kguidonimartins/r-list-diogo.R

## r-list-diogo.R
if (!require("ade4")) install.packages("ade4")
#> Loading required package: ade4

# Where am I?
getwd()
#> [1] "/tmp/RtmpK0kjbc/reprex2437bf19e2d4b1"

folder <- "kleyer-files"
data_zip <- paste0(folder, "/", "data.zip")

if (!dir.exists(folder)) {
  dir.create(folder)
}

if (!file.exists(data_zip)) {
  url <- "https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fj.1654-1103.2012.01402.x&file=jvs1402-sup-0004-AppendixS4.zip"
  download.file(url = url, destfile = data_zip)
  unzip(zipfile = data_zip, exdir = folder)
}

traits <- read.table(file = "kleyer-files/Appendix S4 scripts and data/data/Species_traits.txt", sep = "\t")
spe    <- read.table(file = "kleyer-files/Appendix S4 scripts and data/data/Site_species.txt", sep = "\t")
env    <- read.table(file = "kleyer-files/Appendix S4 scripts and data/data/Site_env.txt", sep = "\t")

coa <- dudi.coa(spe, scannf = F)

coa
#> Duality diagramm
#> class: coa dudi
#> $call: dudi.coa(df = spe, scannf = F)
#>
#> $nf: 2 axis-components saved
#> $rank: 42
#> eigen values: 0.7197 0.6659 0.6099 0.5452 0.5012 ...
#>   vector length mode    content
#> 1 $cw    50     numeric column weights
#> 2 $lw    43     numeric row weights
#> 3 $eig   42     numeric eigen values
#>
#>   data.frame nrow ncol content
#> 1 $tab       43   50   modified array
#> 2 $li        43   2    row coordinates
#> 3 $l1        43   2    row normed scores
#> 4 $co        50   2    column coordinates
#> 5 $c1        50   2    column normed scores
#> other elements: N

traits[, 1] <- as.numeric(traits[, 1])

pca.traits <- dudi.pca(traits, row.w = coa$cw, scannf = FALSE)
pca.env <- dudi.pca(env, row.w = coa$lw, scannf = FALSE)

rlq1 <- rlq(pca.env, coa, pca.traits, scannf = FALSE)
summary(rlq1)
#> RLQ analysis
#>
#> Class: rlq dudi
#> Call: rlq(dudiR = pca.env, dudiL = coa, dudiQ = pca.traits, scannf = FALSE)
#>
#> Total inertia: 0.6076
#>
#> Eigenvalues:
#>      Ax1      Ax2      Ax3
#> 0.347425 0.253025 0.007172
#>
#> Projected inertia (%):
#>     Ax1     Ax2     Ax3
#>   57.18   41.64    1.18
#>
#> Cumulative projected inertia (%):
#>     Ax1   Ax1:2   Ax1:3
#>   57.18   98.82  100.00
#>
#>
#> Eigenvalues decomposition:
#>         eig     covar       sdR      sdQ      corr
#> 1 0.3474245 0.5894273 0.9994426 1.316734 0.4478929
#> 2 0.2530248 0.5030157 1.1859679 1.136397 0.3732319
#>
#> Inertia & coinertia R (pca.env):
#>      inertia      max     ratio
#> 1  0.9988856 1.581479 0.6316149
#> 12 2.4054053 2.552662 0.9423125
#>
#> Inertia & coinertia Q (pca.traits):
#>     inertia      max     ratio
#> 1  1.733789 2.222861 0.7799810
#> 12 3.025187 3.195351 0.9467464
#>
#> Correlation L (coa):
#>        corr       max     ratio
#> 1 0.4478929 0.8483415 0.5279630
#> 2 0.3732319 0.8160086 0.4573872

plot(rlq1)

#' ![](reprex_reprex_files/figure-markdown_strict/reprex-body-1.png)


## Percentage of co-Inertia for each axis
100*rlq1$eig/sum(rlq1$eig)
#> [1] 57.177840 41.641884  1.180276

## weighted correlations axes / env.
t(pca.env$tab)%*%(diag(pca.env$lw))%*%as.matrix(rlq1$mR)
#>                NorS1      NorS2
#> dist.int  0.09551403  0.9599589
#> SOIL.P   -0.99445098 -0.1150855
#> SOIL.WHC  0.17425053  0.7637516

## weighted correlations axes / traits.
t(pca.traits$tab)%*%(diag(pca.traits$lw))%*%as.matrix(rlq1$mQ)
#>                    NorS1      NorS2
#> Polycarpic     0.7171193  0.1551089
#> Cnratio        0.5582854 -0.6262489
#> seed.mass.log  0.4932320  0.1147673
#> SLA           -0.6396080  0.6372234
#> height         0.5220954 -0.3724864
#> Onset.flower   0.4782056 -0.7687494

## correlations traits / env.
rlq1$tab
#>          Polycarpic    Cnratio seed.mass.log        SLA      height
#> dist.int  0.1467609 -0.2182632    0.13662287 0.17193497 -0.08406364
#> SOIL.P   -0.4311989 -0.1728592   -0.25391352 0.16158906 -0.11784596
#> SOIL.WHC  0.1243845 -0.1152605    0.09662426 0.05832776  0.05671719
#>          Onset.flower
#> dist.int  -0.30211986
#> SOIL.P    -0.14185350
#> SOIL.WHC  -0.08218956


devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Arch Linux
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    pt_BR.UTF-8
#>  tz       America/Sao_Paulo
#>  date     2020-07-15
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version  date       lib source
#>  ade4        * 1.7-15   2020-02-13 [1] CRAN (R 4.0.0)
#>  assertthat    0.2.1    2019-03-21 [1] CRAN (R 4.0.0)
#>  backports     1.1.5    2019-10-02 [1] CRAN (R 4.0.2)
#>  callr         3.4.3    2020-03-28 [1] CRAN (R 4.0.0)
#>  cli           2.0.2    2020-02-28 [1] CRAN (R 4.0.0)
#>  crayon        1.3.4    2017-09-16 [1] CRAN (R 4.0.0)
#>  desc          1.2.0    2018-05-01 [1] CRAN (R 4.0.0)
#>  devtools      2.3.0    2020-04-10 [1] CRAN (R 4.0.0)
#>  digest        0.6.25   2020-02-23 [1] CRAN (R 4.0.0)
#>  ellipsis      0.3.0    2019-09-20 [1] CRAN (R 4.0.2)
#>  evaluate      0.14     2019-05-28 [1] CRAN (R 4.0.0)
#>  fansi         0.4.1    2020-01-08 [1] CRAN (R 4.0.0)
#>  fs            1.4.2    2020-06-30 [1] CRAN (R 4.0.2)
#>  glue          1.4.0    2020-04-03 [1] CRAN (R 4.0.2)
#>  highr         0.8      2019-03-20 [1] CRAN (R 4.0.0)
#>  htmltools     0.5.0    2020-06-16 [1] CRAN (R 4.0.1)
#>  knitr         1.29     2020-06-23 [1] CRAN (R 4.0.1)
#>  magrittr      1.5      2014-11-22 [1] CRAN (R 4.0.0)
#>  MASS          7.3-51.6 2020-04-26 [2] CRAN (R 4.0.2)
#>  memoise       1.1.0    2017-04-21 [1] CRAN (R 4.0.0)
#>  pkgbuild      1.0.8    2020-05-07 [1] CRAN (R 4.0.0)
#>  pkgload       1.1.0    2020-05-29 [1] CRAN (R 4.0.0)
#>  prettyunits   1.1.1    2020-01-24 [1] CRAN (R 4.0.0)
#>  processx      3.4.3    2020-07-05 [1] CRAN (R 4.0.2)
#>  ps            1.3.3    2020-05-08 [1] CRAN (R 4.0.0)
#>  R6            2.4.1    2019-11-12 [1] CRAN (R 4.0.0)
#>  remotes       2.1.1    2020-02-15 [1] CRAN (R 4.0.0)
#>  rlang         0.4.6    2020-05-02 [1] CRAN (R 4.0.2)
#>  rmarkdown     2.3      2020-06-18 [1] CRAN (R 4.0.1)
#>  rprojroot     1.3-2    2018-01-03 [1] CRAN (R 4.0.0)
#>  sessioninfo   1.1.1    2018-11-05 [1] CRAN (R 4.0.0)
#>  stringi       1.4.3    2019-03-12 [1] CRAN (R 4.0.2)
#>  stringr       1.4.0    2019-02-10 [1] CRAN (R 4.0.0)
#>  testthat      2.3.2    2020-03-02 [1] CRAN (R 4.0.0)
#>  usethis       1.6.1    2020-04-29 [1] CRAN (R 4.0.0)
#>  withr         2.2.0    2020-04-20 [1] CRAN (R 4.0.0)
#>  xfun          0.15     2020-06-21 [1] CRAN (R 4.0.1)
#>  yaml          2.2.1    2020-02-01 [1] CRAN (R 4.0.0)
#>
#> [1] /home/karlo/.local/lib/R/library/4.0
#> [2] /usr/lib/R/library
	if (!require("ade4")) install.packages("ade4")
	#> Loading required package: ade4

	# Where am I?
	getwd()
	#> [1] "/tmp/RtmpK0kjbc/reprex2437bf19e2d4b1"

	folder <- "kleyer-files"
	data_zip <- paste0(folder, "/", "data.zip")

	if (!dir.exists(folder)) {
	dir.create(folder)
	}

	if (!file.exists(data_zip)) {
	url <- "https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fj.1654-1103.2012.01402.x&file=jvs1402-sup-0004-AppendixS4.zip"
	download.file(url = url, destfile = data_zip)
	unzip(zipfile = data_zip, exdir = folder)
	}

	traits <- read.table(file = "kleyer-files/Appendix S4 scripts and data/data/Species_traits.txt", sep = "\t")
	spe <- read.table(file = "kleyer-files/Appendix S4 scripts and data/data/Site_species.txt", sep = "\t")
	env <- read.table(file = "kleyer-files/Appendix S4 scripts and data/data/Site_env.txt", sep = "\t")

	coa <- dudi.coa(spe, scannf = F)

	coa
	#> Duality diagramm
	#> class: coa dudi
	#> $call: dudi.coa(df = spe, scannf = F)
	#>
	#> $nf: 2 axis-components saved
	#> $rank: 42
	#> eigen values: 0.7197 0.6659 0.6099 0.5452 0.5012 ...
	#> vector length mode content
	#> 1 $cw 50 numeric column weights
	#> 2 $lw 43 numeric row weights
	#> 3 $eig 42 numeric eigen values
	#>
	#> data.frame nrow ncol content
	#> 1 $tab 43 50 modified array
	#> 2 $li 43 2 row coordinates
	#> 3 $l1 43 2 row normed scores
	#> 4 $co 50 2 column coordinates
	#> 5 $c1 50 2 column normed scores
	#> other elements: N

	traits[, 1] <- as.numeric(traits[, 1])

	pca.traits <- dudi.pca(traits, row.w = coa$cw, scannf = FALSE)
	pca.env <- dudi.pca(env, row.w = coa$lw, scannf = FALSE)

	rlq1 <- rlq(pca.env, coa, pca.traits, scannf = FALSE)
	summary(rlq1)
	#> RLQ analysis
	#>
	#> Class: rlq dudi
	#> Call: rlq(dudiR = pca.env, dudiL = coa, dudiQ = pca.traits, scannf = FALSE)
	#>
	#> Total inertia: 0.6076
	#>
	#> Eigenvalues:
	#> Ax1 Ax2 Ax3
	#> 0.347425 0.253025 0.007172
	#>
	#> Projected inertia (%):
	#> Ax1 Ax2 Ax3
	#> 57.18 41.64 1.18
	#>
	#> Cumulative projected inertia (%):
	#> Ax1 Ax1:2 Ax1:3
	#> 57.18 98.82 100.00
	#>
	#>
	#> Eigenvalues decomposition:
	#> eig covar sdR sdQ corr
	#> 1 0.3474245 0.5894273 0.9994426 1.316734 0.4478929
	#> 2 0.2530248 0.5030157 1.1859679 1.136397 0.3732319
	#>
	#> Inertia & coinertia R (pca.env):
	#> inertia max ratio
	#> 1 0.9988856 1.581479 0.6316149
	#> 12 2.4054053 2.552662 0.9423125
	#>
	#> Inertia & coinertia Q (pca.traits):
	#> inertia max ratio
	#> 1 1.733789 2.222861 0.7799810
	#> 12 3.025187 3.195351 0.9467464
	#>
	#> Correlation L (coa):
	#> corr max ratio
	#> 1 0.4478929 0.8483415 0.5279630
	#> 2 0.3732319 0.8160086 0.4573872

	plot(rlq1)

	#' ![](reprex_reprex_files/figure-markdown_strict/reprex-body-1.png)


	## Percentage of co-Inertia for each axis
	100*rlq1$eig/sum(rlq1$eig)
	#> [1] 57.177840 41.641884 1.180276

	## weighted correlations axes / env.
	t(pca.env$tab)%%(diag(pca.env$lw))%%as.matrix(rlq1$mR)
	#> NorS1 NorS2
	#> dist.int 0.09551403 0.9599589
	#> SOIL.P -0.99445098 -0.1150855
	#> SOIL.WHC 0.17425053 0.7637516

	## weighted correlations axes / traits.
	t(pca.traits$tab)%%(diag(pca.traits$lw))%%as.matrix(rlq1$mQ)
	#> NorS1 NorS2
	#> Polycarpic 0.7171193 0.1551089
	#> Cnratio 0.5582854 -0.6262489
	#> seed.mass.log 0.4932320 0.1147673
	#> SLA -0.6396080 0.6372234
	#> height 0.5220954 -0.3724864
	#> Onset.flower 0.4782056 -0.7687494

	## correlations traits / env.
	rlq1$tab
	#> Polycarpic Cnratio seed.mass.log SLA height
	#> dist.int 0.1467609 -0.2182632 0.13662287 0.17193497 -0.08406364
	#> SOIL.P -0.4311989 -0.1728592 -0.25391352 0.16158906 -0.11784596
	#> SOIL.WHC 0.1243845 -0.1152605 0.09662426 0.05832776 0.05671719
	#> Onset.flower
	#> dist.int -0.30211986
	#> SOIL.P -0.14185350
	#> SOIL.WHC -0.08218956








	devtools::session_info()
	#> ─ Session info ───────────────────────────────────────────────────────────────
	#> setting value
	#> version R version 4.0.2 (2020-06-22)
	#> os Arch Linux
	#> system x86_64, linux-gnu
	#> ui X11
	#> language (EN)
	#> collate en_US.UTF-8
	#> ctype pt_BR.UTF-8
	#> tz America/Sao_Paulo
	#> date 2020-07-15
	#>
	#> ─ Packages ───────────────────────────────────────────────────────────────────
	#> package * version date lib source
	#> ade4 * 1.7-15 2020-02-13 [1] CRAN (R 4.0.0)
	#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
	#> backports 1.1.5 2019-10-02 [1] CRAN (R 4.0.2)
	#> callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
	#> cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
	#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
	#> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
	#> devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
	#> digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
	#> ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.2)
	#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
	#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
	#> fs 1.4.2 2020-06-30 [1] CRAN (R 4.0.2)
	#> glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.2)
	#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.0)
	#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.1)
	#> knitr 1.29 2020-06-23 [1] CRAN (R 4.0.1)
	#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
	#> MASS 7.3-51.6 2020-04-26 [2] CRAN (R 4.0.2)
	#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
	#> pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
	#> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
	#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
	#> processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2)
	#> ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
	#> R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
	#> remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
	#> rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.2)
	#> rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.1)
	#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
	#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
	#> stringi 1.4.3 2019-03-12 [1] CRAN (R 4.0.2)
	#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
	#> testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
	#> usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
	#> withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
	#> xfun 0.15 2020-06-21 [1] CRAN (R 4.0.1)
	#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
	#>
	#> [1] /home/karlo/.local/lib/R/library/4.0
	#> [2] /usr/lib/R/library