diff --git a/README.html b/README.html index 2a7bea3..1541b30 100644 --- a/README.html +++ b/README.html @@ -604,7 +604,7 @@

LausanneBasic

-

Binder

+

Binder

This repository contains the material for the course Training in ade4 in R - Module I: Basic methods.

Contents

@@ -672,7 +672,7 @@

How to cite

Please cite this document as:

Dray, S. (2023). Training in ade4 in R - Module I: Basic methods . -Accessed 03 déc. 2023. Online at https://github.com/sdray/LausanneBasic/

+Accessed 06 déc. 2023. Online at https://github.com/sdray/LausanneBasic/

Licenses

Text and figures : CC-BY-4.0

@@ -693,20 +693,32 @@

Session Information

#> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3 #> #> locale: -#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 -#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C -#> -#> attached base packages: -#> [1] stats graphics grDevices utils datasets methods base -#> -#> loaded via a namespace (and not attached): -#> [1] Rcpp_1.0.10 pillar_1.8.1 compiler_4.2.1 later_1.3.0 urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 tools_4.2.1 -#> [10] digest_0.6.29 pkgbuild_1.3.1 pkgload_1.3.0 tibble_3.1.8 memoise_2.0.1 evaluate_0.17 lifecycle_1.0.3 pkgconfig_2.0.3 rlang_1.0.6 -#> [19] shiny_1.7.2 cli_3.4.1 rstudioapi_0.14 yaml_2.3.5 pagedown_0.19 xfun_0.33 fastmap_1.1.0 knitr_1.40 stringr_1.4.1 -#> [28] vctrs_0.4.2 fs_1.5.2 htmlwidgets_1.5.4 devtools_2.4.5 rprojroot_2.0.3 here_1.0.1 glue_1.6.2 R6_2.5.1 processx_3.7.0 -#> [37] fansi_1.0.3 rmarkdown_2.17 sessioninfo_1.2.2 callr_3.7.3 purrr_0.3.5 magrittr_2.0.3 ps_1.7.1 promises_1.2.0.1 ellipsis_0.3.2 -#> [46] htmltools_0.5.3 usethis_2.1.6 mime_0.12 xtable_1.8-4 httpuv_1.6.6 utf8_1.2.2 stringi_1.7.8 miniUI_0.1.1.1 cachem_1.0.6 -#> [55] crayon_1.5.2 +#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 +#> [4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 +#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C +#> [10] LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C +#> +#> attached base packages: +#> [1] stats graphics grDevices utils datasets methods base +#> +#> other attached packages: +#> [1] ade4_1.7-22 +#> +#> loaded via a namespace (and not attached): +#> [1] Rcpp_1.0.10 pillar_1.8.1 compiler_4.2.1 later_1.3.0 +#> [5] urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 +#> [9] tools_4.2.1 digest_0.6.29 pkgbuild_1.3.1 pkgload_1.3.0 +#> [13] tibble_3.1.8 memoise_2.0.1 evaluate_0.17 lifecycle_1.0.3 +#> [17] pkgconfig_2.0.3 rlang_1.0.6 shiny_1.7.2 cli_3.4.1 +#> [21] rstudioapi_0.14 yaml_2.3.5 pagedown_0.19 xfun_0.33 +#> [25] fastmap_1.1.0 knitr_1.40 stringr_1.4.1 vctrs_0.4.2 +#> [29] fs_1.5.2 htmlwidgets_1.5.4 devtools_2.4.5 rprojroot_2.0.3 +#> [33] here_1.0.1 glue_1.6.2 R6_2.5.1 processx_3.7.0 +#> [37] fansi_1.0.3 rmarkdown_2.17 sessioninfo_1.2.2 callr_3.7.3 +#> [41] purrr_0.3.5 magrittr_2.0.3 MASS_7.3-57 ps_1.7.1 +#> [45] promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.3 usethis_2.1.6 +#> [49] mime_0.12 xtable_1.8-4 httpuv_1.6.6 utf8_1.2.2 +#> [53] stringi_1.7.8 miniUI_0.1.1.1 cachem_1.0.6 crayon_1.5.2 diff --git a/README.md b/README.md index f5a5065..a834cff 100644 --- a/README.md +++ b/README.md @@ -83,7 +83,7 @@ An alternative is to use the following code in your R session: Please cite this document as: > Dray, S. (2023). Training in ade4 in R - Module I: Basic methods . -> Accessed 03 déc. 2023. Online at +> Accessed 06 déc. 2023. Online at > ### Licenses @@ -113,18 +113,30 @@ utils::sessionInfo() #> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3 #> #> locale: -#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 -#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C +#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 +#> [4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 +#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C +#> [10] LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> +#> other attached packages: +#> [1] ade4_1.7-22 +#> #> loaded via a namespace (and not attached): -#> [1] Rcpp_1.0.10 pillar_1.8.1 compiler_4.2.1 later_1.3.0 urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 tools_4.2.1 -#> [10] digest_0.6.29 pkgbuild_1.3.1 pkgload_1.3.0 tibble_3.1.8 memoise_2.0.1 evaluate_0.17 lifecycle_1.0.3 pkgconfig_2.0.3 rlang_1.0.6 -#> [19] shiny_1.7.2 cli_3.4.1 rstudioapi_0.14 yaml_2.3.5 pagedown_0.19 xfun_0.33 fastmap_1.1.0 knitr_1.40 stringr_1.4.1 -#> [28] vctrs_0.4.2 fs_1.5.2 htmlwidgets_1.5.4 devtools_2.4.5 rprojroot_2.0.3 here_1.0.1 glue_1.6.2 R6_2.5.1 processx_3.7.0 -#> [37] fansi_1.0.3 rmarkdown_2.17 sessioninfo_1.2.2 callr_3.7.3 purrr_0.3.5 magrittr_2.0.3 ps_1.7.1 promises_1.2.0.1 ellipsis_0.3.2 -#> [46] htmltools_0.5.3 usethis_2.1.6 mime_0.12 xtable_1.8-4 httpuv_1.6.6 utf8_1.2.2 stringi_1.7.8 miniUI_0.1.1.1 cachem_1.0.6 -#> [55] crayon_1.5.2 +#> [1] Rcpp_1.0.10 pillar_1.8.1 compiler_4.2.1 later_1.3.0 +#> [5] urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 +#> [9] tools_4.2.1 digest_0.6.29 pkgbuild_1.3.1 pkgload_1.3.0 +#> [13] tibble_3.1.8 memoise_2.0.1 evaluate_0.17 lifecycle_1.0.3 +#> [17] pkgconfig_2.0.3 rlang_1.0.6 shiny_1.7.2 cli_3.4.1 +#> [21] rstudioapi_0.14 yaml_2.3.5 pagedown_0.19 xfun_0.33 +#> [25] fastmap_1.1.0 knitr_1.40 stringr_1.4.1 vctrs_0.4.2 +#> [29] fs_1.5.2 htmlwidgets_1.5.4 devtools_2.4.5 rprojroot_2.0.3 +#> [33] here_1.0.1 glue_1.6.2 R6_2.5.1 processx_3.7.0 +#> [37] fansi_1.0.3 rmarkdown_2.17 sessioninfo_1.2.2 callr_3.7.3 +#> [41] purrr_0.3.5 magrittr_2.0.3 MASS_7.3-57 ps_1.7.1 +#> [45] promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.3 usethis_2.1.6 +#> [49] mime_0.12 xtable_1.8-4 httpuv_1.6.6 utf8_1.2.2 +#> [53] stringi_1.7.8 miniUI_0.1.1.1 cachem_1.0.6 crayon_1.5.2 ``` diff --git a/course/session1/session1.html b/course/session1/session1.html index e11c192..4fe44e7 100644 --- a/course/session1/session1.html +++ b/course/session1/session1.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -346,8 +346,9 @@ ``` ``` -## [1] "dudi.acm" "dudi.coa" "dudi.dec" "dudi.fca" "dudi.fpca" "dudi.hillsmith" "dudi.mix" "dudi.nsc" "dudi.pca" "dudi.pco" -## [11] "dudi.type" +## [1] "dudi.acm" "dudi.coa" "dudi.dec" "dudi.fca" +## [5] "dudi.fpca" "dudi.hillsmith" "dudi.mix" "dudi.nsc" +## [9] "dudi.pca" "dudi.pco" "dudi.type" ``` --- # Available methods diff --git a/course/session1/session1.pdf b/course/session1/session1.pdf index cb2df82..43e17b1 100644 Binary files a/course/session1/session1.pdf and b/course/session1/session1.pdf differ diff --git a/course/session2/fig/unnamed-chunk-11-1.svg b/course/session2/fig/unnamed-chunk-11-1.svg index 98166c1..b7790ab 100644 --- a/course/session2/fig/unnamed-chunk-11-1.svg +++ b/course/session2/fig/unnamed-chunk-11-1.svg @@ -268,7 +268,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-12-1.svg b/course/session2/fig/unnamed-chunk-12-1.svg index b9c094d..0576f60 100644 --- a/course/session2/fig/unnamed-chunk-12-1.svg +++ b/course/session2/fig/unnamed-chunk-12-1.svg @@ -271,7 +271,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-13-1.svg b/course/session2/fig/unnamed-chunk-13-1.svg index c6d1a55..11ffd08 100644 --- a/course/session2/fig/unnamed-chunk-13-1.svg +++ b/course/session2/fig/unnamed-chunk-13-1.svg @@ -52,7 +52,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-14-1.svg b/course/session2/fig/unnamed-chunk-14-1.svg index a9daeba..0f316ca 100644 --- a/course/session2/fig/unnamed-chunk-14-1.svg +++ b/course/session2/fig/unnamed-chunk-14-1.svg @@ -94,7 +94,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-15-1.svg b/course/session2/fig/unnamed-chunk-15-1.svg index 9a3196a..b9f282c 100644 --- a/course/session2/fig/unnamed-chunk-15-1.svg +++ b/course/session2/fig/unnamed-chunk-15-1.svg @@ -52,7 +52,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-16-1.svg b/course/session2/fig/unnamed-chunk-16-1.svg index 9e0b436..146f2a9 100644 --- a/course/session2/fig/unnamed-chunk-16-1.svg +++ b/course/session2/fig/unnamed-chunk-16-1.svg @@ -97,7 +97,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-17-1.svg b/course/session2/fig/unnamed-chunk-17-1.svg index 534c372..342551f 100644 --- a/course/session2/fig/unnamed-chunk-17-1.svg +++ b/course/session2/fig/unnamed-chunk-17-1.svg @@ -55,7 +55,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-18-1.svg b/course/session2/fig/unnamed-chunk-18-1.svg index 0fbdab0..bd9c281 100644 --- a/course/session2/fig/unnamed-chunk-18-1.svg +++ b/course/session2/fig/unnamed-chunk-18-1.svg @@ -94,7 +94,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-20-1.svg b/course/session2/fig/unnamed-chunk-20-1.svg index b83c77a..bfc417f 100644 --- a/course/session2/fig/unnamed-chunk-20-1.svg +++ b/course/session2/fig/unnamed-chunk-20-1.svg @@ -307,7 +307,7 @@ - + diff --git a/course/session2/fig/unnamed-chunk-21-1.svg b/course/session2/fig/unnamed-chunk-21-1.svg index dee18ca..550ac5d 100644 --- a/course/session2/fig/unnamed-chunk-21-1.svg +++ b/course/session2/fig/unnamed-chunk-21-1.svg @@ -295,7 +295,7 @@ - + diff --git a/course/session2/session2.html b/course/session2/session2.html index 0f19598..b6486b4 100644 --- a/course/session2/session2.html +++ b/course/session2/session2.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -123,7 +123,7 @@ ## [1] "Temp" "Flow" "pH" "Cond" "Bdo5" "Oxyd" "Ammo" "Nitr" "Phos" ``` --- -The data set contains an environmental table with 20 measurements of 9 environmental variables. The measurements have been made in 6 sites at each season along a small French stream (see `?meaudret`) +The data set contains an environmental table with 20 measurements of 9 environmental variables. The measurements have been made in 5 sites at each season along a small French stream (see `?meaudret`) ```r @@ -219,7 +219,8 @@ ``` ``` -## [1] "tab" "cw" "lw" "eig" "rank" "nf" "c1" "li" "co" "l1" "call" "cent" "norm" +## [1] "tab" "cw" "lw" "eig" "rank" "nf" "c1" "li" "co" "l1" "call" +## [12] "cent" "norm" ``` It returns an object of class `dudi` containing: diff --git a/course/session2/session2.pdf b/course/session2/session2.pdf index deb781c..989241f 100644 Binary files a/course/session2/session2.pdf and b/course/session2/session2.pdf differ diff --git a/course/session3/fig/unnamed-chunk-12-1.svg b/course/session3/fig/unnamed-chunk-12-1.svg index a89db36..7048224 100644 --- a/course/session3/fig/unnamed-chunk-12-1.svg +++ b/course/session3/fig/unnamed-chunk-12-1.svg @@ -94,7 +94,7 @@ - + diff --git a/course/session3/fig/unnamed-chunk-13-1.svg b/course/session3/fig/unnamed-chunk-13-1.svg index 9d7df43..c347837 100644 --- a/course/session3/fig/unnamed-chunk-13-1.svg +++ b/course/session3/fig/unnamed-chunk-13-1.svg @@ -49,7 +49,7 @@ - + diff --git a/course/session3/fig/unnamed-chunk-14-1.svg b/course/session3/fig/unnamed-chunk-14-1.svg index e10442f..2a480b7 100644 --- a/course/session3/fig/unnamed-chunk-14-1.svg +++ b/course/session3/fig/unnamed-chunk-14-1.svg @@ -565,7 +565,7 @@ - + diff --git a/course/session3/fig/unnamed-chunk-4-1.svg b/course/session3/fig/unnamed-chunk-4-1.svg index 60c13c5..e1c6114 100644 --- a/course/session3/fig/unnamed-chunk-4-1.svg +++ b/course/session3/fig/unnamed-chunk-4-1.svg @@ -103,7 +103,7 @@ - + diff --git a/course/session3/session3.html b/course/session3/session3.html index 1b977f2..241e31e 100644 --- a/course/session3/session3.html +++ b/course/session3/session3.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -244,7 +244,8 @@ ``` ``` -## [1] "tab" "cw" "lw" "eig" "rank" "nf" "l1" "co" "li" "c1" "call" "cr" +## [1] "tab" "cw" "lw" "eig" "rank" "nf" "l1" "co" "li" "c1" "call" +## [12] "cr" ``` It returns an object of class `dudi` containing: diff --git a/course/session3/session3.pdf b/course/session3/session3.pdf index 113f85d..0276cdf 100644 Binary files a/course/session3/session3.pdf and b/course/session3/session3.pdf differ diff --git a/course/session4/fig/unnamed-chunk-14-1.svg b/course/session4/fig/unnamed-chunk-14-1.svg index a2aa514..5ce2b18 100644 --- a/course/session4/fig/unnamed-chunk-14-1.svg +++ b/course/session4/fig/unnamed-chunk-14-1.svg @@ -151,7 +151,7 @@ - + diff --git a/course/session4/fig/unnamed-chunk-15-1.svg b/course/session4/fig/unnamed-chunk-15-1.svg index 2df00f3..c64d1c8 100644 --- a/course/session4/fig/unnamed-chunk-15-1.svg +++ b/course/session4/fig/unnamed-chunk-15-1.svg @@ -61,7 +61,7 @@ - + diff --git a/course/session4/fig/unnamed-chunk-16-1.svg b/course/session4/fig/unnamed-chunk-16-1.svg index e0ee69b..dc92cab 100644 --- a/course/session4/fig/unnamed-chunk-16-1.svg +++ b/course/session4/fig/unnamed-chunk-16-1.svg @@ -103,7 +103,7 @@ - + @@ -155,29 +155,29 @@ - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + @@ -185,9 +185,9 @@ - - - + + + @@ -195,14 +195,14 @@ - - - + + + - - - + + + @@ -210,14 +210,14 @@ - - - + + + - - - + + + diff --git a/course/session4/fig/unnamed-chunk-17-1.svg b/course/session4/fig/unnamed-chunk-17-1.svg index cd037a0..8da3b30 100644 --- a/course/session4/fig/unnamed-chunk-17-1.svg +++ b/course/session4/fig/unnamed-chunk-17-1.svg @@ -85,7 +85,7 @@ - + @@ -146,22 +146,22 @@ - - - - + + + + - - - - + + + + - - - - + + + + @@ -170,22 +170,22 @@ - - - - + + + + - - - - + + + + - - - - + + + + @@ -194,16 +194,16 @@ - - - - + + + + - - - - + + + + @@ -212,22 +212,22 @@ - - - - + + + + - - - - + + + + - - - - + + + + @@ -248,10 +248,10 @@ - - - - + + + + @@ -260,10 +260,10 @@ - - - - + + + + diff --git a/course/session4/fig/unnamed-chunk-18-1.svg b/course/session4/fig/unnamed-chunk-18-1.svg index e328562..a8acb1b 100644 --- a/course/session4/fig/unnamed-chunk-18-1.svg +++ b/course/session4/fig/unnamed-chunk-18-1.svg @@ -124,7 +124,7 @@ - + diff --git a/course/session4/fig/unnamed-chunk-19-1.svg b/course/session4/fig/unnamed-chunk-19-1.svg index d707155..4d7f2bb 100644 --- a/course/session4/fig/unnamed-chunk-19-1.svg +++ b/course/session4/fig/unnamed-chunk-19-1.svg @@ -97,7 +97,7 @@ - + @@ -176,58 +176,58 @@ - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + @@ -236,10 +236,10 @@ - - - - + + + + @@ -254,10 +254,10 @@ - - - - + + + + @@ -266,10 +266,10 @@ - - - - + + + + @@ -284,10 +284,10 @@ - - - - + + + + diff --git a/course/session4/fig/unnamed-chunk-4-1.svg b/course/session4/fig/unnamed-chunk-4-1.svg index e7f64bf..dc2366d 100644 --- a/course/session4/fig/unnamed-chunk-4-1.svg +++ b/course/session4/fig/unnamed-chunk-4-1.svg @@ -124,7 +124,7 @@ - + diff --git a/course/session4/fig/unnamed-chunk-7-1.svg b/course/session4/fig/unnamed-chunk-7-1.svg index 69a4db5..99571fd 100644 --- a/course/session4/fig/unnamed-chunk-7-1.svg +++ b/course/session4/fig/unnamed-chunk-7-1.svg @@ -156,13 +156,13 @@ - + - + - + @@ -385,7 +385,7 @@ - + @@ -430,7 +430,7 @@ - + diff --git a/course/session4/session4.html b/course/session4/session4.html index 6fb6395..023a6a9 100644 --- a/course/session4/session4.html +++ b/course/session4/session4.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -119,10 +119,11 @@ ``` ``` -## [1] "Ephemera_danica" "Baetis_sp" "Baetis_rhodani" "Baetis_niger" "Baetis_muticus" "Centroptilum_sp" +## [1] "Ephemera_danica" "Baetis_sp" "Baetis_rhodani" "Baetis_niger" +## [5] "Baetis_muticus" "Centroptilum_sp" ``` --- -The data set contains the abundances of 13 Ephemeroptera species in 20 samples. The measurements have been made in 6 sites at each season along a small French stream (see `?meaudret`) +The data set contains the abundances of 13 Ephemeroptera species in 20 samples. The measurements have been made in 5 sites at each season along a small French stream (see `?meaudret`) ```r @@ -199,7 +200,8 @@ ``` ``` -## Warning in chisq.test(meaudret$spe): L’approximation du Chi-2 est peut-être incorrecte +## Warning in chisq.test(meaudret$spe): L’approximation du Chi-2 est peut-être +## incorrecte ``` ``` @@ -284,7 +286,8 @@ ``` ``` -## [1] "tab" "cw" "lw" "eig" "rank" "nf" "c1" "li" "co" "l1" "call" "N" +## [1] "tab" "cw" "lw" "eig" "rank" "nf" "c1" "li" "co" "l1" "call" +## [12] "N" ``` It returns an object of class `dudi` containing: diff --git a/course/session4/session4.pdf b/course/session4/session4.pdf index cd385b9..8f9c353 100644 Binary files a/course/session4/session4.pdf and b/course/session4/session4.pdf differ diff --git a/practical/session1/session1.html b/practical/session1/session1.html index 1539a0c..313fa56 100644 --- a/practical/session1/session1.html +++ b/practical/session1/session1.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -382,7 +382,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -477,8 +477,8 @@ ``` .pull-left[ -
- +
+ ] .pull-right[ diff --git a/practical/session1/session1.pdf b/practical/session1/session1.pdf index fda19dc..f786007 100644 Binary files a/practical/session1/session1.pdf and b/practical/session1/session1.pdf differ diff --git a/practical/session2/fig/unnamed-chunk-10-1.svg b/practical/session2/fig/unnamed-chunk-10-1.svg index ac4852b..92b4f60 100644 --- a/practical/session2/fig/unnamed-chunk-10-1.svg +++ b/practical/session2/fig/unnamed-chunk-10-1.svg @@ -154,7 +154,7 @@ - + @@ -366,106 +366,106 @@ - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + diff --git a/practical/session2/fig/unnamed-chunk-11-1.svg b/practical/session2/fig/unnamed-chunk-11-1.svg index 9b4b000..72ea37a 100644 --- a/practical/session2/fig/unnamed-chunk-11-1.svg +++ b/practical/session2/fig/unnamed-chunk-11-1.svg @@ -46,7 +46,7 @@ - + diff --git a/practical/session2/fig/unnamed-chunk-13-1.svg b/practical/session2/fig/unnamed-chunk-13-1.svg index 0627b5d..b363cf6 100644 --- a/practical/session2/fig/unnamed-chunk-13-1.svg +++ b/practical/session2/fig/unnamed-chunk-13-1.svg @@ -226,7 +226,7 @@ - + diff --git a/practical/session2/fig/unnamed-chunk-3-1.svg b/practical/session2/fig/unnamed-chunk-3-1.svg index c28fbc5..4e76d6f 100644 --- a/practical/session2/fig/unnamed-chunk-3-1.svg +++ b/practical/session2/fig/unnamed-chunk-3-1.svg @@ -109,7 +109,7 @@ - + diff --git a/practical/session2/fig/unnamed-chunk-4-1.svg b/practical/session2/fig/unnamed-chunk-4-1.svg index cd10db8..6485f49 100644 --- a/practical/session2/fig/unnamed-chunk-4-1.svg +++ b/practical/session2/fig/unnamed-chunk-4-1.svg @@ -91,7 +91,7 @@ - + diff --git a/practical/session2/fig/unnamed-chunk-5-1.svg b/practical/session2/fig/unnamed-chunk-5-1.svg index fe6e969..0664333 100644 --- a/practical/session2/fig/unnamed-chunk-5-1.svg +++ b/practical/session2/fig/unnamed-chunk-5-1.svg @@ -76,7 +76,7 @@ - + diff --git a/practical/session2/fig/unnamed-chunk-6-1.svg b/practical/session2/fig/unnamed-chunk-6-1.svg index 055e813..c636a81 100644 --- a/practical/session2/fig/unnamed-chunk-6-1.svg +++ b/practical/session2/fig/unnamed-chunk-6-1.svg @@ -94,7 +94,7 @@ - + diff --git a/practical/session2/fig/unnamed-chunk-9-1.svg b/practical/session2/fig/unnamed-chunk-9-1.svg index bbab654..d1e5b4a 100644 --- a/practical/session2/fig/unnamed-chunk-9-1.svg +++ b/practical/session2/fig/unnamed-chunk-9-1.svg @@ -142,7 +142,7 @@ - + diff --git a/practical/session2/session2-corrected.html b/practical/session2/session2-corrected.html index 036fa64..1837328 100644 --- a/practical/session2/session2-corrected.html +++ b/practical/session2/session2-corrected.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -239,9 +239,12 @@ ``` ``` -## dfs alt slo flo pH har pho nit amm oxy bdo -## RS1 0.8733503 -0.8390535 -0.7602047 0.7777617 -0.02457895 0.7122973 0.8111056 0.9015491 0.7671086 -0.7489949 0.7375260 -## RS2 -0.3963445 0.4537709 0.4145874 -0.5037445 -0.37560694 -0.4011204 0.5033806 0.1066847 0.5785809 -0.4280275 0.5985336 +## dfs alt slo flo pH har pho +## RS1 0.8733503 -0.8390535 -0.7602047 0.7777617 -0.02457895 0.7122973 0.8111056 +## RS2 -0.3963445 0.4537709 0.4145874 -0.5037445 -0.37560694 -0.4011204 0.5033806 +## nit amm oxy bdo +## RS1 0.9015491 0.7671086 -0.7489949 0.7375260 +## RS2 0.1066847 0.5785809 -0.4280275 0.5985336 ``` ```r diff --git a/practical/session2/session2-corrected.pdf b/practical/session2/session2-corrected.pdf index 2e0734b..5403b40 100644 Binary files a/practical/session2/session2-corrected.pdf and b/practical/session2/session2-corrected.pdf differ diff --git a/practical/session2/session2.html b/practical/session2/session2.html index 25007fd..d0ce914 100644 --- a/practical/session2/session2.html +++ b/practical/session2/session2.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- diff --git a/practical/session2/session2.pdf b/practical/session2/session2.pdf index 4618f44..7c5ead2 100644 Binary files a/practical/session2/session2.pdf and b/practical/session2/session2.pdf differ diff --git a/practical/session3/fig/unnamed-chunk-10-1.svg b/practical/session3/fig/unnamed-chunk-10-1.svg index 2952b38..beab345 100644 --- a/practical/session3/fig/unnamed-chunk-10-1.svg +++ b/practical/session3/fig/unnamed-chunk-10-1.svg @@ -301,7 +301,7 @@ - + diff --git a/practical/session3/fig/unnamed-chunk-3-1.svg b/practical/session3/fig/unnamed-chunk-3-1.svg index 3235c59..be568b3 100644 --- a/practical/session3/fig/unnamed-chunk-3-1.svg +++ b/practical/session3/fig/unnamed-chunk-3-1.svg @@ -133,7 +133,7 @@ - + diff --git a/practical/session3/fig/unnamed-chunk-4-1.svg b/practical/session3/fig/unnamed-chunk-4-1.svg index 2a9c153..4ef20d9 100644 --- a/practical/session3/fig/unnamed-chunk-4-1.svg +++ b/practical/session3/fig/unnamed-chunk-4-1.svg @@ -469,7 +469,7 @@ - + diff --git a/practical/session3/fig/unnamed-chunk-5-1.svg b/practical/session3/fig/unnamed-chunk-5-1.svg index ace0ecb..d1e6922 100644 --- a/practical/session3/fig/unnamed-chunk-5-1.svg +++ b/practical/session3/fig/unnamed-chunk-5-1.svg @@ -46,7 +46,7 @@ - + diff --git a/practical/session3/fig/unnamed-chunk-7-1.svg b/practical/session3/fig/unnamed-chunk-7-1.svg index 42c346c..0036dec 100644 --- a/practical/session3/fig/unnamed-chunk-7-1.svg +++ b/practical/session3/fig/unnamed-chunk-7-1.svg @@ -388,7 +388,7 @@ - + diff --git a/practical/session3/session3-corrected.html b/practical/session3/session3-corrected.html index 965eaf9..b236ae5 100644 --- a/practical/session3/session3-corrected.html +++ b/practical/session3/session3-corrected.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -126,9 +126,9 @@ <img src="fig/unnamed-chunk-4-1.svg" style="display: block; margin: auto;" /> --- -# PCA scores on the geographical map +# MCA scores on the geographical map -* Draw maps of PCA scores on the first two axes +* Draw maps of MCA scores on the first two axes * Interpret the maps to describe the environmental structure of the river diff --git a/practical/session3/session3-corrected.pdf b/practical/session3/session3-corrected.pdf index 6be284e..8b4d22b 100644 Binary files a/practical/session3/session3-corrected.pdf and b/practical/session3/session3-corrected.pdf differ diff --git a/practical/session3/session3.html b/practical/session3/session3.html index 9a0fd93..798d143 100644 --- a/practical/session3/session3.html +++ b/practical/session3/session3.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -115,9 +115,9 @@ --- -# PCA scores on the geographical map +# MCA scores on the geographical map -* Draw maps of PCA scores on the first two axes +* Draw maps of MCA scores on the first two axes * Interpret the maps to describe the environmental structure of the river diff --git a/practical/session3/session3.pdf b/practical/session3/session3.pdf index 5758505..d359060 100644 Binary files a/practical/session3/session3.pdf and b/practical/session3/session3.pdf differ diff --git a/practical/session4/fig/unnamed-chunk-2-1.svg b/practical/session4/fig/unnamed-chunk-2-1.svg index 4c34426..2fbc592 100644 --- a/practical/session4/fig/unnamed-chunk-2-1.svg +++ b/practical/session4/fig/unnamed-chunk-2-1.svg @@ -136,7 +136,7 @@ - + diff --git a/practical/session4/fig/unnamed-chunk-4-1.svg b/practical/session4/fig/unnamed-chunk-4-1.svg index 010fd29..04e5a53 100644 --- a/practical/session4/fig/unnamed-chunk-4-1.svg +++ b/practical/session4/fig/unnamed-chunk-4-1.svg @@ -388,7 +388,7 @@ - + diff --git a/practical/session4/fig/unnamed-chunk-5-1.svg b/practical/session4/fig/unnamed-chunk-5-1.svg index 2dfe339..cddfe25 100644 --- a/practical/session4/fig/unnamed-chunk-5-1.svg +++ b/practical/session4/fig/unnamed-chunk-5-1.svg @@ -46,7 +46,7 @@ - + diff --git a/practical/session4/fig/unnamed-chunk-6-1.svg b/practical/session4/fig/unnamed-chunk-6-1.svg index de49b72..2f26896 100644 --- a/practical/session4/fig/unnamed-chunk-6-1.svg +++ b/practical/session4/fig/unnamed-chunk-6-1.svg @@ -379,7 +379,7 @@ - + diff --git a/practical/session4/fig/unnamed-chunk-7-1.svg b/practical/session4/fig/unnamed-chunk-7-1.svg index d109b88..bdaed0e 100644 --- a/practical/session4/fig/unnamed-chunk-7-1.svg +++ b/practical/session4/fig/unnamed-chunk-7-1.svg @@ -385,7 +385,7 @@ - + diff --git a/practical/session4/fig/unnamed-chunk-8-1.svg b/practical/session4/fig/unnamed-chunk-8-1.svg index 426f6fe..0251441 100644 --- a/practical/session4/fig/unnamed-chunk-8-1.svg +++ b/practical/session4/fig/unnamed-chunk-8-1.svg @@ -367,7 +367,7 @@ - + diff --git a/practical/session4/fig/unnamed-chunk-9-1.svg b/practical/session4/fig/unnamed-chunk-9-1.svg index ff9a6d6..b38ab49 100644 --- a/practical/session4/fig/unnamed-chunk-9-1.svg +++ b/practical/session4/fig/unnamed-chunk-9-1.svg @@ -88,7 +88,7 @@ - + diff --git a/practical/session4/session4-corrected.html b/practical/session4/session4-corrected.html index 1e24342..1bf82fb 100644 --- a/practical/session4/session4-corrected.html +++ b/practical/session4/session4-corrected.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -90,8 +90,9 @@ ``` ``` -## [1] "Cogo" "Satr" "Phph" "Neba" "Thth" "Teso" "Chna" "Chto" "Lele" "Lece" "Baba" "Spbi" "Gogo" "Eslu" "Pefl" "Rham" "Legi" "Scer" "Cyca" "Titi" "Abbr" "Icme" "Acce" "Ruru" -## [25] "Blbj" "Alal" "Anan" +## [1] "Cogo" "Satr" "Phph" "Neba" "Thth" "Teso" "Chna" "Chto" "Lele" "Lece" "Baba" +## [12] "Spbi" "Gogo" "Eslu" "Pefl" "Rham" "Legi" "Scer" "Cyca" "Titi" "Abbr" "Icme" +## [23] "Acce" "Ruru" "Blbj" "Alal" "Anan" ``` --- # Correspondence Analysis @@ -109,7 +110,7 @@ --- # Inertia statistics -* Compute the percentage of variation explained bu the first PCA axes +* Compute the percentage of variation explained by the first COA axes ```r @@ -166,7 +167,7 @@ --- # Principal Component Analysis -PCA can also be applied on the abundance table. Perform PCAon `doubs$fish` table. Should we scale or not? +PCA can also be applied on the abundance table. Perform PCA on `doubs$fish` table. Should we scale or not? ```r diff --git a/practical/session4/session4-corrected.pdf b/practical/session4/session4-corrected.pdf index 35837f2..4200da7 100644 Binary files a/practical/session4/session4-corrected.pdf and b/practical/session4/session4-corrected.pdf differ diff --git a/practical/session4/session4.html b/practical/session4/session4.html index 8996c0b..df886d2 100644 --- a/practical/session4/session4.html +++ b/practical/session4/session4.html @@ -4,7 +4,7 @@ Training in ade4 in R - Module I: Basic methods - + @@ -23,7 +23,7 @@ ### Stéphane Dray ] .date[ -### 2023-12-03 +### 2023-12-06 ] --- @@ -90,8 +90,9 @@ ``` ``` -## [1] "Cogo" "Satr" "Phph" "Neba" "Thth" "Teso" "Chna" "Chto" "Lele" "Lece" "Baba" "Spbi" "Gogo" "Eslu" "Pefl" "Rham" "Legi" "Scer" "Cyca" "Titi" "Abbr" "Icme" "Acce" "Ruru" -## [25] "Blbj" "Alal" "Anan" +## [1] "Cogo" "Satr" "Phph" "Neba" "Thth" "Teso" "Chna" "Chto" "Lele" "Lece" "Baba" +## [12] "Spbi" "Gogo" "Eslu" "Pefl" "Rham" "Legi" "Scer" "Cyca" "Titi" "Abbr" "Icme" +## [23] "Acce" "Ruru" "Blbj" "Alal" "Anan" ``` --- # Correspondence Analysis @@ -103,7 +104,7 @@ --- # Inertia statistics -* Compute the percentage of variation explained bu the first PCA axes +* Compute the percentage of variation explained by the first COA axes @@ -123,7 +124,7 @@ --- # Principal Component Analysis -PCA can also be applied on the abundance table. Perform PCAon `doubs$fish` table. Should we scale or not? +PCA can also be applied on the abundance table. Perform PCA on `doubs$fish` table. Should we scale or not? --- diff --git a/practical/session4/session4.pdf b/practical/session4/session4.pdf index 6f2325f..9db118f 100644 Binary files a/practical/session4/session4.pdf and b/practical/session4/session4.pdf differ