/
README.html
724 lines (714 loc) · 22 KB
/
README.html
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<!DOCTYPE html>
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<!-- README.md is generated from README.Rmd. Please edit that file -->
<h1 id="lausannebasic">LausanneBasic</h1>
<p><a href="https://mybinder.org/v2/gh/sdray/LausanneBasic/main?urlpath=rstudio"><img src="https://mybinder.org/badge_logo.svg" alt="Binder" /></a></p>
<p>This repository contains the material for the course <em>Training in
ade4 in R - Module I: Basic methods</em>.</p>
<h2 id="contents">Contents</h2>
<p>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:</p>
<ul>
<li><a href="course"><span class="emoji" data-emoji="file_folder">📁</span> course</a>: 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)</li>
<li><a href="practical"><span class="emoji" data-emoji="file_folder">📁</span> practical</a>: Source and rendered
versions of the slides. Corrections of practical are provided as R codes
to reproduce the different analyses</li>
</ul>
<h2 id="program">Program</h2>
<ul>
<li><strong>Session 1</strong>: Welcome, presentation of participants.
Introduction, packages installation. Theory and 3D explanation of
multivariate methods.
<ul>
<li>Course [<a href="course/session1/session1.html">html</a>|<a href="course/session1/session1.pdf">pdf</a>|<a href="course/session1/session1.Rmd">Rmd</a>]</li>
<li>Practical [<a href="practical/session1/session1.html">html</a>|<a href="practical/session1/session1.pdf">pdf</a>|<a href="practical/session1/session1.Rmd">Rmd</a>]</li>
</ul></li>
<li><strong>Session 2</strong>: Analysis of environmental data:
Principal Component Analysis.
<ul>
<li>Course [<a href="course/session2/session2.html">html</a>|<a href="course/session2/session2.pdf">pdf</a>|<a href="course/session2/session2.Rmd">Rmd</a>]</li>
<li>Practical [<a href="practical/session2/session2.html">html</a>|<a href="practical/session2/session2.pdf">pdf</a>|<a href="practical/session2/session2.Rmd">Rmd</a>] / Correction [<a href="practical/session2/session2-corrected.html">html</a>|<a href="practical/session2/session2-corrected.pdf">pdf</a>]</li>
</ul></li>
<li><strong>Session 3</strong>: Analysis of environmental data: Multiple
Correspondence Analysis. Hill-Smith Analysis
<ul>
<li>Course [<a href="course/session3/session3.html">html</a>|<a href="course/session3/session3.pdf">pdf</a>|<a href="course/session3/session3.Rmd">Rmd</a>]</li>
<li>Practical [<a href="practical/session3/session3.html">html</a>|<a href="practical/session3/session3.pdf">pdf</a>|<a href="practical/session3/session3.Rmd">Rmd</a>] / Correction [<a href="practical/session3/session3-corrected.html">html</a>|<a href="practical/session3/session3-corrected.pdf">pdf</a>]</li>
</ul></li>
<li><strong>Session 4</strong>:Analysis of species data: Correspondence
Analysis and Principal Component Analysis. Principal Coordinates
Analysis.
<ul>
<li>Course [<a href="course/session4/session4.html">html</a>|<a href="course/session4/session4.pdf">pdf</a>|<a href="course/session4/session4.Rmd">Rmd</a>]</li>
<li>Practical [<a href="practical/session4/session4.html">html</a>|<a href="practical/session4/session4.pdf">pdf</a>|<a href="practical/session4/session4.Rmd">Rmd</a>] / Correction [<a href="practical/session4/session4-corrected.html">html</a>|<a href="practical/session4/session4-corrected.pdf">pdf</a>]</li>
</ul></li>
<li><strong>Session 5</strong>: Examples of use of multivariate analysis
methods with ade4 in R. Group work and discussions on data sets
presented by participants.</li>
</ul>
<h2 id="how-to-run-in-your-browser-or-download-and-run-locally">How to
run in your browser or download and run locally</h2>
<p>This course has been developed using the statistical programming
language R. To work with the compendium, you will need installed on your
computer the <a href="https://cloud.r-project.org/">R software</a>
itself and optionally <a href="https://rstudio.com/products/rstudio/download/">RStudio
Desktop</a>.</p>
<p>You can download the compendium as a zip from from this URL: <a href="https://github.com/sdray/LausanneBasic/archive/refs/heads/main.zip">main.zip</a>.
After unzipping:</p>
<ul>
<li>open the <code>.Rproj</code> file in RStudio</li>
<li>source <code>make.R</code> file to compile the different documents
of the course.</li>
</ul>
<p>An alternative is to use the following code in your R session:</p>
<p><code>usethis::use_course("sdray/LausanneBasic", destdir = "~/Bureau/")</code></p>
<h3 id="how-to-cite">How to cite</h3>
<p>Please cite this document as:</p>
<blockquote>
<p>Dray, S. (2023). Training in ade4 in R - Module I: Basic methods .
Accessed 06 déc. 2023. Online at <a href="https://github.com/sdray/LausanneBasic/">https://github.com/sdray/LausanneBasic/</a></p>
</blockquote>
<h3 id="licenses">Licenses</h3>
<p><strong>Text and figures :</strong> <a href="http://creativecommons.org/licenses/by/4.0/">CC-BY-4.0</a></p>
<p><strong>Code :</strong> See the <a href="DESCRIPTION">DESCRIPTION</a>
file</p>
<p><strong>Data :</strong> <a href="http://creativecommons.org/publicdomain/zero/1.0/">CC-0</a>
attribution requested in reuse</p>
<h3 id="contributions">Contributions</h3>
<p>We welcome contributions from everyone.</p>
<h3 id="session-information">Session Information</h3>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>utils<span class="sc">::</span><span class="fu">sessionInfo</span>()</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> R version 4.2.1 (2022-06-23)</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> Platform: x86_64-pc-linux-gnu (64-bit)</span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> Running under: Ubuntu 22.04.3 LTS</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> Matrix products: default</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3</span></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co">#> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3</span></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#> locale:</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 </span></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#> [4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 </span></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C </span></span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="co">#> [10] LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C </span></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="co">#> attached base packages:</span></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] stats graphics grDevices utils datasets methods base </span></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="co">#> other attached packages:</span></span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] ade4_1.7-22</span></span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a><span class="co">#> loaded via a namespace (and not attached):</span></span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] Rcpp_1.0.10 pillar_1.8.1 compiler_4.2.1 later_1.3.0 </span></span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="co">#> [5] urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 </span></span>
<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a><span class="co">#> [9] tools_4.2.1 digest_0.6.29 pkgbuild_1.3.1 pkgload_1.3.0 </span></span>
<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="co">#> [13] tibble_3.1.8 memoise_2.0.1 evaluate_0.17 lifecycle_1.0.3 </span></span>
<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a><span class="co">#> [17] pkgconfig_2.0.3 rlang_1.0.6 shiny_1.7.2 cli_3.4.1 </span></span>
<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a><span class="co">#> [21] rstudioapi_0.14 yaml_2.3.5 pagedown_0.19 xfun_0.33 </span></span>
<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a><span class="co">#> [25] fastmap_1.1.0 knitr_1.40 stringr_1.4.1 vctrs_0.4.2 </span></span>
<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a><span class="co">#> [29] fs_1.5.2 htmlwidgets_1.5.4 devtools_2.4.5 rprojroot_2.0.3 </span></span>
<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a><span class="co">#> [33] here_1.0.1 glue_1.6.2 R6_2.5.1 processx_3.7.0 </span></span>
<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a><span class="co">#> [37] fansi_1.0.3 rmarkdown_2.17 sessioninfo_1.2.2 callr_3.7.3 </span></span>
<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a><span class="co">#> [41] purrr_0.3.5 magrittr_2.0.3 MASS_7.3-57 ps_1.7.1 </span></span>
<span id="cb1-34"><a href="#cb1-34" aria-hidden="true" tabindex="-1"></a><span class="co">#> [45] promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.3 usethis_2.1.6 </span></span>
<span id="cb1-35"><a href="#cb1-35" aria-hidden="true" tabindex="-1"></a><span class="co">#> [49] mime_0.12 xtable_1.8-4 httpuv_1.6.6 utf8_1.2.2 </span></span>
<span id="cb1-36"><a href="#cb1-36" aria-hidden="true" tabindex="-1"></a><span class="co">#> [53] stringi_1.7.8 miniUI_0.1.1.1 cachem_1.0.6 crayon_1.5.2</span></span></code></pre></div>
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