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@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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@ -91,7 +91,7 @@
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website update since they are based on randomly created values and the
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 01 May 2025.</p>
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generated on 02 May 2025.</p>
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<div class="section level2">
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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</h2>
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@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2025-05-01</td>
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<td align="center">2025-05-02</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="center">2025-05-01</td>
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<td align="center">2025-05-02</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">R</td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2025-05-01</td>
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<td align="center">2025-05-02</td>
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<td align="center">efgh</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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<td align="center">R</td>
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@ -817,9 +817,10 @@ prints in the right format when using Quarto or R Markdown (such as this
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page), and even applies italics for taxonomic names (by using
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page), and even applies italics for taxonomic names (by using
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<code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> internally).</p>
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<code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> internally).</p>
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<p>It also uses the language of your OS if this is either English,
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<p>It also uses the language of your OS if this is either English,
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Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian,
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Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German,
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Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish,
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Greek, Hindi, Indonesian, Italian, Japanese, Norwegian, Polish,
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Swedish, Turkish, or Ukrainian. In this next example, we force the
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Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish,
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Ukrainian, Urdu, or Vietnamese. In this next example, we force the
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language to be Spanish using the <code>language</code> argument:</p>
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language to be Spanish using the <code>language</code> argument:</p>
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<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
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<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
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<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -352,7 +352,7 @@ I (intermediate [CLSI], or susceptible, increased exposure
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</tr>
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</tr>
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</tbody>
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</tbody>
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</table>
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</table>
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<p>The <code>AMR</code> package is available in 20 languages, which can
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<p>The <code>AMR</code> package is available in 27 languages, which can
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all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></code> function too:</p>
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all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></code> function too:</p>
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<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
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<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
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<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -80,7 +80,7 @@
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<main id="main" class="col-md-9"><div class="page-header">
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
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<h4 data-toc-skip class="date">01 May 2025</h4>
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<h4 data-toc-skip class="date">02 May 2025</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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34
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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</div>
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</div>
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<ul>
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<ul>
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<li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li>
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<li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li>
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<li>Peer-reviewed, used in over 175 countries, available in 20 languages</li>
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<li>Peer-reviewed, used in over 175 countries, available in 27 languages</li>
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<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
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<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
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<li>Provides the <strong>full microbiological taxonomy</strong> of ~79 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
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<li>Provides the <strong>full microbiological taxonomy</strong> of ~79 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
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<li>Applies <strong>CLSI 2011-2025</strong> and <strong>EUCAST 2011-2025</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
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<li>Applies <strong>CLSI 2011-2025</strong> and <strong>EUCAST 2011-2025</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
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@ -114,11 +114,11 @@
|
|||||||
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
|
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
|
||||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||||||
<div class="section level5">
|
<div class="section level5">
|
||||||
<h5 id="used-in-over-175-countries-available-in-20-languages">Used in over 175 countries, available in 20 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-20-languages"></a>
|
<h5 id="used-in-over-175-countries-available-in-27-languages">Used in over 175 countries, available in 27 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-27-languages"></a>
|
||||||
</h5>
|
</h5>
|
||||||
<p><a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;"></a></p>
|
<p><a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;"></a></p>
|
||||||
<p>Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.</p>
|
<p>Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.</p>
|
||||||
<p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, and <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
<p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_ar.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Arabic, <img src="lang_bn.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Bengali, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_hi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Hindi, <img src="lang_id.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Indonesian, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sw.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swahili, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian, <img src="lang_ur.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Urdu, and <img src="lang_vi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
@ -145,10 +145,8 @@
|
|||||||
<span><span class="co">#> ℹ Using column 'mo' as input for mo_fullname()</span></span>
|
<span><span class="co">#> ℹ Using column 'mo' as input for mo_fullname()</span></span>
|
||||||
<span><span class="co">#> ℹ Using column 'mo' as input for mo_is_gram_negative()</span></span>
|
<span><span class="co">#> ℹ Using column 'mo' as input for mo_is_gram_negative()</span></span>
|
||||||
<span><span class="co">#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()</span></span>
|
<span><span class="co">#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()</span></span>
|
||||||
<span><span class="co">#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
|
<span><span class="co">#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
|
||||||
<span><span class="co">#> Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
|
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
|
|
||||||
<span><span class="co">#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
|
||||||
<span><span class="co">#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
|
<span><span class="co">#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
|
||||||
<span><span class="co">#> # A tibble: 35 × 7</span></span>
|
<span><span class="co">#> # A tibble: 35 × 7</span></span>
|
||||||
<span><span class="co">#> bacteria GEN TOB AMK KAN IPM MEM </span></span>
|
<span><span class="co">#> bacteria GEN TOB AMK KAN IPM MEM </span></span>
|
||||||
@ -174,9 +172,9 @@
|
|||||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||||
<span> antimicrobials <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="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
|
<span> antimicrobials <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="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
|
||||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
|
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||||
<span><span class="co">#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
<span><span class="co">#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
|
||||||
<span><span class="co">#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></code></pre></div>
|
<span><span class="co">#> ℹ 502 combinations had less than minimum = 30 results and were ignored</span></span></code></pre></div>
|
||||||
<table style="width:100%;" class="table">
|
<table style="width:100%;" class="table">
|
||||||
<colgroup>
|
<colgroup>
|
||||||
<col width="14%">
|
<col width="14%">
|
||||||
@ -293,7 +291,8 @@
|
|||||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||||
<span> antimicrobials <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
|
<span> antimicrobials <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
|
||||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
|
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span>
|
||||||
|
<span><span class="co">#> ℹ 3 combinations had less than minimum = 30 results and were ignored</span></span></code></pre></div>
|
||||||
<table class="table">
|
<table class="table">
|
||||||
<colgroup>
|
<colgroup>
|
||||||
<col width="25%">
|
<col width="25%">
|
||||||
@ -322,13 +321,14 @@
|
|||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
<p>Like many other functions in this package, <code><a href="reference/antibiogram.html">antibiogram()</a></code> comes with support for 20 languages that are often detected automatically based on system language:</p>
|
<p>Like many other functions in this package, <code><a href="reference/antibiogram.html">antibiogram()</a></code> comes with support for 27 languages that are often detected automatically based on system language:</p>
|
||||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||||
<span> antimicrobials <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">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
|
<span> antimicrobials <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">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
|
||||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
|
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
|
||||||
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
|
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
|
||||||
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div>
|
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span>
|
||||||
|
<span><span class="co">#> ℹ 3 combinations had less than minimum = 30 results and were ignored</span></span></code></pre></div>
|
||||||
<table class="table">
|
<table class="table">
|
||||||
<colgroup>
|
<colgroup>
|
||||||
<col width="19%">
|
<col width="19%">
|
||||||
@ -421,15 +421,13 @@
|
|||||||
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
|
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
|
||||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><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="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
|
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><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="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
|
||||||
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
|
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
|
||||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
|
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||||
<span><span class="co">#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
|
||||||
<span><span class="co">#> ℹ For polymyxins() using column 'COL' (colistin)</span></span>
|
<span><span class="co">#> ℹ For polymyxins() using column 'COL' (colistin)</span></span>
|
||||||
<span><span class="co">#> Warning: There was 1 warning in `summarise()`.</span></span>
|
<span><span class="co">#> Warning: There was 1 warning in `summarise()`.</span></span>
|
||||||
<span><span class="co">#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
|
<span><span class="co">#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
|
||||||
<span><span class="co">#> ℹ In group 3: `ward = "Outpatient"`.</span></span>
|
<span><span class="co">#> ℹ In group 3: `ward = "Outpatient"`.</span></span>
|
||||||
<span><span class="co">#> Caused by warning:</span></span>
|
<span><span class="co">#> Caused by warning:</span></span>
|
||||||
<span><span class="co">#> ! Introducing NA: only 23 results available for KAN in group: ward =</span></span>
|
<span><span class="co">#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (minimum = 30).</span></span>
|
||||||
<span><span class="co">#> "Outpatient" (minimum = 30).</span></span>
|
|
||||||
<span><span class="va">out</span></span>
|
<span><span class="va">out</span></span>
|
||||||
<span><span class="co">#> # A tibble: 3 × 6</span></span>
|
<span><span class="co">#> # A tibble: 3 × 6</span></span>
|
||||||
<span><span class="co">#> ward GEN TOB AMK KAN COL</span></span>
|
<span><span class="co">#> ward GEN TOB AMK KAN COL</span></span>
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||||||
|
|||||||
105
lang_ar.svg
Normal file
105
lang_ar.svg
Normal file
@ -0,0 +1,105 @@
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|
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<path id="sword" d="m1558.8 1170.7c-1.1729-3.3554-4.7649-5.8169-9.0607-5.8169s-7.8806 2.4615-9.0608 5.8169h-40.678c-0.4105-4.5128-0.01-9.0477 1.2683-13.465l83.981-0.051 2.3385 3.9414c2.1113 3.5531 4.7797 6.7619 7.8731 9.5751zm55.596-39.026h-100.92c7.7559-5.5971 11.824-13.766 10.732-22.029-0.6964-5.2089-5.8571-9.099-12.147-9.6264h-3.1596c-7.6532 0.7472-13.203 6.2637-12.396 12.322l0.3079 2.3297 0.3738 3.5824c0.4106 4.4982 0.015 9.0183-1.2535 13.421h-745.97c11.077 16.117 31.273 26 53.082 25.985l680.71-0.4178c-7.7852 5.6044-11.868 13.788-10.769 22.066 0.8064 6.0585 7.6533 10.374 15.307 9.6263 7.6459-0.7472 13.195-6.2637 12.396-12.33l-0.3079-2.3223h40.004c0.7037 3.9048 4.6037 6.9011 9.354 6.9011s8.6502-2.9963 9.3613-6.9011h40.693v-0.095c8.4963 6.0294 19.294 9.4946 30.716 9.4946 10.747 0 19.456-7.4652 19.456-16.681v-4.8205c0-16.842-15.922-30.506-35.569-30.506" fill="#fff"/>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 10 6"><rect width="10" height="6" fill="#006a4e"/><circle cx="4.5" cy="3" r="2" fill="#f42a41"/></svg>
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<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="900" height="600" viewBox="-45 -30 90 60" fill="#07038D">
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<title>Flag of India</title>
|
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<path fill="#FFF" d="m-45-30h90v60h-90z"/>
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<path fill="#FF6820" d="m-45-30h90v20h-90z"/>
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<svg xmlns="http://www.w3.org/2000/svg" width="900" height="600"><path fill="#fff" d="M0 0H900V600H0z"/><path fill="red" d="M0 0H900V300H0z"/></svg>
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<svg xmlns="http://www.w3.org/2000/svg" width="900" height="600" viewBox="0 0 72 48">
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<title>Flag of Tanzania</title>
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<defs>
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<path fill="none" stroke="#fcd116" stroke-width="19" d="m0 48L72 0"/>
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<?xml version="1.0" encoding="UTF-8"?>
|
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<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
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<svg xmlns="http://www.w3.org/2000/svg" width="900" height="600" viewBox="-75 -40 120 80" version="1.1">
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<title>Flag of Pakistan</title>
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<rect x="-75" y="-40" width="120" height="80" fill="#fff"/>
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<rect x="-45" y="-40" width="90" height="80" fill="#01411C"/>
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<circle r="22" cx="-7" cy="-40" fill="#01411C" transform="rotate(-41.63354, 45, -40)"/>
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<polygon points="0,-513674 301930,415571 -488533,-158734 488533,-158734 -301930,415571" fill="#fff" transform="rotate(-41.63354) translate(16) rotate(18) scale(0.00001557408)"/>
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<?xml version="1.0" encoding="UTF-8"?>
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<svg width="900" height="600" viewBox="0 0 30 20" xmlns="http://www.w3.org/2000/svg" version="1.1">
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<polygon points="15,4 11.47,14.85 20.71,8.15 9.29,8.15 18.53,14.85" fill="#ff0"/>
|
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</svg>
|
||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -49,11 +49,11 @@
|
|||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 class="pkg-version" data-toc-text="2.1.1.9268" id="amr-2119268">AMR 2.1.1.9268<a class="anchor" aria-label="anchor" href="#amr-2119268"></a></h2>
|
<h2 class="pkg-version" data-toc-text="2.1.1.9269" id="amr-2119269">AMR 2.1.1.9269<a class="anchor" aria-label="anchor" href="#amr-2119269"></a></h2>
|
||||||
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
|
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
|
||||||
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="tldr-2-1-1-9268">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9268"></a></h3>
|
<h3 id="tldr-2-1-1-9269">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9269"></a></h3>
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<strong>Scope Expansion</strong>: One Health support (Human + Veterinary + Environmental microbiology).</li>
|
<strong>Scope Expansion</strong>: One Health support (Human + Veterinary + Environmental microbiology).</li>
|
||||||
<li>
|
<li>
|
||||||
@ -113,15 +113,15 @@
|
|||||||
</ul></li>
|
</ul></li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="full-changelog-2-1-1-9268">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9268"></a></h3>
|
<h3 id="full-changelog-2-1-1-9269">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9269"></a></h3>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="breaking-2-1-1-9268">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9268"></a></h4>
|
<h4 id="breaking-2-1-1-9269">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9269"></a></h4>
|
||||||
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
|
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
|
||||||
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
|
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
|
||||||
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> are now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
|
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> are now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="new-2-1-1-9268">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9268"></a></h4>
|
<h4 id="new-2-1-1-9269">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9269"></a></h4>
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<strong>One Health implementation</strong>
|
<strong>One Health implementation</strong>
|
||||||
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
||||||
@ -137,6 +137,10 @@
|
|||||||
<ul><li>The <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in datasets with sparse data. A dedicated <code><a href="../reference/antibiogram.html">wisca()</a></code> function is also available for easy usage.</li>
|
<ul><li>The <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in datasets with sparse data. A dedicated <code><a href="../reference/antibiogram.html">wisca()</a></code> function is also available for easy usage.</li>
|
||||||
</ul></li>
|
</ul></li>
|
||||||
<li>
|
<li>
|
||||||
|
<strong>More global coverage of languages</strong>
|
||||||
|
<ul><li>Added full support for 7 new languages: Arabic, Bengali, Hindi, Indonesian, Swahili, Urdu, and Vietnamese. The <code>AMR</code> package is now available in 27 languages.</li>
|
||||||
|
</ul></li>
|
||||||
|
<li>
|
||||||
<strong>Major update to fungal taxonomy and tools for mycologists</strong>
|
<strong>Major update to fungal taxonomy and tools for mycologists</strong>
|
||||||
<ul><li>MycoBank has now been integrated as the primary taxonomic source for fungi. The <code>microorganisms</code> data set has been enriched with new columns (<code>mycobank</code>, <code>mycobank_parent</code>, and <code>mycobank_renamed_to</code>) that provide detailed information for fungal species.</li>
|
<ul><li>MycoBank has now been integrated as the primary taxonomic source for fungi. The <code>microorganisms</code> data set has been enriched with new columns (<code>mycobank</code>, <code>mycobank_parent</code>, and <code>mycobank_renamed_to</code>) that provide detailed information for fungal species.</li>
|
||||||
<li>A remarkable addition of over 20,000 new fungal records</li>
|
<li>A remarkable addition of over 20,000 new fungal records</li>
|
||||||
@ -176,7 +180,7 @@
|
|||||||
</ul></li>
|
</ul></li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="changed-2-1-1-9268">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9268"></a></h4>
|
<h4 id="changed-2-1-1-9269">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9269"></a></h4>
|
||||||
<ul><li>SIR interpretation
|
<ul><li>SIR interpretation
|
||||||
<ul><li>Support for parallel computing to greatly improve speed using the <code>parallel</code> package (part of base R). Use <code>as.sir(your_data, parallel = TRUE)</code> to run SIR interpretation using multiple cores.</li>
|
<ul><li>Support for parallel computing to greatly improve speed using the <code>parallel</code> package (part of base R). Use <code>as.sir(your_data, parallel = TRUE)</code> to run SIR interpretation using multiple cores.</li>
|
||||||
<li>It is now possible to use column names for arguments <code>guideline</code>, <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
<li>It is now possible to use column names for arguments <code>guideline</code>, <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
||||||
@ -258,7 +262,7 @@
|
|||||||
<li>Added console colours support of <code>sir</code> class for Positron</li>
|
<li>Added console colours support of <code>sir</code> class for Positron</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="other-2-1-1-9268">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9268"></a></h4>
|
<h4 id="other-2-1-1-9269">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9269"></a></h4>
|
||||||
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org/" class="external-link uri">http://amr-for-r.org/</a>) will remain to work.</li>
|
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org/" class="external-link uri">http://amr-for-r.org/</a>) will remain to work.</li>
|
||||||
<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
|
<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
|
||||||
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
|
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
|
||||||
@ -269,7 +273,7 @@
|
|||||||
</ul></div>
|
</ul></div>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="older-versions-2-1-1-9268">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9268"></a></h3>
|
<h3 id="older-versions-2-1-1-9269">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9269"></a></h3>
|
||||||
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
|
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
|
||||||
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
|
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
|
||||||
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
|
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
|
||||||
|
|||||||
@ -11,7 +11,7 @@ articles:
|
|||||||
PCA: PCA.html
|
PCA: PCA.html
|
||||||
WHONET: WHONET.html
|
WHONET: WHONET.html
|
||||||
WISCA: WISCA.html
|
WISCA: WISCA.html
|
||||||
last_built: 2025-05-01T12:49Z
|
last_built: 2025-05-02T17:33Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://amr-for-r.org/reference
|
reference: https://amr-for-r.org/reference
|
||||||
article: https://amr-for-r.org/articles
|
article: https://amr-for-r.org/articles
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -71,7 +71,7 @@
|
|||||||
<li><p><code>AMR_substitute_missing_r_breakpoint</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that missing R breakpoints must be substituted with <code>"R"</code> - the default is <code>FALSE</code>.</p></li>
|
<li><p><code>AMR_substitute_missing_r_breakpoint</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that missing R breakpoints must be substituted with <code>"R"</code> - the default is <code>FALSE</code>.</p></li>
|
||||||
<li><p><code>AMR_include_screening</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>.</p></li>
|
<li><p><code>AMR_include_screening</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>.</p></li>
|
||||||
<li><p><code>AMR_keep_synonyms</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>.</p></li>
|
<li><p><code>AMR_keep_synonyms</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>.</p></li>
|
||||||
<li><p><code>AMR_locale</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the language for the <code>AMR</code> package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported, English otherwise).</p></li>
|
<li><p><code>AMR_locale</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the language for the <code>AMR</code> package, can be one of these supported language names or <a href="https://en.wikipedia.org/wiki/ISO_639-1" class="external-link">ISO 639-1 codes</a>: English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr), Ukrainian (uk), Urdu (ur), or Vietnamese (vi). The default is the current system language (if supported, English otherwise).</p></li>
|
||||||
<li><p><code>AMR_mo_source</code> <br> A file location for a manual code list to be used in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions. This is explained in <code><a href="mo_source.html">set_mo_source()</a></code>.</p></li>
|
<li><p><code>AMR_mo_source</code> <br> A file location for a manual code list to be used in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions. This is explained in <code><a href="mo_source.html">set_mo_source()</a></code>.</p></li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
|
|||||||
@ -6,14 +6,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
|
|||||||
and doi:10.33612/diss.192486375
|
and doi:10.33612/diss.192486375
|
||||||
).
|
).
|
||||||
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
|
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
|
||||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
|
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
|
||||||
The AMR package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of many different researchers from around the globe to make this a successful and durable project!
|
The AMR package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of many different researchers from around the globe to make this a successful and durable project!
|
||||||
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
|
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
|
||||||
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
|
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
|
||||||
and doi:10.33612/diss.192486375
|
and doi:10.33612/diss.192486375
|
||||||
).
|
).
|
||||||
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
|
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
|
||||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
||||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||||
|
|
||||||
|
|
||||||
@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -71,7 +71,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
|||||||
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
|
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
|
||||||
).</p>
|
).</p>
|
||||||
<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||||||
<p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
<p>The <code>AMR</code> package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
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|
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|
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|
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@ -7,7 +7,7 @@
|
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|
|
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
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||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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||||||
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|
||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -112,16 +112,16 @@
|
|||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 25 25.83562 0</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 25 25.83836 0</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 57 57.25205 31</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 57 57.25479 31</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 59 59.40274 34</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 59 59.40548 34</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 45 45.16712 19</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 45 45.16986 19</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 75 75.49589 50</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 75 75.49863 50</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 78 78.20822 52</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 78 78.21096 52</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 85 85.19452 59</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 85 85.19726 59</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 37 37.30411 11</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 37 37.30685 11</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 27 27.67671 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 27 27.67945 2</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 47 47.26027 21</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 47 47.26301 21</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
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|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
||||||
|
|||||||
@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</small>
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
|
|||||||
@ -1,11 +1,11 @@
|
|||||||
<!DOCTYPE html>
|
<!DOCTYPE html>
|
||||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><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, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><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><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
|
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><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, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><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><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
|
||||||
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:
|
Simply puy, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class, code or name: column names "cefazolin", "kefzol", "CZO" and "J01DB04" would all be included in the following selection:
|
||||||
library(dplyr)
|
library(dplyr)
|
||||||
my_data_with_all_these_columns %&gt;%
|
my_data_with_all_these_columns %&gt;%
|
||||||
select(cephalosporins())
|
select(cephalosporins())
|
||||||
'><meta property="og:description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
|
'><meta property="og:description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
|
||||||
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:
|
Simply puy, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class, code or name: column names "cefazolin", "kefzol", "CZO" and "J01DB04" would all be included in the following selection:
|
||||||
library(dplyr)
|
library(dplyr)
|
||||||
my_data_with_all_these_columns %&gt;%
|
my_data_with_all_these_columns %&gt;%
|
||||||
select(cephalosporins())
|
select(cephalosporins())
|
||||||
@ -17,7 +17,7 @@ my_data_with_all_these_columns %&gt;%
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -61,7 +61,7 @@ my_data_with_all_these_columns %&gt;%
|
|||||||
|
|
||||||
<div class="ref-description section level2">
|
<div class="ref-description section level2">
|
||||||
<p>These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base <span style="R">R</span>, tidyverse, tidymodels, and <code>data.table</code>.</p>
|
<p>These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base <span style="R">R</span>, tidyverse, tidymodels, and <code>data.table</code>.</p>
|
||||||
<p>In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:</p>
|
<p>Simply puy, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class, code or name: column names "cefazolin", "kefzol", "CZO" and "J01DB04" would all be included in the following selection:</p>
|
||||||
<p></p><div class="sourceCode r"><pre><code><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>
|
<p></p><div class="sourceCode r"><pre><code><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 class="va">my_data_with_all_these_columns</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
<span><span class="va">my_data_with_all_these_columns</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div>
|
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div>
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
|
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|
|
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|
|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -76,7 +76,7 @@
|
|||||||
|
|
||||||
|
|
||||||
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
|
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
|
||||||
<dd><p>Language to coerce input values from any of the 20 supported languages - default to the system language if supported (see <code><a href="translate.html">get_AMR_locale()</a></code>).</p></dd>
|
<dd><p>Language to coerce input values from any of the 27 supported languages - default to the system language if supported (see <code><a href="translate.html">get_AMR_locale()</a></code>).</p></dd>
|
||||||
|
|
||||||
|
|
||||||
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
|
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -196,7 +196,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
|||||||
|
|
||||||
|
|
||||||
<dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt>
|
<dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt>
|
||||||
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s to indicate the host. Only useful for veterinary breakpoints, as it requires <code>breakpoint_type = "animal"</code>. The values can be any text resembling the animal species, even in any of the 20 supported languages of this package. For foreign languages, be sure to set the language with <code><a href="translate.html">set_AMR_locale()</a></code> (though it will be automatically guessed based on the system language).</p></dd>
|
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s to indicate the host. Only useful for veterinary breakpoints, as it requires <code>breakpoint_type = "animal"</code>. The values can be any text resembling the animal species, even in any of the 27 supported languages of this package. For foreign languages, be sure to set the language with <code><a href="translate.html">set_AMR_locale()</a></code> (though it will be automatically guessed based on the system language).</p></dd>
|
||||||
|
|
||||||
|
|
||||||
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
|
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
|
||||||
@ -409,10 +409,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-05-02 <span style="color: #949494;">17:34:18</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 MIC cipro Escherich… human 0.256 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-05-02 <span style="color: #949494;">17:34:18</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 DISK tobra Escherich… human 16 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-05-02 <span style="color: #949494;">17:34:18</span> 1 DISK tobra Escherich… human 16 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 DISK genta Escherich… human 18 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-05-02 <span style="color: #949494;">17:34:19</span> 1 DISK genta Escherich… human 18 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
|
||||||
|
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||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
|
||||||
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||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
|
||||||
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|
||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -274,7 +274,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
|||||||
<h3 id="the-scale-sir-functions">The <code>scale_*_sir()</code> Functions<a class="anchor" aria-label="anchor" href="#the-scale-sir-functions"></a></h3>
|
<h3 id="the-scale-sir-functions">The <code>scale_*_sir()</code> Functions<a class="anchor" aria-label="anchor" href="#the-scale-sir-functions"></a></h3>
|
||||||
|
|
||||||
|
|
||||||
<p>The functions <code>scale_x_sir()</code>, <code>scale_colour_sir()</code>, and <code>scale_fill_sir()</code> functions allow to plot the <a href="as.sir.html">sir</a> class in the right order (S < SDD < I < R < NI). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 20 supported languages (use <code>language = NULL</code> to keep S/I/R). Also, except for <code>scale_x_sir()</code>, they set colour-blind friendly colours to the <code>colour</code> and <code>fill</code> aesthetics.</p>
|
<p>The functions <code>scale_x_sir()</code>, <code>scale_colour_sir()</code>, and <code>scale_fill_sir()</code> functions allow to plot the <a href="as.sir.html">sir</a> class in the right order (S < SDD < I < R < NI). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 27 supported languages (use <code>language = NULL</code> to keep S/I/R). Also, except for <code>scale_x_sir()</code>, they set colour-blind friendly colours to the <code>colour</code> and <code>fill</code> aesthetics.</p>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="section">
|
<div class="section">
|
||||||
@ -310,7 +310,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
|||||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||||
<span class="r-plt img"><img src="plot-2.png" alt="" width="700" height="433"></span>
|
<span class="r-plt img"><img src="plot-2.png" alt="" width="700" height="433"></span>
|
||||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
<span class="r-in"><span> <span class="co"># support for 20 languages, various guidelines, and many options</span></span></span>
|
<span class="r-in"><span> <span class="co"># support for 27 languages, various guidelines, and many options</span></span></span>
|
||||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>,</span></span>
|
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>,</span></span>
|
||||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>,</span></span>
|
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>,</span></span>
|
||||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI 2024"</span>, language <span class="op">=</span> <span class="st">"no"</span>,</span></span>
|
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI 2024"</span>, language <span class="op">=</span> <span class="st">"no"</span>,</span></span>
|
||||||
@ -438,7 +438,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
|||||||
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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="fl">0.005</span>, <span class="fl">32</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Our MICs!"</span><span class="op">)</span> <span class="op">+</span></span></span>
|
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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="fl">0.005</span>, <span class="fl">32</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Our MICs!"</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||||
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span></span></span>
|
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span></span></span>
|
||||||
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"pt"</span>,</span></span>
|
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"pt"</span>,</span></span>
|
||||||
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Support in 20 languages"</span></span></span>
|
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Support in 27 languages"</span></span></span>
|
||||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||||
<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
|
<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
|
||||||
|
|||||||
@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</small>
|
||||||
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||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9268</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9269</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -69,7 +69,7 @@
|
|||||||
|
|
||||||
|
|
||||||
<dl><dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
|
<dl><dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
|
||||||
<dd><p>Language to choose. Use one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk).</p></dd>
|
<dd><p>Language to choose. Use one of these supported language names or <a href="https://en.wikipedia.org/wiki/ISO_639-1" class="external-link">ISO 639-1 codes</a>: English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr), Ukrainian (uk), Urdu (ur), or Vietnamese (vi).</p></dd>
|
||||||
|
|
||||||
|
|
||||||
<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
|
<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
|
||||||
@ -78,7 +78,7 @@
|
|||||||
</dl></div>
|
</dl></div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||||
<p>The currently 20 supported languages are English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.</p>
|
<p>The currently 27 supported languages are English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr), Ukrainian (uk), Urdu (ur), and Vietnamese (vi). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.</p>
|
||||||
<p>To permanently silence the once-per-session language note on a non-English operating system, you can set the package option <code><a href="AMR-options.html">AMR_locale</a></code> in your <code>.Rprofile</code> file like this:</p>
|
<p>To permanently silence the once-per-session language note on a non-English operating system, you can set the package option <code><a href="AMR-options.html">AMR_locale</a></code> in your <code>.Rprofile</code> file like this:</p>
|
||||||
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Open .Rprofile file</span></span>
|
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Open .Rprofile file</span></span>
|
||||||
<span><span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span>
|
<span><span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span>
|
||||||
@ -122,7 +122,7 @@
|
|||||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Koagulase-negative Staphylococcus (KNS)"</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Koagulase-negative Staphylococcus (KNS)"</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1:</span></span></span>
|
<span class="r-in"><span><span class="co"># set_AMR_locale() understands endonyms, English exonyms, and ISO 639-1:</span></span></span>
|
||||||
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Deutsch"</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Deutsch"</span><span class="op">)</span></span></span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using German (Deutsch) for the AMR package for this session.</span></span>
|
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using German (Deutsch) for the AMR package for this session.</span></span>
|
||||||
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"German"</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"German"</span><span class="op">)</span></span></span>
|
||||||
|
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Reference in New Issue
Block a user