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LausanneBasic

Binder

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

Contents

The directory contains the material for the first four sessions (course and practical). The last session is designed for open discussion and personal work. The structure of this compendium is as follows:

  • 📁 course: Source (R Markdown) to reproduce the slides of the course. It contains also rendered versions (html and pdf documents) suitable for reading (the code is replaced by figures and tables in these files)
  • 📁 practical: Source and rendered versions of the slides. Corrections of practical are provided as R codes to reproduce the different analyses

Program

  • Session 1: Welcome, presentation of participants. Introduction, packages installation. Theory and 3D explanation of multivariate methods.
  • Session 2: Analysis of environmental data: Principal Component Analysis.
  • Session 3: Analysis of environmental data: Multiple Correspondence Analysis. Hill-Smith Analysis
  • Session 4:Analysis of species data: Correspondence Analysis and Principal Component Analysis. Principal Coordinates Analysis.
  • Session 5: Examples of use of multivariate analysis methods with ade4 in R. Group work and discussions on data sets presented by participants.

How to run in your browser or download and run locally

This course has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software itself and optionally RStudio Desktop.

You can download the compendium as a zip from from this URL: main.zip. After unzipping:

  • open the .Rproj file in RStudio
  • source make.R file to compile the different documents of the course.

An alternative is to use the following code in your R session:

usethis::use_course("sdray/LausanneBasic", destdir = "~/Bureau/")

How to cite

Please cite this document as:

Dray, S. (2023). Training in ade4 in R - Module I: Basic methods . Accessed 06 déc. 2023. Online at https://github.com/sdray/LausanneBasic/

Licenses

Text and figures : CC-BY-4.0

Code : See the DESCRIPTION file

Data : CC-0 attribution requested in reuse

Contributions

We welcome contributions from everyone.

Session Information

utils::sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
#> 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       
#>  [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

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