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@ -36,7 +36,7 @@
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/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="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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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@ -10,7 +10,7 @@
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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="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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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@ -38,7 +38,7 @@
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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="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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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@ -187,7 +187,7 @@
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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 12 May 2023.</p>
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generated on 17 May 2023.</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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@ -243,21 +243,21 @@ 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">2023-05-12</td>
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<td align="center">2023-05-17</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">2023-05-12</td>
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<td align="center">2023-05-17</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">2023-05-12</td>
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<td align="center">2023-05-17</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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@ -492,13 +492,12 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
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<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
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<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
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<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
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<span><span class="co">#> Determining first isolates using an episode length of 365 days</span></span>
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<span><span class="co">#> ℹ Determining first isolates using an episode length of 365 days</span></span>
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<span><span class="co">#> ℹ Using column 'bacteria' as input for col_mo.</span></span>
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<span><span class="co">#> ℹ Using column 'bacteria' as input for col_mo.</span></span>
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<span><span class="co">#> ℹ Using column 'date' as input for col_date.</span></span>
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<span><span class="co">#> ℹ Using column 'date' as input for col_date.</span></span>
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<span><span class="co">#> ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
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<span><span class="co">#> ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
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<span><span class="co">#> Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
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<span><span class="co">#> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
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<span><span class="co">#> 2</span></span>
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<span><span class="co">#> of 2</span></span>
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<span><span class="co">#> Including isolates from ICU.</span></span>
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<span><span class="co">#> => Found 2,626 'phenotype-based' first isolates (87.6% within scope and</span></span>
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<span><span class="co">#> => Found 2,626 'phenotype-based' first isolates (87.6% within scope and</span></span>
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<span><span class="co">#> 87.5% of total where a microbial ID was available)</span></span></code></pre></div>
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<span><span class="co">#> 87.5% of total where a microbial ID was available)</span></span></code></pre></div>
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<p>So only 88% is suitable for resistance analysis! We can now filter on
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<p>So only 88% is suitable for resistance analysis! We can now filter on
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@ -38,7 +38,7 @@
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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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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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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@ -38,7 +38,7 @@
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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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||||||
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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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@ -385,18 +385,18 @@ names or codes, this would have worked exactly the same way:</p>
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
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<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
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<span><span class="co">#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
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<span><span class="co">#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
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<span><span class="co">#> 1 S I I I S S</span></span>
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<span><span class="co">#> 1 R R S I I R</span></span>
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<span><span class="co">#> 2 R R I I S R</span></span>
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<span><span class="co">#> 2 S I R I R S</span></span>
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<span><span class="co">#> 3 R I S S R R</span></span>
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<span><span class="co">#> 3 R S S S R I</span></span>
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<span><span class="co">#> 4 I S R I I S</span></span>
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<span><span class="co">#> 4 S R S R R I</span></span>
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<span><span class="co">#> 5 S R R I R R</span></span>
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<span><span class="co">#> 5 R I S R R R</span></span>
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<span><span class="co">#> 6 S R S I I I</span></span>
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<span><span class="co">#> 6 R R I S I I</span></span>
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<span><span class="co">#> kanamycin</span></span>
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<span><span class="co">#> kanamycin</span></span>
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<span><span class="co">#> 1 S</span></span>
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<span><span class="co">#> 1 I</span></span>
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<span><span class="co">#> 2 R</span></span>
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<span><span class="co">#> 2 R</span></span>
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<span><span class="co">#> 3 S</span></span>
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<span><span class="co">#> 3 S</span></span>
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<span><span class="co">#> 4 S</span></span>
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<span><span class="co">#> 4 S</span></span>
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<span><span class="co">#> 5 I</span></span>
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<span><span class="co">#> 5 S</span></span>
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<span><span class="co">#> 6 R</span></span></code></pre></div>
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<span><span class="co">#> 6 R</span></span></code></pre></div>
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<p>We can now add the interpretation of MDR-TB to our data set. You can
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<p>We can now add the interpretation of MDR-TB to our data set. You can
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use:</p>
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use:</p>
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@ -438,40 +438,40 @@ Unique: 5</p>
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<tr class="odd">
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<tr class="odd">
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<td align="left">1</td>
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<td align="left">1</td>
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<td align="left">Mono-resistant</td>
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<td align="left">Mono-resistant</td>
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<td align="right">3190</td>
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<td align="right">3221</td>
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<td align="right">63.80%</td>
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<td align="right">64.42%</td>
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<td align="right">3190</td>
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<td align="right">3221</td>
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<td align="right">63.80%</td>
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<td align="right">64.42%</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="left">2</td>
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<td align="left">2</td>
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<td align="left">Negative</td>
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<td align="left">Negative</td>
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<td align="right">1008</td>
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<td align="right">942</td>
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<td align="right">20.16%</td>
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<td align="right">18.84%</td>
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<td align="right">4198</td>
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<td align="right">4163</td>
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<td align="right">83.96%</td>
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<td align="right">83.26%</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="left">3</td>
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<td align="left">3</td>
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<td align="left">Multi-drug-resistant</td>
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<td align="left">Multi-drug-resistant</td>
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<td align="right">477</td>
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<td align="right">465</td>
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<td align="right">9.54%</td>
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<td align="right">9.30%</td>
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<td align="right">4675</td>
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<td align="right">4628</td>
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<td align="right">93.50%</td>
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<td align="right">92.56%</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="left">4</td>
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<td align="left">4</td>
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<td align="left">Poly-resistant</td>
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<td align="left">Poly-resistant</td>
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<td align="right">224</td>
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<td align="right">255</td>
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<td align="right">4.48%</td>
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<td align="right">5.10%</td>
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<td align="right">4899</td>
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<td align="right">4883</td>
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<td align="right">97.98%</td>
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<td align="right">97.66%</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="left">5</td>
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<td align="left">5</td>
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<td align="left">Extensively drug-resistant</td>
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<td align="left">Extensively drug-resistant</td>
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<td align="right">101</td>
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<td align="right">117</td>
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<td align="right">2.02%</td>
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<td align="right">2.34%</td>
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<td align="right">5000</td>
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<td align="right">5000</td>
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<td align="right">100.00%</td>
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<td align="right">100.00%</td>
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</tr>
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</tr>
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@ -38,7 +38,7 @@
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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="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
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@ -38,7 +38,7 @@
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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="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
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@ -178,7 +178,7 @@
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<h4 data-toc-skip class="author">Dr. Matthijs
|
<h4 data-toc-skip class="author">Dr. Matthijs
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Berends</h4>
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Berends</h4>
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<h4 data-toc-skip class="date">12 May 2023</h4>
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<h4 data-toc-skip class="date">17 May 2023</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
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<div class="d-none name"><code>SPSS.Rmd</code></div>
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<div class="d-none name"><code>SPSS.Rmd</code></div>
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@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
|
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<li>
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<li>
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<p><strong>R has a huge community.</strong></p>
|
<p><strong>R has a huge community.</strong></p>
|
||||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
|
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
|
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online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">489 114
|
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">489 583
|
||||||
R-related questions</a> have already been asked on this platform (that
|
R-related questions</a> have already been asked on this platform (that
|
||||||
covers questions and answers for any programming language). In my own
|
covers questions and answers for any programming language). In my own
|
||||||
experience, most questions are answered within a couple of
|
experience, most questions are answered within a couple of
|
||||||
|
|||||||
@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -176,7 +176,7 @@
|
|||||||
<main id="main" class="col-md-9"><div class="page-header">
|
<main id="main" class="col-md-9"><div class="page-header">
|
||||||
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
||||||
|
|
||||||
<h4 data-toc-skip class="date">12 May 2023</h4>
|
<h4 data-toc-skip class="date">17 May 2023</h4>
|
||||||
|
|
||||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -42,7 +42,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -142,24 +142,26 @@
|
|||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 class="pkg-version" data-toc-text="2.0.0.9015" id="amr-2009015">AMR 2.0.0.9015<a class="anchor" aria-label="anchor" href="#amr-2009015"></a></h2>
|
<h2 class="pkg-version" data-toc-text="2.0.0.9018" id="amr-2009018">AMR 2.0.0.9018<a class="anchor" aria-label="anchor" href="#amr-2009018"></a></h2>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="changed-2-0-0-9015">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9015"></a></h3>
|
<h3 id="changed-2-0-0-9018">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9018"></a></h3>
|
||||||
<ul><li>Added oxygen tolerance to over 25,000 bacteria in the <code>microorganisms</code> data set
|
<ul><li>Added oxygen tolerance to over 25,000 bacteria in the <code>microorganisms</code> data set
|
||||||
<ul><li>Added <code><a href="../reference/mo_property.html">mo_oxygen_tolerance()</a></code> to retrieve the values</li>
|
<ul><li>Added <code><a href="../reference/mo_property.html">mo_oxygen_tolerance()</a></code> to retrieve the values</li>
|
||||||
<li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which species are obligate anaerobic bacteria</li>
|
<li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which species are obligate anaerobic bacteria</li>
|
||||||
</ul></li>
|
</ul></li>
|
||||||
<li>Added LPSN and GBIF identifiers, and oxygen tolerance to <code><a href="../reference/mo_property.html">mo_info()</a></code>
|
<li>Added LPSN and GBIF identifiers, and oxygen tolerance to <code><a href="../reference/mo_property.html">mo_info()</a></code>
|
||||||
</li>
|
</li>
|
||||||
<li>formatting fix for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
|
<li>Added SAS Transport files (file extension <code>.xpt</code>) to <a href="https://msberends.github.io/AMR/articles/datasets.html">our download page</a> to use in SAS software</li>
|
||||||
</li>
|
|
||||||
<li>Fixed some WHONET codes for microorganisms and consequently a couple of entries in <code>clinical_breakpoints</code>
|
|
||||||
</li>
|
|
||||||
<li>Added microbial codes for Gram-negative/positive anaerobic bacteria</li>
|
<li>Added microbial codes for Gram-negative/positive anaerobic bacteria</li>
|
||||||
<li>
|
<li>
|
||||||
<code><a href="../reference/mo_property.html">mo_rank()</a></code> now returns <code>NA</code> for ‘unknown’ microorganisms (<code>B_ANAER</code>, <code>B_ANAER-NEG</code>, <code>B_ANAER-POS</code>, <code>B_GRAMN</code>, <code>B_GRAMP</code>, <code>F_FUNGUS</code>, <code>F_YEAST</code>, and <code>UNKNOWN</code>)</li>
|
<code><a href="../reference/mo_property.html">mo_rank()</a></code> now returns <code>NA</code> for ‘unknown’ microorganisms (<code>B_ANAER</code>, <code>B_ANAER-NEG</code>, <code>B_ANAER-POS</code>, <code>B_GRAMN</code>, <code>B_GRAMP</code>, <code>F_FUNGUS</code>, <code>F_YEAST</code>, and <code>UNKNOWN</code>)</li>
|
||||||
|
<li>Fixed formatting for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
|
||||||
|
</li>
|
||||||
|
<li>Fixed some WHONET codes for microorganisms and consequently a couple of entries in <code>clinical_breakpoints</code>
|
||||||
|
</li>
|
||||||
<li>Fixed a bug for <code><a href="../reference/as.mo.html">as.mo()</a></code> that led to coercion of <code>NA</code> values when using custom microorganism codes</li>
|
<li>Fixed a bug for <code><a href="../reference/as.mo.html">as.mo()</a></code> that led to coercion of <code>NA</code> values when using custom microorganism codes</li>
|
||||||
<li>Added SAS Transport files (file extension <code>.xpt</code>) to <a href="https://msberends.github.io/AMR/articles/datasets.html">our download page</a> to use in SAS software</li>
|
<li>Fixed usage of <code>icu_exclude</code> in <code>first_isolates()</code>
|
||||||
|
</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
|
|||||||
@ -11,7 +11,7 @@ articles:
|
|||||||
datasets: datasets.html
|
datasets: datasets.html
|
||||||
resistance_predict: resistance_predict.html
|
resistance_predict: resistance_predict.html
|
||||||
welcome_to_AMR: welcome_to_AMR.html
|
welcome_to_AMR: welcome_to_AMR.html
|
||||||
last_built: 2023-05-12T08:39Z
|
last_built: 2023-05-17T20:16Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://msberends.github.io/AMR/reference
|
reference: https://msberends.github.io/AMR/reference
|
||||||
article: https://msberends.github.io/AMR/articles
|
article: https://msberends.github.io/AMR/articles
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -24,7 +24,7 @@ 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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
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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>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -205,16 +205,16 @@
|
|||||||
<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 1935-04-26 88 88.04384 64</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 1973-10-03 49 49.61918 26</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 1939-12-20 83 83.39178 60</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 1982-04-23 41 41.06575 17</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 1940-09-26 82 82.62466 59</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 1977-12-04 45 45.44932 22</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 1981-04-16 42 42.07123 18</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 1982-03-29 41 41.13425 17</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 1946-10-07 76 76.59452 53</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 1970-07-24 52 52.81370 29</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 1974-10-27 48 48.53973 25</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 1982-04-15 41 41.08767 17</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 1938-08-21 84 84.72329 61</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 1990-06-30 32 32.87945 9</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 1941-05-13 81 81.99726 58</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 1932-03-06 91 91.19726 67</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 1933-07-19 89 89.81370 66</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 1966-09-16 56 56.66575 33</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 1977-01-31 46 46.27671 22</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 1932-01-09 91 91.35068 67</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -609,8 +609,8 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 1</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 1</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> kefzol</span>
|
<span class="r-out co"><span class="r-pr">#></span> kefzol</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> I </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> S </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> R </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> I </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> R </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> R </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> I </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> I </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> R </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> R </span>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_guideline mo_input mo_guideline </span>
|
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_guideline mo_input mo_guideline </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;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></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;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-05-12 <span style="color: #949494;">08:40:42</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-05-17 <span style="color: #949494;">20:17:18</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-05-12 <span style="color: #949494;">08:40:42</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-05-17 <span style="color: #949494;">20:17:18</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-05-12 <span style="color: #949494;">08:40:42</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-05-17 <span style="color: #949494;">20:17:17</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-05-12 <span style="color: #949494;">08:40:41</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-05-17 <span style="color: #949494;">20:17:17</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-05-12 <span style="color: #949494;">08:40:37</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-05-17 <span style="color: #949494;">20:17:11</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-05-12 <span style="color: #949494;">08:40:37</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-05-17 <span style="color: #949494;">20:17:11</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-05-12 <span style="color: #949494;">08:40:37</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-05-17 <span style="color: #949494;">20:17:11</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-05-12 <span style="color: #949494;">08:40:37</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-05-17 <span style="color: #949494;">20:17:11</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-05-12 <span style="color: #949494;">08:40:37</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-05-17 <span style="color: #949494;">20:17:11</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-05-12 <span style="color: #949494;">08:40:37</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-05-17 <span style="color: #949494;">20:17:11</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 6 more variables: guideline <chr>, ref_table <chr>, method <chr>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 6 more variables: guideline <chr>, ref_table <chr>, method <chr>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># input <dbl>, outcome <sir>, breakpoint_S_R <chr></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># input <dbl>, outcome <sir>, breakpoint_S_R <chr></span></span>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@ 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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@ 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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -338,13 +338,12 @@
|
|||||||
<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
|
<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Determining first isolates using an episode length of 365 days</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Determining first isolates using an episode length of 365 days</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'date' as input for col_date.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'date' as input for col_date.</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'patient' as input for col_patient_id.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'patient' as input for col_patient_id.</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> 2</span>
|
<span class="r-msg co"><span class="r-pr">#></span> of 2</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a</span>
|
<span class="r-msg co"><span class="r-pr">#></span> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> microbial ID was available)</span>
|
<span class="r-msg co"><span class="r-pr">#></span> microbial ID was available)</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
|
||||||
@ -397,11 +396,10 @@
|
|||||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
|
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</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-msg co"><span class="r-pr">#></span> Determining first isolates using an episode length of 365 days</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Determining first isolates using an episode length of 365 days</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> 2</span>
|
<span class="r-msg co"><span class="r-pr">#></span> of 2</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a</span>
|
<span class="r-msg co"><span class="r-pr">#></span> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> microbial ID was available)</span>
|
<span class="r-msg co"><span class="r-pr">#></span> microbial ID was available)</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
|
||||||
@ -456,25 +454,22 @@
|
|||||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||||
<span class="r-in"><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="va">ward</span>, <span class="va">date</span>, <span class="va">patient</span>, <span class="va">mo</span>, <span class="va">first</span><span class="op">)</span></span></span>
|
<span class="r-in"><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="va">ward</span>, <span class="va">date</span>, <span class="va">patient</span>, <span class="va">mo</span>, <span class="va">first</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-msg co"><span class="r-pr">#></span> Determining first isolates using an episode length of 365 days</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Determining first isolates using an episode length of 365 days</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> 2</span>
|
<span class="r-msg co"><span class="r-pr">#></span> of 2</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "Clinical"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "Clinical"</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluded 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> => Found 861 'phenotype-based' first isolates (69.8% of total where a</span>
|
<span class="r-msg co"><span class="r-pr">#></span> => Found 861 'phenotype-based' first isolates (69.8% of total where a</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> microbial ID was available)</span>
|
<span class="r-msg co"><span class="r-pr">#></span> microbial ID was available)</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "ICU"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "ICU"</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluded 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> => Found 449 'phenotype-based' first isolates (69.6% within scope and 69.5%</span>
|
<span class="r-msg co"><span class="r-pr">#></span> => Found 449 'phenotype-based' first isolates (69.6% within scope and 69.5%</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> of total where a microbial ID was available)</span>
|
<span class="r-msg co"><span class="r-pr">#></span> of total where a microbial ID was available)</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "Outpatient"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> Group: ward = "Outpatient"</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluded 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> => Found 98 'phenotype-based' first isolates (82.4% within scope and 81.7%</span>
|
<span class="r-msg co"><span class="r-pr">#></span> => Found 98 'phenotype-based' first isolates (82.4% within scope and 81.7%</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> of total where a microbial ID was available)</span>
|
<span class="r-msg co"><span class="r-pr">#></span> of total where a microbial ID was available)</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -246,27 +246,27 @@
|
|||||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 45 13 42 35 36 17 26 23 21 32 27 48 22 10 19 4 37 5 18 11 7 15 3 38 28</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 12 21 4 9 13 34 31 14 43 33 40 37 45 5 41 35 34 30 8 5 25 7 26 39 22</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [26] 47 51 35 6 41 16 25 24 26 4 38 24 35 2 26 10 44 43 1 46 19 12 15 49 41</span>
|
<span class="r-out co"><span class="r-pr">#></span> [26] 30 17 36 5 42 9 17 4 13 17 24 43 5 16 16 19 8 10 14 38 13 14 35 23 9</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [51] 29 5 31 11 33 18 9 48 12 20 25 47 36 46 16 52 8 30 34 51 7 27 50 40 47</span>
|
<span class="r-out co"><span class="r-pr">#></span> [51] 35 37 39 1 6 33 29 31 2 11 18 33 29 3 40 7 30 40 14 20 33 32 26 44 44</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [76] 39 34 35 15 32 27 10 26 36 26 11 34 44 37 50 48 14 22 2 45 5 26 30 51 5</span>
|
<span class="r-out co"><span class="r-pr">#></span> [76] 43 13 14 6 40 14 10 21 27 42 39 7 7 32 18 25 8 14 28 38 35 9 24 15 5</span>
|
||||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [73] TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE TRUE FALSE</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
|
||||||
@ -300,19 +300,19 @@
|
|||||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
|
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [99]</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [94]</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 023456 2009-11-02 A TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 010257 2004-04-03 C TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 036063 2010-01-28 B TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 022060 2004-05-04 C TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 0DBB93 2003-10-02 A TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 023456 2009-11-02 C TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 0DBF93 2015-10-12 B TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 067927 2002-01-07 A TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0E2483 2007-06-21 A TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0E2483 2007-05-29 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 114570 2003-04-08 B TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 0E2483 2007-06-21 A TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 14D826 2006-09-14 A TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 0E2483 2007-06-21 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 156730 2012-04-12 B TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 0E2483 2007-11-10 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 1710B8 2008-01-22 C TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 114570 2003-04-08 B TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 180928 2008-06-13 A TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 141061 2014-10-22 C TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
@ -326,19 +326,19 @@
|
|||||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
|
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [93]</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-11-02 023456 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2004-04-03 010257 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2010-01-28 036063 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2004-05-04 022060 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ICU 2003-10-02 0DBB93 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2009-11-02 023456 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2015-10-12 0DBF93 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2002-01-07 067927 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU 2007-06-21 0E2483 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2003-04-08 114570 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2007-11-10 0E2483 2 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2006-09-14 14D826 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2007-06-21 0E2483 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2012-04-12 156730 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2007-06-21 0E2483 1 FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-01-22 1710B8 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2003-04-08 114570 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2008-06-14 180928 1 FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2014-10-22 141061 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
@ -354,9 +354,9 @@
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 64 14 40 49</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 53 13 35 42</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 23 9 20 21</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 34 10 24 29</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 7 5 6 7</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 6 4 6 6</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
|
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
|
||||||
@ -385,19 +385,19 @@
|
|||||||
<span class="r-in"><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="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
|
<span class="r-in"><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="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> A76045 B_ENTRC_FACM ICU TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 964998 B_STRPT_PNMN Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 452212 B_ENTRC_FACM ICU TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> DF0749 B_ESCHR_COLI Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 419568 B_STRPT_PNMN Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 496896 B_STPHY_CONS ICU TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> BC9909 B_ESCHR_COLI Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> E48302 B_STRPT_PNMN ICU TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 443847 B_KLBSL_PNMN Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> E19440 B_ESCHR_COLI ICU TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F32657 B_STPHY_EPDR ICU TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 545388 B_STPHY_CPTS Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 180928 B_STRPT_AGLC Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 824233 B_STPHY_AURS Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B82692 B_STPHY_CONS Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 54890C B_ESCHR_COLI Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 89F578 B_STPHY_CONS Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> CD8C33 B_STPHY_HMNS Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 597301 B_ESCHR_COLI ICU TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 966513 B_STPHY_HMNS Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
|
||||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -182,9 +182,9 @@
|
|||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.027601</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 2.983447</span>
|
||||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.04687044</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] -0.05816737</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -201,30 +201,30 @@
|
|||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="va">sir</span></span></span>
|
<span class="r-in"><span><span class="va">sir</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] R R R I S R S I S R</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] I R R I R I R R R S</span>
|
||||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.9486833 0.9486833 0.9486833 -0.9486833 -0.9486833 0.9486833</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] -1.1618950 0.7745967 0.7745967 -1.1618950 0.7745967 -1.1618950</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 -0.9486833 -0.9486833 0.9486833</span>
|
<span class="r-out co"><span class="r-pr">#></span> [7] 0.7745967 0.7745967 0.7745967 -1.1618950</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="va">mic</span></span></span>
|
<span class="r-in"><span><span class="va">mic</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 128 0.5 0.025 0.002 32 128 16 0.5 128 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 4 128 0.0625 0.002 0.001 8 0.001 4 4 </span>
|
||||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.07714511 0.97675198 -0.46261901 -1.24022626 -1.89583387 0.61690923</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] -0.3120147 0.6680004 1.4846796 -0.3120147 -1.1231053 -1.2864411</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.97675198 0.43698786 -0.46261901 0.97675198</span>
|
<span class="r-out co"><span class="r-pr">#></span> [7] 0.8313362 -1.2864411 0.6680004 0.6680004</span>
|
||||||
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
|
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
|
||||||
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.07714511 0.97675198 -0.46261901 -1.24022626 -1.89583387 0.61690923</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] -0.3120147 0.6680004 1.4846796 -0.3120147 -1.1231053 -1.2864411</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.97675198 0.43698786 -0.46261901 0.97675198</span>
|
<span class="r-out co"><span class="r-pr">#></span> [7] 0.8313362 -1.2864411 0.6680004 0.6680004</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="va">disk</span></span></span>
|
<span class="r-in"><span><span class="va">disk</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 9 46 37 23 13 47 10 23 6 38</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 10 15 33 50 37 6 50 7 27 42</span>
|
||||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.0287932 1.3209197 0.7493679 -0.1397127 -0.7747702 1.3844254</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] -1.02416943 -0.73485604 0.30667220 1.29033776 0.53812292 -1.25562015</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.9652875 -0.1397127 -1.2193105 0.8128737</span>
|
<span class="r-out co"><span class="r-pr">#></span> [7] 1.29033776 -1.19775747 -0.04050388 0.82743632</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||||
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
||||||
@ -234,22 +234,22 @@
|
|||||||
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</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="va">y</span></span></span>
|
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 A I 18 4 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 A R 22 1 >=4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 23 16 0.25</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 B R 27 0.5 1</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 20 2 1</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 C I 27 8 2</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 20 8 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 8 >=4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 <=0.5 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 E S 18 0.5 >=4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 22 1 1</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 F I 19 8 >=4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 1 0.25</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 G S 27 2 >=4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 2 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 8 2</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 2 0.25</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 I S 30 4 1</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 8 0.25</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 4 2</span>
|
||||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.14918777 -0.03570087 0.13005928 0.13771386 -0.17506383 0.10002806</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 0.16915536 -0.32319888 0.10243586 1.05012543 -0.67969116 -0.02029945</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.47691376 0.43333913 0.00264067 0.03308522</span>
|
<span class="r-out co"><span class="r-pr">#></span> [7] 0.10305622 0.26675770 -0.19285261 -0.47548846</span>
|
||||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||||
@ -265,17 +265,17 @@
|
|||||||
<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-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 20 2 1 0.13005928 0.000000000</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 C I 27 8 2 0.10243586 0.0000000000</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 D I 20 8 2 0.13771386 0.007654579</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 G S 27 2 >=4 0.10305622 0.0006203605</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 F R 22 1 1 0.10002806 0.030031221</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 A R 22 1 >=4 0.16915536 0.0667195016</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 J R 19 8 0.25 0.03308522 0.096974059</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 F I 19 8 >=4 -0.02029945 0.1227353089</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 I I 31 2 0.25 0.00264067 0.127418609</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 H R 21 8 2 0.26675770 0.1643218437</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 B I 23 16 0.25 -0.03570087 0.165760150</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 I S 30 4 1 -0.19285261 0.2952884682</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 A I 18 4 2 -0.14918777 0.279247046</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 B R 27 0.5 1 -0.32319888 0.4256347323</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 2 2 0.43333913 0.303279854</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 J S 19 4 2 -0.47548846 0.5779243144</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 E S 25 <=0.5 2 -0.17506383 0.305123107</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 E S 18 0.5 >=4 -0.67969116 0.7821270147</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 G I 26 1 0.25 -0.47691376 0.606973037</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 D R 30 8 >=4 1.05012543 0.9476895794</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://dplyr.tidyverse.org" class="external-link">"dplyr"</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://dplyr.tidyverse.org" class="external-link">"dplyr"</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 groups</span></span></span>
|
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
|
||||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@ 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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
Binary file not shown.
|
Before Width: | Height: | Size: 26 KiB After Width: | Height: | Size: 25 KiB |
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|
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|
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|
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|
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@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@ 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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -193,42 +193,43 @@
|
|||||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 4 128 4 4 2 0.25 0.002 2 128 1 0.25 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 32 0.125 0.002 0.0625 16 32 0.25 0.005 32 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [13] 128 0.5 0.005 0.025 4 256 64 16 16 0.01 0.25 0.001</span>
|
<span class="r-out co"><span class="r-pr">#></span> [10] 32 0.025 0.025 0.01 16 0.25 32 0.005 8 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [25] 0.002</span>
|
<span class="r-out co"><span class="r-pr">#></span> [19] >=128 0.002 0.01 0.002 8 <=0.001 0.01 </span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 42 9 27 42 18 9 46 39 38 20 26 48 6 47 40 23 13 29 22 6 8 16 40 20 16</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 39 44 20 34 35 49 41 9 45 26 38 38 43 44 43 27 44 29 42 27 11 46 7 43 46</span>
|
||||||
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] S S I I S S S I R R I R I I S R R R R I I S R I I</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] S I R S S R R I S R S S S R R I I I R S I R S I R</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 0.125 0.025 0.001 0.01 64 0.125 0.01 2 2 64 1 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 2 1 0.0625 0.01 1 0.25 0.125 0.005 0.125 >=64 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [13] 0.025 0.25 0.125 16 8 0.125 0.002 4 0.025 128 256 0.002</span>
|
<span class="r-out co"><span class="r-pr">#></span> [11] 0.25 0.025 0.125 1 0.005 0.25 0.025 32 0.25 32 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [25] 16 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [21] 32 0.0625 0.125 0.01 0.125 </span>
|
||||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 16 32 1 16 2 4 32 32 32 2 4 2 16 1 16 16 2 16 2 8 8 1 8 32 2 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 2 1 2 8 2 4 <=0.5 <=0.5 >=16 >=16 1 4 </span>
|
||||||
|
<span class="r-out co"><span class="r-pr">#></span> [13] 4 4 >=16 1 4 <=0.5 4 2 1 2 1 2 </span>
|
||||||
|
<span class="r-out co"><span class="r-pr">#></span> [25] 2 </span>
|
||||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=0.0625 0.25 4 0.5 0.5 2 16 1 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.25 1 <=0.025 2 2 0.125 0.5 1 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [9] 0.5 <=0.0625 <=0.0625 0.25 0.125 8 1 0.125 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [10] 0.0625 <=0.025 1 0.5 0.125 >=4 >=4 0.25 0.125 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [17] 0.25 0.25 0.5 4 <=0.0625 0.5 2 0.5 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [19] 0.125 0.5 <=0.025 <=0.025 0.25 0.5 0.5 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [25] <=0.0625</span>
|
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 40 46 17 10 19 38 43 35 33 44 9 22 30 24 49 11 48 8 18 8 12 21 24 33</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 14 34 36 16 21 47 29 46 32 45 27 45 25 37 42 36 34 30 49 28 22 45 46 41 34</span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 13 15 12 15 17 11 14 17 15 15 13 13 13 13 13 11 17 16 13 12 13 13 12 17</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 15 14 14 11 13 11 16 17 12 11 11 15 15 16 14 11 12 13 14 14 16 17 14 16 12</span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 21 23 23 18 25 24 16 19 20 22 15 22 23 24 21 24 23 17 22 17 23 27 23 26 19</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 27 19 26 21 24 27 23 22 19 25 23 27 25 25 21 20 20 27 21 19 26 22 26 27 24</span>
|
||||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
@ -12,7 +12,7 @@ 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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.02857046</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 0.04370586</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||||
|
|||||||
@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<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="">2.0.0.9015</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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">
|
||||||
|
|||||||
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Reference in New Issue
Block a user