:
##   cannot open URL 'https://github.com/tidyverse/ggplot2/src/contrib/PACKAGES'
## Warning: package 'ggplot2' 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/tidyverse/ggplot2/bin/windows/contrib/4.4:
##   cannot open URL 'https://github.com/tidyverse/ggplot2/bin/windows/contrib/4.4/PACKAGES'

#Once installed, then need to load these r packages…

library(vegan)
## Warning: package 'vegan' was built under R version 4.4.1
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.6-8
library(ggplot2)

#Loading the data files… Make sure to set your directory before loading data on your #system.

BarrowPS <-read.csv("BarrowPlantSpecies.csv", header = TRUE)

BarrowPC <-read.csv("BARROW_PLANT_CHEMISTRY_MG_KG.csv", header = TRUE)

head(BarrowPS)
##   Anthyllis.vulneraria Aphanes.arvensis Arrhenatherum.elatius Bellis.perennis
## 1                    4                0                     0               4
## 2                    0                0                     0               6
## 3                  127                0                     0               1
## 4                    0                0                     0               0
## 5                   32                0                     0               6
## 6                    0                0                     8               0
##   Blackstonia.perfoliata Brachythecium.albicans Brachythecium.rutabulum
## 1                      0                      0                       0
## 2                      0                     30                      30
## 3                      0                      0                       0
## 4                      0                      0                       0
## 5                      0                      0                       0
## 6                      0                      0                       0
##   Briza.media Bromus.hordeaceus Calliergonella.cupsidata Carex.flacca
## 1           0                 0                        0            0
## 2           0                 0                       30            0
## 3         138                 0                       20            0
## 4           9                 0                      110            0
## 5           8                 0                        0            0
## 6           0                 1                        0            0
##   Carlina.vulgaris Centaurium.erythraea Cerastium.fontanum Cynosurus.cristatus
## 1                0                    0                  0                   0
## 2                0                    0                  0                   0
## 3                0                    0                  1                   0
## 4                0                    0                  2                   0
## 5                0                    0                  1                   0
## 6                0                    0                  0                   0
##   Daucus.carrota Erigeron.acer Euphrasia.agg Festuca.ovina Festuca.rubra
## 1              0             0             0            66             0
## 2              0             0             0             0            19
## 3              0             0            14             0             1
## 4              0             0             0             0            39
## 5              2             0             0             2             2
## 6              0             0             0             0            54
##   Galium.verum Helicotrichon.spp. Hieracium.spp. Holcus.spp. Holcus.lanatus
## 1            0                  0              0           0              0
## 2           87                  0              0          55              5
## 3           88                  0              0           0              1
## 4            0                  0              0          50             25
## 5            1                  0              1           3              2
## 6            0                  1              0         169              0
##   Holcus.mollis Hypericum.perforatum Hypochaeris.radicata Lathyrus.pratensis
## 1             0                    0                    0                  0
## 2             0                    0                    0                  0
## 3             0                    0                    0                  0
## 4             0                    0                    1                  0
## 5             0                    0                    0                  0
## 6             0                    0                    0                  0
##   Leontodon.hispidus Leontodon.saxatilis Leucanthemum.vulgare Lolium.perenne
## 1                 18                   1                    0              0
## 2                  0                   0                   12              0
## 3                  0                   0                    0              0
## 4                  0                   0                    1              0
## 5                 30                   0                    3              0
## 6                  0                   0                    2             85
##   Lotus.corniculatus Medicago.lupulina Ononis.repens Pastinaca.sativa
## 1                  0                 3             0                0
## 2                 67                 3             0                0
## 3                 18                 0             0                0
## 4                 31                 0             0                0
## 5                 12                 0             0                0
## 6                140                 0             0                0
##   Pillosella.officinarum Plantago.lanceolata Potentilla.reptans
## 1                     22                   0                  0
## 2                      0                   0                  0
## 3                      0                   0                  0
## 4                      0                   0                  0
## 5                      4                   3                  0
## 6                      0                   0                  0
##   Prunella.vulgaris Pseudoscleropidum.purum Ranunculus.repens Reseda.lutea
## 1                 0                       0                 0            0
## 2                 0                       0                 0            0
## 3                 0                       0                 0            0
## 4                 0                       0                 1            0
## 5                 0                     160                 0            0
## 6                 0                       0                 0            0
##   Sanguisorba.minor.spp.minor Sedum.anglicum Senecio.jacobaea Senecio.vulgaris
## 1                           0              0                0                4
## 2                          34              0                0                0
## 3                          10              0                0                0
## 4                           0              0                0                0
## 5                           0              0                0                0
## 6                           0              0                1                0
##   Stellaria.apetala Taraxacum.agg. Trifolium.campestre Trifolium.pratense
## 1                 0              2                   8                  0
## 2                 0              0                  64                  2
## 3                 0              1                  22                  0
## 4                 0              0                   8                  0
## 5                 0              0                   2                  0
## 6                 0              0                   0                  0
##   Trifolium.repens Trisetum.flavescens
## 1                0                   0
## 2                0                   0
## 3                4                   0
## 4               17                   0
## 5                0                   3
## 6                0                   0
head(BarrowPC)
##   pH_level     SiO2    Al2O3     Fe2O3       CaO       MgO     Na2O       K2O
## 1    9.921 143502.5 47579.61  8393.106 255144.60 18513.202 4302.770  3569.635
## 2    8.850 221096.7 53189.66 27907.078  95053.87  8201.288 5415.555 15772.808
## 3    7.701 215954.9 88649.43 53506.051  34876.91  7960.074 8308.797 23161.123
## 4    8.295 260828.7 43292.68 22381.616  79688.02  6633.395 5934.855 14444.571
## 5    8.363 188376.3 63774.67 25389.146 147226.30  7115.824 2893.242  8218.463
## 6    8.047 284200.4 51760.68 31474.148  30874.64  9045.538 6602.526 16602.956
##       Cr2O3     TiO2      MnO      P2O5       SrO       BaO   LOI  Ag As  B
## 1  20.52607 2936.780 4491.853  599.9225 676.47564 3045.2147 16.55 0.2  5 30
## 2  95.78834 3536.123 1239.132 1399.8192 169.11891  626.9560 19.60 0.2 15 20
## 3 191.57668 8031.195 2710.601 3699.5223  84.55946  447.8257 15.80 0.2 60 10
## 4  75.26227 3056.649  619.566 1399.8192  84.55946  447.8257 15.80 0.2 11 10
## 5  75.26227 2876.846 2942.938 1499.8063 253.67837 3224.3449 18.60 0.5  8 20
## 6 102.63036 3056.649 1239.132 1599.7934  84.55946  806.0862 14.80 0.7 12 10
##     Be  Bi   Cd Co Cu Ga  Hg La Li  Mo Ni  Pb    S  Sb Sc Th Tl U  V W  Zn
## 1 10.3 1.5 0.25  2 28  5 0.5 40 70 0.5  6  11 7000 1.5 15 10  5 5 18 5  24
## 2  2.1 1.5 0.25 11 44  5 0.5 20 30 1.0 29  61 1600 3.0  5 10  5 5 25 5  88
## 3  1.1 1.5 0.25 31 97  5 0.5 20 40 1.0 60  14  500 5.0 15 10  5 5 39 5  57
## 4  0.7 1.5 0.25  9 37  5 0.5 10 20 1.0 23  43  600 1.5  3 10  5 5 21 5  68
## 5  5.8 1.5 1.00  4 32  5 0.5 20 40 1.0 10 158 2400 5.0  5 10  5 5 11 5 210
## 6  1.5 1.5 1.80  9 41  5 1.0 10 20 1.0 24 240  900 5.0  3 10  5 5 23 5 544
##   Akermanite Albite Aluminium.oxide.hydroxide Anhydrite Aragonite Augite
## 1          0      0                         0         0         0      0
## 2          0      0                         0         0         0      0
## 3          0      1                         0         0         0      1
## 4          0      0                         1         0         0      0
## 5          0      0                         0         0         0      0
## 6          0      0                         0         0         0      0
##   Biotite Birnessite Calcite Clinochlore Cuspidine Diaspore Dickite Gehlenite
## 1       0          0       1           0         0        0       0         1
## 2       0          0       1           0         0        0       0         0
## 3       0          0       1           1         0        0       0         0
## 4       0          0       1           0         0        0       0         0
## 5       0          0       1           0         0        1       0         1
## 6       0          0       0           0         0        0       0         0
##   Goethite Haematite Illite Kaolinite Langite Linnaeite Magnesioferrite
## 1        0         0      0         0       0         0               0
## 2        0         0      0         1       0         0               0
## 3        0         0      1         0       0         0               0
## 4        0         0      0         1       0         0               0
## 5        0         0      0         1       0         0               0
## 6        0         0      0         1       0         0               0
##   Melilite Merwinite Microcline Mullite Muscovite Nitratine Orthoclase
## 1        1         0          0       0         0         0          0
## 2        0         0          0       0         1         1          0
## 3        0         0          0       0         1         0          0
## 4        0         0          0       0         1         0          0
## 5        0         0          0       1         0         0          0
## 6        0         0          0       0         1         0          0
##   Orthopyroxene Periclase Pigeonite Phengite Pseudowollastonite Quartz
## 1             0         0         1        0                  0      0
## 2             0         0         1        0                  0      1
## 3             0         0         0        0                  0      1
## 4             0         1         1        0                  0      1
## 5             0         0         0        0                  0      1
## 6             0         0         1        0                  0      1
##   Staurolite Valentinite
## 1          0           0
## 2          0           0
## 3          0           0
## 4          0           0
## 5          0           0
## 6          0           0
sapply(BarrowPS, class)
##        Anthyllis.vulneraria            Aphanes.arvensis 
##                   "integer"                   "integer" 
##       Arrhenatherum.elatius             Bellis.perennis 
##                   "integer"                   "integer" 
##      Blackstonia.perfoliata      Brachythecium.albicans 
##                   "integer"                   "integer" 
##     Brachythecium.rutabulum                 Briza.media 
##                   "integer"                   "integer" 
##           Bromus.hordeaceus    Calliergonella.cupsidata 
##                   "integer"                   "integer" 
##                Carex.flacca            Carlina.vulgaris 
##                   "integer"                   "integer" 
##        Centaurium.erythraea          Cerastium.fontanum 
##                   "integer"                   "integer" 
##         Cynosurus.cristatus              Daucus.carrota 
##                   "integer"                   "integer" 
##               Erigeron.acer               Euphrasia.agg 
##                   "integer"                   "integer" 
##               Festuca.ovina               Festuca.rubra 
##                   "integer"                   "integer" 
##                Galium.verum          Helicotrichon.spp. 
##                   "integer"                   "integer" 
##              Hieracium.spp.                 Holcus.spp. 
##                   "integer"                   "integer" 
##              Holcus.lanatus               Holcus.mollis 
##                   "integer"                   "integer" 
##        Hypericum.perforatum        Hypochaeris.radicata 
##                   "integer"                   "integer" 
##          Lathyrus.pratensis          Leontodon.hispidus 
##                   "integer"                   "integer" 
##         Leontodon.saxatilis        Leucanthemum.vulgare 
##                   "integer"                   "integer" 
##              Lolium.perenne          Lotus.corniculatus 
##                   "integer"                   "integer" 
##           Medicago.lupulina               Ononis.repens 
##                   "integer"                   "integer" 
##            Pastinaca.sativa      Pillosella.officinarum 
##                   "integer"                   "integer" 
##         Plantago.lanceolata          Potentilla.reptans 
##                   "integer"                   "integer" 
##           Prunella.vulgaris     Pseudoscleropidum.purum 
##                   "integer"                   "integer" 
##           Ranunculus.repens                Reseda.lutea 
##                   "integer"                   "integer" 
## Sanguisorba.minor.spp.minor              Sedum.anglicum 
##                   "integer"                   "integer" 
##            Senecio.jacobaea            Senecio.vulgaris 
##                   "integer"                   "integer" 
##           Stellaria.apetala              Taraxacum.agg. 
##                   "integer"                   "integer" 
##         Trifolium.campestre          Trifolium.pratense 
##                   "integer"                   "integer" 
##            Trifolium.repens         Trisetum.flavescens 
##                   "integer"                   "integer"
sapply(BarrowPC, class)
##                  pH_level                      SiO2                     Al2O3 
##                 "numeric"                 "numeric"                 "numeric" 
##                     Fe2O3                       CaO                       MgO 
##                 "numeric"                 "numeric"                 "numeric" 
##                      Na2O                       K2O                     Cr2O3 
##                 "numeric"                 "numeric"                 "numeric" 
##                      TiO2                       MnO                      P2O5 
##                 "numeric"                 "numeric"                 "numeric" 
##                       SrO                       BaO                       LOI 
##                 "numeric"                 "numeric"                 "numeric" 
##                        Ag                        As                         B 
##                 "numeric"                 "integer"                 "integer" 
##                        Be                        Bi                        Cd 
##                 "numeric"                 "numeric"                 "numeric" 
##                        Co                        Cu                        Ga 
##                 "integer"                 "integer"                 "integer" 
##                        Hg                        La                        Li 
##                 "numeric"                 "integer"                 "integer" 
##                        Mo                        Ni                        Pb 
##                 "numeric"                 "integer"                 "integer" 
##                         S                        Sb                        Sc 
##                 "integer"                 "numeric"                 "integer" 
##                        Th                        Tl                         U 
##                 "integer"                 "integer"                 "integer" 
##                         V                         W                        Zn 
##                 "integer"                 "integer"                 "integer" 
##                Akermanite                    Albite Aluminium.oxide.hydroxide 
##                 "integer"                 "integer"                 "integer" 
##                 Anhydrite                 Aragonite                    Augite 
##                 "integer"                 "integer"                 "integer" 
##                   Biotite                Birnessite                   Calcite 
##                 "integer"                 "integer"                 "integer" 
##               Clinochlore                 Cuspidine                  Diaspore 
##                 "integer"                 "integer"                 "integer" 
##                   Dickite                 Gehlenite                  Goethite 
##                 "integer"                 "integer"                 "integer" 
##                 Haematite                    Illite                 Kaolinite 
##                 "integer"                 "integer"                 "integer" 
##                   Langite                 Linnaeite           Magnesioferrite 
##                 "integer"                 "integer"                 "integer" 
##                  Melilite                 Merwinite                Microcline 
##                 "integer"                 "integer"                 "integer" 
##                   Mullite                 Muscovite                 Nitratine 
##                 "integer"                 "integer"                 "integer" 
##                Orthoclase             Orthopyroxene                 Periclase 
##                 "integer"                 "integer"                 "integer" 
##                 Pigeonite                  Phengite        Pseudowollastonite 
##                 "integer"                 "integer"                 "integer" 
##                    Quartz                Staurolite               Valentinite 
##                 "integer"                 "integer"                 "integer"
rowSums(BarrowPS)
##  [1] 132 444 446 294 277 461 328 428  82 250 155
BarrowPSna <- na.omit(BarrowPS)

print(BarrowPS)
##    Anthyllis.vulneraria Aphanes.arvensis Arrhenatherum.elatius Bellis.perennis
## 1                     4                0                     0               4
## 2                     0                0                     0               6
## 3                   127                0                     0               1
## 4                     0                0                     0               0
## 5                    32                0                     0               6
## 6                     0                0                     8               0
## 7                     0                1                     0               0
## 8                     0                5                     0               2
## 9                     0                0                     0               0
## 10                    0                0                     5               0
## 11                    0                0                     0               4
##    Blackstonia.perfoliata Brachythecium.albicans Brachythecium.rutabulum
## 1                       0                      0                       0
## 2                       0                     30                      30
## 3                       0                      0                       0
## 4                       0                      0                       0
## 5                       0                      0                       0
## 6                       0                      0                       0
## 7                       0                      0                       0
## 8                       2                      0                       0
## 9                       0                      0                       0
## 10                      0                      0                       0
## 11                      0                      0                       0
##    Briza.media Bromus.hordeaceus Calliergonella.cupsidata Carex.flacca
## 1            0                 0                        0            0
## 2            0                 0                       30            0
## 3          138                 0                       20            0
## 4            9                 0                      110            0
## 5            8                 0                        0            0
## 6            0                 1                        0            0
## 7            0                 0                       10          120
## 8            0                 0                        0           40
## 9            0                 0                        0            0
## 10           0                 0                        0            0
## 11           0                 0                        0            0
##    Carlina.vulgaris Centaurium.erythraea Cerastium.fontanum Cynosurus.cristatus
## 1                 0                    0                  0                   0
## 2                 0                    0                  0                   0
## 3                 0                    0                  1                   0
## 4                 0                    0                  2                   0
## 5                 0                    0                  1                   0
## 6                 0                    0                  0                   0
## 7                 0                    0                  1                  54
## 8                 0                   14                  0                  15
## 9                 2                    1                  0                   0
## 10                0                    0                  0                   0
## 11                5                    0                  0                   0
##    Daucus.carrota Erigeron.acer Euphrasia.agg Festuca.ovina Festuca.rubra
## 1               0             0             0            66             0
## 2               0             0             0             0            19
## 3               0             0            14             0             1
## 4               0             0             0             0            39
## 5               2             0             0             2             2
## 6               0             0             0             0            54
## 7               0             0             0             0            42
## 8               0             0             7             0            19
## 9               0            25             2             0            22
## 10              1             0             1             0            41
## 11              0             6             4             0            44
##    Galium.verum Helicotrichon.spp. Hieracium.spp. Holcus.spp. Holcus.lanatus
## 1             0                  0              0           0              0
## 2            87                  0              0          55              5
## 3            88                  0              0           0              1
## 4             0                  0              0          50             25
## 5             1                  0              1           3              2
## 6             0                  1              0         169              0
## 7             0                  0              0          10              0
## 8             0                  0              0          30              0
## 9             0                  0              0           0              0
## 10            2                  0              0          82              5
## 11            0                  0              0           4              0
##    Holcus.mollis Hypericum.perforatum Hypochaeris.radicata Lathyrus.pratensis
## 1              0                    0                    0                  0
## 2              0                    0                    0                  0
## 3              0                    0                    0                  0
## 4              0                    0                    1                  0
## 5              0                    0                    0                  0
## 6              0                    0                    0                  0
## 7              0                    0                    0                 42
## 8              0                    0                    0                  0
## 9              0                    0                    0                  0
## 10            10                    0                    0                  0
## 11             0                   22                    0                  0
##    Leontodon.hispidus Leontodon.saxatilis Leucanthemum.vulgare Lolium.perenne
## 1                  18                   1                    0              0
## 2                   0                   0                   12              0
## 3                   0                   0                    0              0
## 4                   0                   0                    1              0
## 5                  30                   0                    3              0
## 6                   0                   0                    2             85
## 7                   0                   0                    0              2
## 8                   0                   0                    0              0
## 9                   0                   0                    2              2
## 10                  0                   0                    0              5
## 11                  0                   0                   24              0
##    Lotus.corniculatus Medicago.lupulina Ononis.repens Pastinaca.sativa
## 1                   0                 3             0                0
## 2                  67                 3             0                0
## 3                  18                 0             0                0
## 4                  31                 0             0                0
## 5                  12                 0             0                0
## 6                 140                 0             0                0
## 7                   0                 0             0                0
## 8                  14                 0           153                0
## 9                   2                 3             0                1
## 10                 98                 0             0                0
## 11                 17                 0             0                0
##    Pillosella.officinarum Plantago.lanceolata Potentilla.reptans
## 1                      22                   0                  0
## 2                       0                   0                  0
## 3                       0                   0                  0
## 4                       0                   0                  0
## 5                       4                   3                  0
## 6                       0                   0                  0
## 7                       0                   1                 37
## 8                       0                   3                  1
## 9                       3                   0                  0
## 10                      0                   0                  0
## 11                     14                   3                  2
##    Prunella.vulgaris Pseudoscleropidum.purum Ranunculus.repens Reseda.lutea
## 1                  0                       0                 0            0
## 2                  0                       0                 0            0
## 3                  0                       0                 0            0
## 4                  0                       0                 1            0
## 5                  0                     160                 0            0
## 6                  0                       0                 0            0
## 7                  2                       0                 0            0
## 8                  0                       0                 0            0
## 9                  5                       0                 0            1
## 10                 0                       0                 0            0
## 11                 0                       0                 0            0
##    Sanguisorba.minor.spp.minor Sedum.anglicum Senecio.jacobaea Senecio.vulgaris
## 1                            0              0                0                4
## 2                           34              0                0                0
## 3                           10              0                0                0
## 4                            0              0                0                0
## 5                            0              0                0                0
## 6                            0              0                1                0
## 7                            0              0                0                0
## 8                            0              0                0                0
## 9                            0              6                0                0
## 10                           0              0                0                0
## 11                           0              0                0                0
##    Stellaria.apetala Taraxacum.agg. Trifolium.campestre Trifolium.pratense
## 1                  0              2                   8                  0
## 2                  0              0                  64                  2
## 3                  0              1                  22                  0
## 4                  0              0                   8                  0
## 5                  0              0                   2                  0
## 6                  0              0                   0                  0
## 7                  2              0                   2                  0
## 8                  0              0                   0                  0
## 9                  0              4                   0                  0
## 10                 0              0                   0                  0
## 11                 0              6                   0                  0
##    Trifolium.repens Trisetum.flavescens
## 1                 0                   0
## 2                 0                   0
## 3                 4                   0
## 4                17                   0
## 5                 0                   3
## 6                 0                   0
## 7                 2                   0
## 8                 0                 123
## 9                 0                   1
## 10                0                   0
## 11                0                   0

#Need to do this to make sure the datasets are good to go.

#Now to do some ANOSIM tests to assess any significant differences between plant species in #different chemical variables.

#anoBSiO2 <- anosim(BarrowPS, BarrowPC$SiO2, distance = “bray”, permutations = 9999)

#When this ANOSIM is run, the error message: “there should be replicates within groups” #comes up. This error message comes up for another substrate variables for the Barrow #data. From now on, only variables that were tested successfully will be included.

anoBK2O <- anosim(BarrowPS, BarrowPC$K2O, distance = "bray", permutations = 9999)

anoBK2O
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$K2O, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.3704 
##       Significance: 0.324 
## 
## Permutation: free
## Number of permutations: 9999

#Not statistically significant, will mention statistically significant results when #they are generated.

anoBCr2O3 <- anosim(BarrowPS, BarrowPC$Cr2O3, distance = "bray", permutations = 9999)

anoBCr2O3
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Cr2O3, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: -0.009804 
##       Significance: 0.5134 
## 
## Permutation: free
## Number of permutations: 9999
anoBTiO2 <- anosim(BarrowPS, BarrowPC$TiO2, distance = "bray", permutations = 9999)

anoBTiO2
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$TiO2, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: -0.01701 
##       Significance: 0.5136 
## 
## Permutation: free
## Number of permutations: 9999
anoBMnO <- anosim(BarrowPS, BarrowPC$MnO, distance = "bray", permutations = 9999)

anoBMnO
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$MnO, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.2051 
##       Significance: 0.322 
## 
## Permutation: free
## Number of permutations: 9999
anoBP2O5 <- anosim(BarrowPS, BarrowPC$P2O5, distance = "bray", permutations = 9999)

anoBP2O5
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$P2O5, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.6981 
##       Significance: 0.045 
## 
## Permutation: free
## Number of permutations: 9999

#R statistic of 0.6981 and p value of 0.0456 for P2O5.

anoBSrO <- anosim(BarrowPS, BarrowPC$SrO, distance = "bray", permutations = 9999)

anoBSrO
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$SrO, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.1506 
##       Significance: 0.2081 
## 
## Permutation: free
## Number of permutations: 9999
anoBBaO <- anosim(BarrowPS, BarrowPC$BaO, distance = "bray", permutations = 9999)

anoBBaO
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$BaO, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.3333 
##       Significance: 0.3542 
## 
## Permutation: free
## Number of permutations: 9999
anoBAg <- anosim(BarrowPS, BarrowPC$Ag, distance = "bray", permutations = 9999)

anoBAg
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Ag, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.2128 
##       Significance: 0.1986 
## 
## Permutation: free
## Number of permutations: 9999
anoBAs <- anosim(BarrowPS, BarrowPC$As, distance = "bray", permutations = 9999)

anoBAs
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$As, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.2564 
##       Significance: 0.2248 
## 
## Permutation: free
## Number of permutations: 9999
anoBB <- anosim(BarrowPS, BarrowPC$B, distance = "bray", permutations = 9999)

anoBB
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$B, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.09158 
##       Significance: 0.3112 
## 
## Permutation: free
## Number of permutations: 9999
anoBCd <- anosim(BarrowPS, BarrowPC$Cd, distance = "bray", permutations = 9999)

anoBCd
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Cd, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.01333 
##       Significance: 0.4531 
## 
## Permutation: free
## Number of permutations: 9999
anoBCo <- anosim(BarrowPS, BarrowPC$Co, distance = "bray", permutations = 9999)

anoBCo
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Co, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R:   0.5 
##       Significance: 0.0612 
## 
## Permutation: free
## Number of permutations: 9999

#R statistic of 0.5 and a close-to-significant p value of 0.0586 for Co.

anoBCu <- anosim(BarrowPS, BarrowPC$Cu, distance = "bray", permutations = 9999)

anoBCu
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Cu, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: -0.4444 
##       Significance: 0.7262 
## 
## Permutation: free
## Number of permutations: 9999
anoBNi <- anosim(BarrowPS, BarrowPC$Ni, distance = "bray", permutations = 9999)

anoBNi
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Ni, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.434 
##       Significance: 0.1584 
## 
## Permutation: free
## Number of permutations: 9999
anoBS <- anosim(BarrowPS, BarrowPC$S, distance = "bray", permutations = 9999)

anoBS
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$S, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: -0.4444 
##       Significance: 0.7284 
## 
## Permutation: free
## Number of permutations: 9999
anoBSb <- anosim(BarrowPS, BarrowPC$Sb, distance = "bray", permutations = 9999)

anoBSb
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Sb, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: -0.1795 
##       Significance: 0.8406 
## 
## Permutation: free
## Number of permutations: 9999
anoBSc <- anosim(BarrowPS, BarrowPC$Sc, distance = "bray", permutations = 9999)

anoBSc
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$Sc, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.07979 
##       Significance: 0.3496 
## 
## Permutation: free
## Number of permutations: 9999
anoBV <- anosim(BarrowPS, BarrowPC$V, distance = "bray", permutations = 9999)

anoBV
## 
## Call:
## anosim(x = BarrowPS, grouping = BarrowPC$V, permutations = 9999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R:     1 
##       Significance: 0.0201 
## 
## Permutation: free
## Number of permutations: 9999

#A high R statistic of 1, with a p value of 0.0186, for V.

#With two of the variables showing significant differences in different Barrow #samples, CCAs will be appropriate to demonstrate what is going on in the data.

BarrowCCA <-cca(BarrowPS, BarrowPC)
## 
## Some constraints or conditions were aliased because they were redundant. This
## can happen if terms are linearly dependent (collinear): 'MnO', 'P2O5', 'SrO',
## 'BaO', 'LOI', 'Ag', 'As', 'B', 'Be', 'Bi', 'Cd', 'Co', 'Cu', 'Ga', 'Hg', 'La',
## 'Li', 'Mo', 'Ni', 'Pb', 'S', 'Sb', 'Sc', 'Th', 'Tl', 'U', 'V', 'W', 'Zn',
## 'Akermanite', 'Albite', 'Aluminium.oxide.hydroxide', 'Anhydrite', 'Aragonite',
## 'Augite', 'Biotite', 'Birnessite', 'Calcite', 'Clinochlore', 'Cuspidine',
## 'Diaspore', 'Dickite', 'Gehlenite', 'Goethite', 'Haematite', 'Illite',
## 'Kaolinite', 'Langite', 'Linnaeite', 'Magnesioferrite', 'Melilite',
## 'Merwinite', 'Microcline', 'Mullite', 'Muscovite', 'Nitratine', 'Orthoclase',
## 'Orthopyroxene', 'Periclase', 'Pigeonite', 'Phengite', 'Pseudowollastonite',
## 'Quartz', 'Staurolite', 'Valentinite'
## 
## The model is overfitted with no unconstrained (residual) component
print(BarrowCCA)
## Call: cca(X = BarrowPS, Y = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total           4.781      1.000     
## Constrained     4.781      1.000   10
## Unconstrained   0.000      0.000    0
## 
## Inertia is scaled Chi-square
## 
## -- Note --
## 
## Some constraints or conditions were aliased because they were redundant.
## This can happen if terms are linearly dependent (collinear): 'MnO', 'P2O5',
## 'SrO', 'BaO', 'LOI', 'Ag', 'As', 'B', 'Be', 'Bi', 'Cd', 'Co', 'Cu', 'Ga',
## 'Hg', 'La', 'Li', 'Mo', 'Ni', 'Pb', 'S', 'Sb', 'Sc', 'Th', 'Tl', 'U', 'V',
## 'W', 'Zn', 'Akermanite', 'Albite', 'Aluminium.oxide.hydroxide',
## 'Anhydrite', 'Aragonite', 'Augite', 'Biotite', 'Birnessite', 'Calcite',
## 'Clinochlore', 'Cuspidine', 'Diaspore', 'Dickite', 'Gehlenite', 'Goethite',
## 'Haematite', 'Illite', 'Kaolinite', 'Langite', 'Linnaeite',
## 'Magnesioferrite', 'Melilite', 'Merwinite', 'Microcline', 'Mullite',
## 'Muscovite', 'Nitratine', 'Orthoclase', 'Orthopyroxene', 'Periclase',
## 'Pigeonite', 'Phengite', 'Pseudowollastonite', 'Quartz', 'Staurolite',
## 'Valentinite'
## 
## The model is overfitted with no unconstrained (residual) component.
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6   CCA7   CCA8   CCA9  CCA10 
## 0.8172 0.7280 0.6486 0.5715 0.5650 0.4821 0.3262 0.2994 0.2659 0.0770
summary(BarrowCCA)
## 
## Call:
## cca(X = BarrowPS, Y = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total           4.781          1
## Constrained     4.781          1
## Unconstrained   0.000          0
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5   CCA6    CCA7    CCA8
## Eigenvalue            0.8172 0.7280 0.6486 0.5715 0.5650 0.4821 0.32617 0.29936
## Proportion Explained  0.1709 0.1523 0.1357 0.1195 0.1182 0.1008 0.06822 0.06262
## Cumulative Proportion 0.1709 0.3232 0.4589 0.5784 0.6966 0.7974 0.86565 0.92827
##                          CCA9   CCA10
## Eigenvalue            0.26592 0.07702
## Proportion Explained  0.05562 0.01611
## Cumulative Proportion 0.98389 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5   CCA6    CCA7    CCA8
## Eigenvalue            0.8172 0.7280 0.6486 0.5715 0.5650 0.4821 0.32617 0.29936
## Proportion Explained  0.1709 0.1523 0.1357 0.1195 0.1182 0.1008 0.06822 0.06262
## Cumulative Proportion 0.1709 0.3232 0.4589 0.5784 0.6966 0.7974 0.86565 0.92827
##                          CCA9   CCA10
## Eigenvalue            0.26592 0.07702
## Proportion Explained  0.05562 0.01611
## Cumulative Proportion 0.98389 1.00000
plot(BarrowCCA)

#This CCA uses all of the plant data and substrate data. As before, substrate samples will #be selected for CCAs that can be further examined using anova tests.

BarrowCCA1.1 <-cca(BarrowPS ~ pH_level + CaO + MgO + K2O + MgO + Al2O3 + Cr2O3, 
data = BarrowPC)

print(BarrowCCA1.1)
## Call: cca(formula = BarrowPS ~ pH_level + CaO + MgO + K2O + MgO + Al2O3 +
## Cr2O3, data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total           4.781      1.000     
## Constrained     3.394      0.710    6
## Unconstrained   1.387      0.290    4
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6 
## 0.8007 0.6692 0.6292 0.5455 0.4623 0.2875 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3    CA4 
## 0.5419 0.3504 0.2938 0.2003
summary(BarrowCCA1.1)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + CaO + MgO + K2O + MgO + Al2O3 +      Cr2O3, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total           4.781       1.00
## Constrained     3.394       0.71
## Unconstrained   1.386       0.29
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4    CCA5    CCA6    CA1    CA2
## Eigenvalue            0.8007 0.6692 0.6292 0.5455 0.46235 0.28751 0.5419 0.3504
## Proportion Explained  0.1675 0.1400 0.1316 0.1141 0.09671 0.06014 0.1134 0.0733
## Cumulative Proportion 0.1675 0.3075 0.4391 0.5531 0.64986 0.70999 0.8233 0.8966
##                           CA3    CA4
## Eigenvalue            0.29381 0.2003
## Proportion Explained  0.06145 0.0419
## Cumulative Proportion 0.95810 1.0000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5   CCA6
## Eigenvalue            0.8007 0.6692 0.6292 0.5455 0.4623 0.2875
## Proportion Explained  0.2359 0.1971 0.1854 0.1607 0.1362 0.0847
## Cumulative Proportion 0.2359 0.4330 0.6184 0.7791 0.9153 1.0000
plot(BarrowCCA1.1)

anova(BarrowCCA1.1)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + CaO + MgO + K2O + MgO + Al2O3 + Cr2O3, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)    
## Model     6    3.3944 1.6321  0.001 ***
## Residual  4    1.3865                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

#F statistic of 1.6299 and p value of 0.001.

BarrowCCA1.2 <-cca(BarrowPS ~ pH_level + CaO + K2O + Al2O3 + Pb + BaO + Calcite,
                   data = BarrowPC)

print(BarrowCCA1.2)
## Call: cca(formula = BarrowPS ~ pH_level + CaO + K2O + Al2O3 + Pb + BaO +
## Calcite, data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total          4.7808     1.0000     
## Constrained    3.8197     0.7990    7
## Unconstrained  0.9612     0.2010    3
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6   CCA7 
## 0.7990 0.7089 0.6200 0.5650 0.4758 0.3491 0.3018 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3 
## 0.4930 0.3464 0.1218
summary(BarrowCCA1.2)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + CaO + K2O + Al2O3 + Pb +      BaO + Calcite, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total          4.7808      1.000
## Constrained    3.8197      0.799
## Unconstrained  0.9612      0.201
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4    CCA5    CCA6    CCA7
## Eigenvalue            0.7990 0.7089 0.6200 0.5650 0.47584 0.34908 0.30177
## Proportion Explained  0.1671 0.1483 0.1297 0.1182 0.09953 0.07302 0.06312
## Cumulative Proportion 0.1671 0.3154 0.4451 0.5633 0.66282 0.73583 0.79895
##                          CA1     CA2     CA3
## Eigenvalue            0.4930 0.34639 0.12182
## Proportion Explained  0.1031 0.07245 0.02548
## Cumulative Proportion 0.9021 0.97452 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.7990 0.7089 0.6200 0.5650 0.4758 0.34908 0.30177
## Proportion Explained  0.2092 0.1856 0.1623 0.1479 0.1246 0.09139 0.07901
## Cumulative Proportion 0.2092 0.3948 0.5571 0.7050 0.8296 0.92099 1.00000
anova(BarrowCCA1.2)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + CaO + K2O + Al2O3 + Pb + BaO + Calcite, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)    
## Model     7    3.8197 1.7031  0.001 ***
## Residual  3    0.9612                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(BarrowCCA1.2)

#F statistic of 1.7012 and p value of 0.001

BarrowCCA1.3 <-cca(BarrowPS ~ pH_level + Cd + K2O + Al2O3 + Pb + BaO + Calcite,
                   data = BarrowPC)

print(BarrowCCA1.3)
## Call: cca(formula = BarrowPS ~ pH_level + Cd + K2O + Al2O3 + Pb + BaO +
## Calcite, data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total          4.7808     1.0000     
## Constrained    3.7670     0.7879    7
## Unconstrained  1.0138     0.2121    3
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6   CCA7 
## 0.8040 0.6864 0.6149 0.5649 0.4426 0.3389 0.3153 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3 
## 0.4643 0.4117 0.1378
summary(BarrowCCA1.3)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + Cd + K2O + Al2O3 + Pb + BaO +      Calcite, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total           4.781     1.0000
## Constrained     3.767     0.7879
## Unconstrained   1.014     0.2121
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4    CCA5   CCA6    CCA7
## Eigenvalue            0.8040 0.6864 0.6149 0.5649 0.44262 0.3389 0.31525
## Proportion Explained  0.1682 0.1436 0.1286 0.1182 0.09258 0.0709 0.06594
## Cumulative Proportion 0.1682 0.3118 0.4404 0.5585 0.65111 0.7220 0.78794
##                           CA1     CA2     CA3
## Eigenvalue            0.46430 0.41167 0.13785
## Proportion Explained  0.09712 0.08611 0.02883
## Cumulative Proportion 0.88506 0.97117 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.8040 0.6864 0.6149 0.5649 0.4426 0.33894 0.31525
## Proportion Explained  0.2134 0.1822 0.1632 0.1500 0.1175 0.08998 0.08369
## Cumulative Proportion 0.2134 0.3957 0.5589 0.7088 0.8263 0.91631 1.00000
anova(BarrowCCA1.3)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + Cd + K2O + Al2O3 + Pb + BaO + Calcite, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)   
## Model     7    3.7670 1.5925  0.002 **
## Residual  3    1.0138                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(BarrowCCA1.3)

#F statistic of 1.5915 and p value of 0.002

BarrowCCA1.4 <-cca(BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Calcite,
                   data = BarrowPC)

print(BarrowCCA1.4)
## Call: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Calcite, data
## = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total           4.781      1.000     
## Constrained     2.792      0.584    5
## Unconstrained   1.989      0.416    5
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5 
## 0.7867 0.6794 0.6048 0.3841 0.3370 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3    CA4    CA5 
## 0.6168 0.5218 0.4209 0.3203 0.1090
summary(BarrowCCA1.4)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Calcite,      data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total           4.781      1.000
## Constrained     2.792      0.584
## Unconstrained   1.989      0.416
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3    CCA4    CCA5    CA1    CA2
## Eigenvalue            0.7867 0.6794 0.6048 0.38411 0.33701 0.6168 0.5218
## Proportion Explained  0.1646 0.1421 0.1265 0.08034 0.07049 0.1290 0.1091
## Cumulative Proportion 0.1646 0.3067 0.4332 0.51353 0.58402 0.7130 0.8222
##                           CA3     CA4     CA5
## Eigenvalue            0.42091 0.32028 0.10897
## Proportion Explained  0.08804 0.06699 0.02279
## Cumulative Proportion 0.91021 0.97721 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5
## Eigenvalue            0.7867 0.6794 0.6048 0.3841 0.3370
## Proportion Explained  0.2818 0.2433 0.2166 0.1376 0.1207
## Cumulative Proportion 0.2818 0.5251 0.7417 0.8793 1.0000
anova(BarrowCCA1.4)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Calcite, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)   
## Model     5    2.7921 1.4039  0.005 **
## Residual  5    1.9888                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(BarrowCCA1.4)

#F statistic of 1.4032 and p value of 0.002

BarrowCCA1.5 <-cca(BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + Pb + Calcite,
                   data = BarrowPC)

print(BarrowCCA1.5)
## Call: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + Pb +
## Calcite, data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total          4.7808     1.0000     
## Constrained    3.8369     0.8026    7
## Unconstrained  0.9439     0.1974    3
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6   CCA7 
## 0.7987 0.7203 0.6122 0.5661 0.5003 0.3363 0.3030 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3 
## 0.4612 0.3326 0.1501
summary(BarrowCCA1.5)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni +      Pb + Calcite, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total          4.7808     1.0000
## Constrained    3.8369     0.8026
## Unconstrained  0.9439     0.1974
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.7987 0.7203 0.6122 0.5661 0.5003 0.33630 0.30305
## Proportion Explained  0.1671 0.1507 0.1281 0.1184 0.1047 0.07034 0.06339
## Cumulative Proportion 0.1671 0.3177 0.4458 0.5642 0.6688 0.73917 0.80256
##                           CA1     CA2    CA3
## Eigenvalue            0.46124 0.33258 0.1501
## Proportion Explained  0.09648 0.06956 0.0314
## Cumulative Proportion 0.89904 0.96860 1.0000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.7987 0.7203 0.6122 0.5661 0.5003 0.33630 0.30305
## Proportion Explained  0.2082 0.1877 0.1596 0.1475 0.1304 0.08765 0.07898
## Cumulative Proportion 0.2082 0.3959 0.5554 0.7030 0.8334 0.92102 1.00000
anova(BarrowCCA1.5)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + Pb + Calcite, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)    
## Model     7    3.8369 1.7421  0.001 ***
## Residual  3    0.9439                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(BarrowCCA1.5)

#F statistic of 1.7394 and p value of 0.001

BarrowCCA1.6 <-cca(BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + Cd + Calcite,
                   data = BarrowPC)

print(BarrowCCA1.6)
## Call: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + Cd +
## Calcite, data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total          4.7808     1.0000     
## Constrained    3.8557     0.8065    7
## Unconstrained  0.9251     0.1935    3
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6   CCA7 
## 0.8032 0.7096 0.6098 0.5606 0.5210 0.3367 0.3147 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3 
## 0.4590 0.3245 0.1417
summary(BarrowCCA1.6)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni +      Cd + Calcite, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total          4.7808     1.0000
## Constrained    3.8557     0.8065
## Unconstrained  0.9251     0.1935
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.8032 0.7096 0.6098 0.5606 0.5210 0.33671 0.31475
## Proportion Explained  0.1680 0.1484 0.1276 0.1173 0.1090 0.07043 0.06584
## Cumulative Proportion 0.1680 0.3164 0.4440 0.5613 0.6702 0.74065 0.80649
##                           CA1     CA2     CA3
## Eigenvalue            0.45900 0.32449 0.14165
## Proportion Explained  0.09601 0.06787 0.02963
## Cumulative Proportion 0.90250 0.97037 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.8032 0.7096 0.6098 0.5606 0.5210 0.33671 0.31475
## Proportion Explained  0.2083 0.1840 0.1582 0.1454 0.1351 0.08733 0.08163
## Cumulative Proportion 0.2083 0.3924 0.5505 0.6959 0.8310 0.91837 1.00000
anova(BarrowCCA1.6)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + Cd + Calcite, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)    
## Model     7    3.8557 1.7862  0.001 ***
## Residual  3    0.9251                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(BarrowCCA1.6)

#F statistic of 1.7839 and p value of 0.001

BarrowCCA1.7 <-cca(BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + As + Calcite,
                   data = BarrowPC)

print(BarrowCCA1.7)
## Call: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + As +
## Calcite, data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total          4.7808     1.0000     
## Constrained    3.7645     0.7874    7
## Unconstrained  1.0163     0.2126    3
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6   CCA7 
## 0.8129 0.7055 0.6141 0.5341 0.4616 0.3363 0.2999 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3 
## 0.4718 0.3935 0.1510
summary(BarrowCCA1.7)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni +      As + Calcite, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total           4.781     1.0000
## Constrained     3.764     0.7874
## Unconstrained   1.016     0.2126
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4    CCA5    CCA6    CCA7
## Eigenvalue            0.8129 0.7055 0.6141 0.5341 0.46162 0.33626 0.29990
## Proportion Explained  0.1700 0.1476 0.1284 0.1117 0.09656 0.07034 0.06273
## Cumulative Proportion 0.1700 0.3176 0.4461 0.5578 0.65435 0.72468 0.78741
##                           CA1     CA2     CA3
## Eigenvalue            0.47176 0.39355 0.15103
## Proportion Explained  0.09868 0.08232 0.03159
## Cumulative Proportion 0.88609 0.96841 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.8129 0.7055 0.6141 0.5341 0.4616 0.33626 0.29990
## Proportion Explained  0.2160 0.1874 0.1631 0.1419 0.1226 0.08933 0.07967
## Cumulative Proportion 0.2160 0.4034 0.5665 0.7084 0.8310 0.92033 1.00000
anova(BarrowCCA1.7)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Ni + As + Calcite, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)   
## Model     7    3.7645 1.5874  0.003 **
## Residual  3    1.0163                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(BarrowCCA1.7)

#F statistic of 1.585 and p value of 0.001

BarrowCCA1.8 <-cca(BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Pb + As + Calcite,
                   data = BarrowPC)

print(BarrowCCA1.8)
## Call: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Pb + As +
## Calcite, data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total          4.7808     1.0000     
## Constrained    3.8030     0.7955    7
## Unconstrained  0.9778     0.2045    3
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6   CCA7 
## 0.7980 0.6956 0.6116 0.5703 0.4899 0.3362 0.3015 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3 
## 0.4734 0.3519 0.1524
summary(BarrowCCA1.8)
## 
## Call:
## cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Pb +      As + Calcite, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total          4.7808     1.0000
## Constrained    3.8030     0.7955
## Unconstrained  0.9778     0.2045
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CCA7
## Eigenvalue            0.7980 0.6956 0.6116 0.5703 0.4899 0.33619 0.30146
## Proportion Explained  0.1669 0.1455 0.1279 0.1193 0.1025 0.07032 0.06305
## Cumulative Proportion 0.1669 0.3124 0.4403 0.5596 0.6621 0.73242 0.79547
##                           CA1     CA2     CA3
## Eigenvalue            0.47344 0.35194 0.15244
## Proportion Explained  0.09903 0.07361 0.03189
## Cumulative Proportion 0.89450 0.96811 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5   CCA6    CCA7
## Eigenvalue            0.7980 0.6956 0.6116 0.5703 0.4899 0.3362 0.30146
## Proportion Explained  0.2098 0.1829 0.1608 0.1499 0.1288 0.0884 0.07927
## Cumulative Proportion 0.2098 0.3927 0.5536 0.7035 0.8323 0.9207 1.00000
anova(BarrowCCA1.8)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ pH_level + K2O + Al2O3 + BaO + Pb + As + Calcite, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)    
## Model     7    3.8030 1.6668  0.001 ***
## Residual  3    0.9778                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(BarrowCCA1.8)

#F statistic of 1.6644 and p value of 0.001

BarrowCCA2 <- cca(BarrowPS ~ Na2O + pH_level + MgO + CaO + Al2O3 + Cr2O3, data = BarrowPC)

print(BarrowCCA2)
## Call: cca(formula = BarrowPS ~ Na2O + pH_level + MgO + CaO + Al2O3 + Cr2O3,
## data = BarrowPC)
## 
## -- Model Summary --
## 
##               Inertia Proportion Rank
## Total          4.7808     1.0000     
## Constrained    3.3904     0.7092    6
## Unconstrained  1.3905     0.2908    4
## 
## Inertia is scaled Chi-square
## 
## -- Eigenvalues --
## 
## Eigenvalues for constrained axes:
##   CCA1   CCA2   CCA3   CCA4   CCA5   CCA6 
## 0.8022 0.6642 0.6288 0.5404 0.4589 0.2958 
## 
## Eigenvalues for unconstrained axes:
##    CA1    CA2    CA3    CA4 
## 0.5674 0.3790 0.3068 0.1372
summary(BarrowCCA2)
## 
## Call:
## cca(formula = BarrowPS ~ Na2O + pH_level + MgO + CaO + Al2O3 +      Cr2O3, data = BarrowPC) 
## 
## Partitioning of scaled Chi-square:
##               Inertia Proportion
## Total           4.781     1.0000
## Constrained     3.390     0.7092
## Unconstrained   1.390     0.2908
## 
## Eigenvalues, and their contribution to the scaled Chi-square 
## 
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6    CA1     CA2
## Eigenvalue            0.8022 0.6642 0.6288 0.5404 0.4589 0.29578 0.5674 0.37905
## Proportion Explained  0.1678 0.1389 0.1315 0.1130 0.0960 0.06187 0.1187 0.07928
## Cumulative Proportion 0.1678 0.3067 0.4383 0.5513 0.6473 0.70916 0.8278 0.90713
##                           CA3     CA4
## Eigenvalue            0.30685 0.13716
## Proportion Explained  0.06418 0.02869
## Cumulative Proportion 0.97131 1.00000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         CCA1   CCA2   CCA3   CCA4   CCA5    CCA6
## Eigenvalue            0.8022 0.6642 0.6288 0.5404 0.4589 0.29578
## Proportion Explained  0.2366 0.1959 0.1855 0.1594 0.1354 0.08724
## Cumulative Proportion 0.2366 0.4325 0.6180 0.7774 0.9128 1.00000
plot(BarrowCCA2)

anova(BarrowCCA2)
## Permutation test for cca under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: cca(formula = BarrowPS ~ Na2O + pH_level + MgO + CaO + Al2O3 + Cr2O3, data = BarrowPC)
##          Df ChiSquare      F Pr(>F)   
## Model     6    3.3904 1.6255  0.002 **
## Residual  4    1.3905                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

#F statistic of 1.6234 and a p value of 0.001

#After carrying out multiple CCAs with different substrate variables, the one with the #highest F statistic and lowest p value is BarrowCCA1.6, with an F statistic of 1.7839 and #a p value of 0.001. The plot for this CCA is also satisfying from a visual point of view.

#To better visualise the BarrowCCA1.6 graph…

BarrowCCA1.6$CCA$v
##                                    CCA1        CCA2        CCA3        CCA4
## Anthyllis.vulneraria        -1.31679829  0.35564071  1.72401074  0.11463673
## Aphanes.arvensis             1.47807999 -1.45442717  0.89999121 -1.01786706
## Arrhenatherum.elatius        0.41742445  0.91955813 -1.21737609 -0.58064722
## Bellis.perennis             -0.82627680 -0.77854942 -0.29129238 -0.11027422
## Blackstonia.perfoliata       1.50711422 -1.54071702  1.05177611 -1.85700942
## Brachythecium.albicans       0.10636765  0.52481121  0.38045396  0.28773345
## Brachythecium.rutabulum      0.10636765  0.52481121  0.38045396  0.28773345
## Briza.media                 -1.08363603  0.84358952  2.03050100  0.26997196
## Bromus.hordeaceus            0.43058718  1.01127788 -0.94046695 -0.91847546
## Calliergonella.cupsidata    -0.13143713  1.08575923  0.03857636  0.43413397
## Carex.flacca                 1.37646016 -1.15241271  0.36874405  1.91913120
## Carlina.vulgaris            -0.07212621  0.11689979 -1.65648422 -0.37684550
## Centaurium.erythraea         1.39303436 -1.43535934  0.79919209 -1.77724344
## Cerastium.fontanum          -0.44032882  0.23678114  0.25744161  0.60767346
## Cynosurus.cristatus          1.37077955 -1.13552991  0.33904701  2.08331122
## Daucus.carrota              -1.29373458 -0.84396368 -0.69963169 -0.65682312
## Erigeron.acer               -0.16832748  0.06058089 -2.44420361 -0.58365314
## Euphrasia.agg               -0.16787580  0.14055693  0.99555842 -0.37876225
## Festuca.ovina               -2.16514749 -2.37790298 -1.75304460  1.41594491
## Festuca.rubra                0.38635804  0.30320703 -0.76546675  0.12052076
## Galium.verum                -0.49095899  0.72477083  1.31531647  0.30455923
## Helicotrichon.spp.           0.43058718  1.01127788 -0.94046695 -0.91847546
## Hieracium.spp.              -2.13878391 -1.65234879 -0.21923217 -0.96517365
## Holcus.spp.                  0.38548226  0.68261764 -0.67181493 -0.39332973
## Holcus.lanatus              -0.17782166  1.06624832 -0.43432521  0.14945173
## Holcus.mollis                0.39636408  0.77280653 -1.66043073 -0.04012204
## Hypericum.perforatum        -0.01934321  0.14780042 -1.22428420 -0.26337583
## Hypochaeris.radicata        -0.15641500  1.45542663 -0.47962535  0.24111999
## Lathyrus.pratensis           1.33290880 -1.02297794  0.14106670  3.17784474
## Leontodon.hispidus          -2.14896984 -1.93267655 -0.81184152 -0.04519603
## Leontodon.saxatilis         -2.16594639 -2.39988948 -1.79952377  1.48810002
## Leucanthemum.vulgare        -0.12062693  0.19193584 -0.75703631 -0.19728658
## Lolium.perenne               0.43446150  0.93463822 -0.99397531 -0.77911036
## Lotus.corniculatus           0.19199985  0.69137600 -0.64189233 -0.35830099
## Medicago.lupulina           -0.75455415 -0.61181002 -1.38535136  0.37177126
## Ononis.repens                1.50711422 -1.54071702  1.05177611 -1.85700942
## Pastinaca.sativa            -0.20408370  0.03964820 -2.73698427 -0.66051970
## Pillosella.officinarum      -1.32765145 -1.33067007 -1.53063682  0.53973687
## Plantago.lanceolata         -0.06201299 -1.01587741 -0.10341541 -0.60788320
## Potentilla.reptans           1.26965134 -0.97738250  0.09556689  2.87991235
## Prunella.vulgaris            0.23505701 -0.26395927 -1.91468399  0.43615585
## Pseudoscleropidum.purum     -2.13878391 -1.65234879 -0.21923217 -0.96517365
## Ranunculus.repens           -0.15641500  1.45542663 -0.47962535  0.24111999
## Reseda.lutea                -0.20408370  0.03964820 -2.73698427 -0.66051970
## Sanguisorba.minor.spp.minor -0.16392931  0.62107666  0.82231083  0.30039773
## Sedum.anglicum              -0.20408370  0.03964820 -2.73698427 -0.66051970
## Senecio.jacobaea             0.43058718  1.01127788 -0.94046695 -0.91847546
## Senecio.vulgaris            -2.16594639 -2.39988948 -1.79952377  1.48810002
## Stellaria.apetala            1.33290880 -1.02297794  0.14106670  3.17784474
## Taraxacum.agg.              -0.48824814 -0.21584649 -1.50523581 -0.06943673
## Trifolium.campestre         -0.35101669  0.39194248  0.53869115  0.41726491
## Trifolium.pratense           0.10636765  0.52481121  0.38045396  0.28773345
## Trifolium.repens            -0.18804319  1.15173102  0.06204345  0.51428497
## Trisetum.flavescens          1.40751665 -1.53091017  0.99191953 -1.82652125
##                                    CCA5        CCA6        CCA7
## Anthyllis.vulneraria        -0.16719387 -0.04152376 -1.27618222
## Aphanes.arvensis            -0.37097811  0.17174175  0.20841641
## Arrhenatherum.elatius        0.83862301  0.97428159 -1.75348572
## Bellis.perennis             -0.15514291 -0.86188280  0.47612436
## Blackstonia.perfoliata      -0.65252954  0.24440902  0.34652057
## Brachythecium.albicans      -0.47118488  0.08952356  2.10840230
## Brachythecium.rutabulum     -0.47118488  0.08952356  2.10840230
## Briza.media                 -0.53321206  0.00640023 -1.32555398
## Bromus.hordeaceus            1.38806320  1.49439252 -1.35887362
## Calliergonella.cupsidata    -0.02684092  0.08724823  2.65116800
## Carex.flacca                 0.61445190 -0.08259368 -0.27494814
## Carlina.vulgaris            -1.97675239 -4.80039110 -0.83503778
## Centaurium.erythraea        -0.93625051  0.26631232  0.27573541
## Cerastium.fontanum           0.59582364 -0.12775295  1.21531912
## Cynosurus.cristatus          0.66953805 -0.09681119 -0.30196852
## Daucus.carrota               1.60851718 -0.43885846 -0.42434891
## Erigeron.acer               -4.11397727 -0.88304592 -0.74771359
## Euphrasia.agg               -1.00421994 -0.86490300 -1.06311256
## Festuca.ovina               -2.37175341  2.71659598 -0.08594059
## Festuca.rubra               -0.13686446 -0.72469366 -0.17085161
## Galium.verum                -0.58705237  0.06183401  0.12946480
## Helicotrichon.spp.           1.38806320  1.49439252 -1.35887362
## Hieracium.spp.               2.43301643 -0.72933975  0.55590918
## Holcus.spp.                  0.51281442  0.62176589 -0.27567993
## Holcus.lanatus               0.12579460  0.07231280  2.50456022
## Holcus.mollis               -0.04048131  0.14210410 -2.38486509
## Hypericum.perforatum        -0.80411573 -6.94973094 -0.88295016
## Hypochaeris.radicata         0.12883348  0.12027209  3.88873884
## Lathyrus.pratensis           1.03677905 -0.19159458 -0.48210438
## Leontodon.hispidus           0.57662808  0.60204451  0.30792177
## Leontodon.saxatilis         -2.51735250  2.82101827 -0.10539058
## Leucanthemum.vulgare        -0.55831079 -3.71937057  0.12541430
## Lolium.perenne               1.17063655  1.36698524 -1.38109899
## Lotus.corniculatus           0.36563926  0.27891495 -0.49876707
## Medicago.lupulina           -2.63229380  1.16116677  0.42925163
## Ononis.repens               -0.65252954  0.24440902  0.34652057
## Pastinaca.sativa            -4.90834404  0.57295848 -0.71525682
## Pillosella.officinarum      -1.66586841 -0.84726313 -0.33958207
## Plantago.lanceolata          0.39658925 -2.24955796 -0.04236656
## Potentilla.reptans           0.90250159 -0.51860131 -0.48143105
## Prunella.vulgaris           -3.20973744  0.35451475 -0.64864183
## Pseudoscleropidum.purum      2.43301643 -0.72933975  0.55590918
## Ranunculus.repens            0.12883348  0.12027209  3.88873884
## Reseda.lutea                -4.90834404  0.57295848 -0.71525682
## Sanguisorba.minor.spp.minor -0.53417564  0.07863762  1.22588203
## Sedum.anglicum              -4.90834404  0.57295848 -0.71525682
## Senecio.jacobaea             1.38806320  1.49439252 -1.35887362
## Senecio.vulgaris            -2.51735250  2.82101827 -0.10539058
## Stellaria.apetala            1.03677905 -0.19159458 -0.48210438
## Taraxacum.agg.              -2.32623998 -2.59406844 -0.78032279
## Trifolium.campestre         -0.55460345  0.26729925  1.19159464
## Trifolium.pratense          -0.47118488  0.08952356  2.10840230
## Trifolium.repens             0.05523263  0.07947556  2.52372191
## Trisetum.flavescens         -0.61315298  0.22399408  0.34310631

#The “v values” show the positions of individual species on the graph, with the CCA1 value #representing the x axis and the CCA2 value representing the y axis, in the case of the #graph created in R.

plot(BarrowCCA1.6, choices = c(1,2), display = c("wa", "bp"), xlim = c(-4, 3),
     ylim = c(-3, 2))


#Increasing the xlim and ylim to give more room for writing on graph

points(x = -2.14035453, y = -1.64782243, pch = 15, col = "black")

#This point represents Pseudoscleropodium purum

text('P. purum', x = -2.14035453, y = -1.64782243, cex = 0.88, pos = 2, col = "black")

#Adding text for Pseudoscleropodium purum

points(x = -1.08445495, y = 0.84019621, pch = 15, col = "black")

#This point represents Briza media

text('Briza media', x = -1.08445495, y = 0.84019621, cex = 0.88, pos = 2, col = "black")

#Adding text for Briza media

points(x = -0.06301341, y = -1.01639484, pch = 15, col = "black")

#This point represents Plantago lanceolata

text('P. lanceolata', x = 1.1, y = -1.3, cex = 0.88, pos = 2, col = "black")

#Adding text for Plantago lanceolata

points(x = -2.16781758, y = -2.37668105, pch = 15, col = "black")

#This point represents Festuca ovina

text('F. ovina', x = -2.16781758, y = -2.37668105, cex = 0.88, pos = 2, col = "black")

#Adding text for Festuca ovina

points(x = 1.50629701, y = -1.54369063, pch = 15, col = "black")

#This point represents Blackstonia perfoliata

text('B. perfoliata', x = 3.5, y = -1.54369063, cex = 0.88, pos = 2, col = "black")

#Adding text for Blackstonia perfoliata

points(x = 0.43181039, y = 1.01456410, pch = 15, col = "black")

#This point represents Bromus hordeaceus

text('B. hordeaceus', x = 1.64, y = 1.01456410, pch = 15, col = "black")

#Adding text for Bromus hordeaceus