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@ -34,7 +34,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
@ -132,7 +132,7 @@
<p>One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a>, which work in base R, <code>dplyr</code> and <code>data.table</code>.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
<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://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
<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://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span>
<span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -441,7 +441,7 @@
<p>The <code>AMR</code> package allows interpretation of MIC and disk diffusion values based on CLSI and EUCAST. Moreover, the <code>ggplot2</code> package is extended with new scale functions, to allow plotting of log2-distributed MIC values and SIR values.</p>
<div class="sourceCode" id="cb5"><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://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<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://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
<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://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># generate some random values</span></span>
<span><span class="va">some_mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
@ -466,7 +466,7 @@
<span> <span class="co"># NEW scale function: write out S/I/R in any of the 20 supported languages</span></span>
<span> <span class="co"># and set colourblind-friendly colours</span></span>
<span> <span class="fu"><a href="reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis"> <img src="./plot_readme.png" style="max-width: 600px;"></a></p>
<p><a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis"> <img src="./plot_readme.png" style="width: 600px; max-width: 100%;"></a></p>
</div>
<div class="section level4">
<h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
@ -515,7 +515,7 @@
</table>
<p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
<div class="sourceCode" id="cb7"><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://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
<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://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span>
<span><span class="va">out</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -691,22 +691,25 @@
<div class="sourceCode" id="cb10"><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">"AMR"</span><span class="op">)</span></span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest beta version.</p>
</div>
<div class="section level4">
<h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
<h4 id="latest-beta-version">Latest beta version<a class="anchor" aria-label="anchor" href="#latest-beta-version"></a>
</h4>
<p><a href="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml/badge.svg?branch=main" alt="check-old"></a> <a href="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml/badge.svg?branch=main" alt="check-recent"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
<p>Please read our <a href="https://github.com/msberends/AMR/wiki/Developer-Guideline" class="external-link">Developer Guideline here</a>.</p>
<p>To install the latest and unpublished development version:</p>
<p>To install the latest and unpublished beta version:</p>
<div class="sourceCode" id="cb11"><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">"AMR"</span>, repos <span class="op">=</span> <span class="st">"beta.amr-for-r.org"</span><span class="op">)</span></span></code></pre></div>
<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">"AMR"</span>, repos <span class="op">=</span> <span class="st">"beta.amr-for-r.org"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># if this does not work, try to install directly from GitHub using the 'remotes' package:</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
</div>
</div>
<div class="section level3">
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
</h3>
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://amr-for-r.org/articles/">‘How to’ menu</a>.</p>
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="./articles/">‘How to’ menu</a>.</p>
</div>
<div class="section level3">
<h3 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>