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diff --git a/docs/index.html b/docs/index.html index c64ae68..2c6303f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -4,139 +4,209 @@ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>Chemical Entities as R Objects • chents</title> -<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"> -<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> -<script src="pkgdown.js"></script><meta property="og:title" content="Chemical Entities as R Objects"> -<meta property="og:description" content="Utilities for dealing with chemical entities and associated - data as R objects. If Python and RDKit (> 2015.03) are installed and - configured for use with reticulate, some basic chemoinformatics functions - like the calculation of molecular weight and plotting of chemical - structures in R graphics are available. For plotting, you need - grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN."> -<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> +<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"> +<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"> +<link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"> +<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Chemical Entities as R Objects"> +<meta name="description" content="Utilities for dealing with chemical entities and associated data as R objects. If Python and RDKit (> 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available."> +<meta property="og:description" content="Utilities for dealing with chemical entities and associated data as R objects. If Python and RDKit (> 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available."> </head> -<body data-spy="scroll" data-target="#toc"> - <div class="container template-home"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="index.html">chents</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> -<li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="reference/index.html">Reference</a> -</li> +<body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="index.html">chents</a> + + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"> +<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li> </ul> -<ul class="nav navbar-nav navbar-right"> -<li> - <a href="https://github.com/jranke/chents/"> - <span class="fab fa-github fa-lg"></span> - - </a> -</li> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/chents/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> +</nav><div class="container template-home"> +<div class="row"> + <main id="main" class="col-md-9"><div class="section level1"> +<div class="page-header"><h1 id="chents">chents<a class="anchor" aria-label="anchor" href="#chents"></a> +</h1></div> +<p><a href="https://pkgdown.jrwb.de/chents/"><img src="https://img.shields.io/badge/docs-jrwb.de-blue.svg" alt="Online documentation"></a> <a href="https://jranke.r-universe.dev/chents" class="external-link"><img src="https://jranke.r-universe.dev/badges/chents" alt="R-Universe status"></a> <a href="https://pkgdown.jrwb.de/chents/coverage/coverage.html"><img src="https://img.shields.io/badge/coverage-jrwb.de-blue.svg" alt="Code coverage"></a></p> +<p>When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package <strong>chents</strong> provides a way to define an R object corresponding to a chemically defined substances (“chemical entity”) and to collect related information.</p> +<p>When first defining a chemical entity, some chemical information is retrieved from the <a href="https://pubchem.ncbi.nlm.nih.gov/" class="external-link">PubChem</a> website using the <a href="https://docs.ropensci.org/webchem/" class="external-link">webchem</a> package.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/chents/">chents</a></span><span class="op">)</span></span> +<span><span class="va">caffeine</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Caffeine"</span><span class="op">)</span></span> +<span><span class="co">#> Querying PubChem for name Caffeine ...</span></span> +<span><span class="co">#> Get chemical information from RDKit using PubChem SMILES</span></span> +<span><span class="co">#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></span></code></pre></div> +<p>If Python and <a href="https://rdkit.org" class="external-link">RDKit</a> (> 2015.03) are installed and configured for use with the <a href="https://rstudio.github.io/reticulate/" class="external-link">reticulate</a> package, some additional chemical information including a 2D graph are computed.</p> +<p>The print method gives an overview of the information that was collected.</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span> +<span><span class="co">#> <chent></span></span> +<span><span class="co">#> Identifier $identifier Caffeine </span></span> +<span><span class="co">#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span></span> +<span><span class="co">#> SMILES string $smiles:</span></span> +<span><span class="co">#> PubChem </span></span> +<span><span class="co">#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span></span> +<span><span class="co">#> Molecular weight $mw: 194.2 </span></span> +<span><span class="co">#> PubChem synonyms (up to 10):</span></span> +<span><span class="co">#> [1] "caffeine" "58-08-2" </span></span> +<span><span class="co">#> [3] "Guaranine" "1,3,7-Trimethylxanthine"</span></span> +<span><span class="co">#> [5] "Methyltheobromine" "Theine" </span></span> +<span><span class="co">#> [7] "Thein" "Cafeina" </span></span> +<span><span class="co">#> [9] "Caffein" "Cafipel"</span></span></code></pre></div> +<p>There is a very simple plotting method for the chemical structure.</p> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></code></pre></div> +<p><img src="reference/figures/README-unnamed-chunk-4-1.png"><!-- --></p> +<p>If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the <a href="http://www.bcpcpesticidecompendium.org/" class="external-link">BCPC compendium</a> first.</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">delta</span> <span class="op"><-</span> <span class="va"><a href="reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Deltamethrin"</span><span class="op">)</span></span> +<span><span class="co">#> Querying BCPC for Deltamethrin ...</span></span> +<span><span class="co">#> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ...</span></span> +<span><span class="co">#> Get chemical information from RDKit using PubChem SMILES</span></span> +<span><span class="co">#> CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">delta</span><span class="op">)</span></span></code></pre></div> +<p><img src="reference/figures/README-unnamed-chunk-5-1.png"><!-- --></p> +<p>Additional information can be read from a local .yaml file. This information can be leveraged e.g. by the <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html" class="external-link">PEC_soil</a> function of the ‘pfm’ package. However, this functionality is to be superseded by a dedicated package, defining data for the environmental risk assessment on chemicals, in particular on active ingredients of plant protection products.</p> +<div class="section level2"> +<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> +</h2> +<p>You can conveniently install chents from the repository kindly made available by the R-Universe project:</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"chents"</span>,</span> +<span> repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"https://jranke.r-universe.dev"</span>, <span class="st">"https://cran.r-project.org"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p>In order to profit from the chemoinformatics, you need to install RDKit and its python bindings. On a Debian type Linux distribution, just use</p> +<div class="sourceCode" id="cb6"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="fu">sudo</span> apt install python3-rdkit</span></code></pre></div> +<p>If you use this package on Windows or MacOS, I would be happy to include installation instructions here if you share them with me, e.g. via a Pull Request.</p> </div> -<!--/.navbar --> - - - - </header><div class="row"> - <div class="contents col-md-9"> -<div id="chents" class="section level1"> -<div class="page-header"><h1 class="hasAnchor"> -<a href="#chents" class="anchor"></a>chents</h1></div> - -<p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R.</p> -<div id="features" class="section level2"> -<h2 class="hasAnchor"> -<a href="#features" class="anchor"></a>Features</h2> -<ul> -<li>Some chemical information is retrieved from the PubChem website using the webchem package</li> -<li>If PythonInR is installed and configured, and RDKit is available via PythonInR, some additional chemical information is computed and a 2D graph can be plotted</li> -<li>Additional information can be read from a local .yaml file</li> -</ul> +<div class="section level2"> +<h2 id="configuration-of-the-python-version-to-use">Configuration of the Python version to use<a class="anchor" aria-label="anchor" href="#configuration-of-the-python-version-to-use"></a> +</h2> +<p>On Debian type Linux distributions, you can use the following line in your global or project specific <code>.Rprofile</code> file to tell the <code>reticulate</code> package to use the system Python version that will find the RDKit installed in the system location.</p> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html" class="external-link">Sys.setenv</a></span><span class="op">(</span>RETICULATE_PYTHON<span class="op">=</span><span class="st">"/usr/bin/python3"</span><span class="op">)</span></span></code></pre></div> </div> -<div id="examples" class="section level2"> -<h2 class="hasAnchor"> -<a href="#examples" class="anchor"></a>Examples</h2> -<p>Some examples are available from the <a href="http://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>.</p> +<div class="section level2"> +<h2 id="using-r6-classes">Using R6 classes<a class="anchor" aria-label="anchor" href="#using-r6-classes"></a> +</h2> +<p>Note that the <code>chent</code> objects defined by this package are <a href="https://r6.r-lib.org/articles/Introduction.html" class="external-link">R6</a> classes. Therefore, if you think you make a copy by assigning them to a new name, the objects will still be connected, because only the reference is copied. For example, you can create a molecule without retrieving data from PubChem</p> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">but</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Butane"</span>, smiles <span class="op">=</span> <span class="st">"CCCC"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span><span class="co">#> Get chemical information from RDKit using user SMILES</span></span> +<span><span class="co">#> CCCC</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">but</span><span class="op">)</span></span> +<span><span class="co">#> <chent></span></span> +<span><span class="co">#> Identifier $identifier Butane </span></span> +<span><span class="co">#> InChI Key $inchikey NA </span></span> +<span><span class="co">#> SMILES string $smiles:</span></span> +<span><span class="co">#> user </span></span> +<span><span class="co">#> "CCCC" </span></span> +<span><span class="co">#> Molecular weight $mw: 58.1</span></span></code></pre></div> +<p>If you then assign a new name and add PubChem information to the object with the new name, the information will also be added to the original <code>chent</code> object:</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">but_pubchem</span> <span class="op"><-</span> <span class="va">but</span></span> +<span><span class="va">but_pubchem</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="op">)</span></span> +<span><span class="co">#> Querying PubChem for name Butane ...</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">but</span><span class="op">)</span></span> +<span><span class="co">#> <chent></span></span> +<span><span class="co">#> Identifier $identifier Butane </span></span> +<span><span class="co">#> InChI Key $inchikey IJDNQMDRQITEOD-UHFFFAOYSA-N </span></span> +<span><span class="co">#> SMILES string $smiles:</span></span> +<span><span class="co">#> user PubChem </span></span> +<span><span class="co">#> "CCCC" "CCCC" </span></span> +<span><span class="co">#> Molecular weight $mw: 58.1 </span></span> +<span><span class="co">#> PubChem synonyms (up to 10):</span></span> +<span><span class="co">#> [1] "BUTANE" "n-Butane" "106-97-8" </span></span> +<span><span class="co">#> [4] "Diethyl" "Methylethylmethane" "Butanen" </span></span> +<span><span class="co">#> [7] "Butani" "Butyl hydride" "HC 600" </span></span> +<span><span class="co">#> [10] "A 21 (lowing agent)"</span></span></code></pre></div> +<p>You can create a derived, independent object using the <code>clone()</code> method that will not be affected by operations on the original object:</p> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">but_new</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Butane"</span>, smiles <span class="op">=</span> <span class="st">"CCCC"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span><span class="co">#> Get chemical information from RDKit using user SMILES</span></span> +<span><span class="co">#> CCCC</span></span> +<span><span class="va">but_clone</span> <span class="op"><-</span> <span class="va">but_new</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span><span class="op">)</span></span> +<span><span class="va">but_new</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="op">)</span></span> +<span><span class="co">#> Querying PubChem for name Butane ...</span></span> +<span><span class="va">but_clone</span></span> +<span><span class="co">#> <chent></span></span> +<span><span class="co">#> Identifier $identifier Butane </span></span> +<span><span class="co">#> InChI Key $inchikey NA </span></span> +<span><span class="co">#> SMILES string $smiles:</span></span> +<span><span class="co">#> user </span></span> +<span><span class="co">#> "CCCC" </span></span> +<span><span class="co">#> Molecular weight $mw: 58.1</span></span></code></pre></div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <div class="links"> -<h2>Links</h2> + </main><aside class="col-md-3"><div class="links"> +<h2 data-toc-skip>Links</h2> <ul class="list-unstyled"> -<li>Browse source code at <br><a href="https://github.com/jranke/chents/">https://github.com/jranke/chents/</a> -</li> +<li><a href="https://github.com/jranke/chents/" class="external-link">Browse source code</a></li> </ul> </div> + <div class="license"> -<h2>License</h2> +<h2 data-toc-skip>License</h2> <ul class="list-unstyled"> <li>GPL</li> </ul> </div> -<div class="developers"> -<h2>Developers</h2> + + +<div class="citation"> +<h2 data-toc-skip>Citation</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +<li><a href="authors.html#citation">Citing chents</a></li> </ul> </div> - <div class="dev-status"> -<h2>Dev status</h2> +<div class="developers"> +<h2 data-toc-skip>Developers</h2> <ul class="list-unstyled"> -<li><a href="https://travis-ci.com/jranke/chents"><img src="https://travis-ci.com/jranke/chents.svg?branch=main" alt="Build Status"></a></li> -<li><a href="https://codecov.io/github/jranke/chents"><img src="https://codecov.io/github/jranke/chents/branch/main/graphs/badge.svg" alt="codecov"></a></li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> </ul> </div> -</div> + + + + </aside> </div> - 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