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articles/EUCAST.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">

90
articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@ -348,46 +348,46 @@ Unique: 2</p>
<p>For another example, I will create a data set to determine multi-drug
resistant TB:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># random_rsi() is a helper function to generate</span></span>
<code class="sourceCode R"><span><span class="co"># random_sir() is a helper function to generate</span></span>
<span><span class="co"># a random vector with values S, I and R</span></span>
<span><span class="va">my_TB_data</span> <span class="op">&lt;-</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> rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
<span> rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p>Because all column names are automatically verified for valid drug
names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">my_TB_data</span> <span class="op">&lt;-</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> RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
<span> RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
<span> KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<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>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R I I I R I</span></span>
<span><span class="co"># 2 I R I I R S</span></span>
<span><span class="co"># 3 R S I S S I</span></span>
<span><span class="co"># 4 S R S R I I</span></span>
<span><span class="co"># 5 S R R R I I</span></span>
<span><span class="co"># 6 R I S S S R</span></span>
<span><span class="co"># 1 I S S I S I</span></span>
<span><span class="co"># 2 R R R R I S</span></span>
<span><span class="co"># 3 R I R R I R</span></span>
<span><span class="co"># 4 R S I S S I</span></span>
<span><span class="co"># 5 I I S S S I</span></span>
<span><span class="co"># 6 I I I R R I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3201</td>
<td align="right">64.02%</td>
<td align="right">3201</td>
<td align="right">64.02%</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">981</td>
<td align="right">19.62%</td>
<td align="right">4182</td>
<td align="right">83.64%</td>
<td align="right">994</td>
<td align="right">19.88%</td>
<td align="right">4232</td>
<td align="right">84.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">441</td>
<td align="right">8.82%</td>
<td align="right">4623</td>
<td align="right">92.46%</td>
<td align="right">425</td>
<td align="right">8.50%</td>
<td align="right">4657</td>
<td align="right">93.14%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">258</td>
<td align="right">5.16%</td>
<td align="right">4881</td>
<td align="right">97.62%</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">119</td>
<td align="right">2.38%</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

84
articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@ -196,46 +196,46 @@ is currently being developed.</strong></p>
<span><span class="co"># $ gender <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M", "M", "M…</span></span>
<span><span class="co"># $ ward <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "Clinical", "Clinical", "ICU", "ICU", "ICU", "ICU", "Clinical"…</span></span>
<span><span class="co"># $ mo <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPHY_EPDR",…</span></span>
<span><span class="co"># $ PEN <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co"># $ OXA <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ FLC <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R…</span></span>
<span><span class="co"># $ AMX <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
<span><span class="co"># $ AMC <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N…</span></span>
<span><span class="co"># $ AMP <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
<span><span class="co"># $ TZP <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ CZO <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
<span><span class="co"># $ FEP <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ CXM <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S…</span></span>
<span><span class="co"># $ FOX <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
<span><span class="co"># $ CTX <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co"># $ CAZ <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, …</span></span>
<span><span class="co"># $ CRO <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co"># $ GEN <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ TOB <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA…</span></span>
<span><span class="co"># $ AMK <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ KAN <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ TMP <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, …</span></span>
<span><span class="co"># $ SXT <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N…</span></span>
<span><span class="co"># $ NIT <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,…</span></span>
<span><span class="co"># $ FOS <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ LNZ <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
<span><span class="co"># $ CIP <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S…</span></span>
<span><span class="co"># $ MFX <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ VAN <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, …</span></span>
<span><span class="co"># $ TEC <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
<span><span class="co"># $ TCY <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, …</span></span>
<span><span class="co"># $ TGC <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
<span><span class="co"># $ DOX <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
<span><span class="co"># $ ERY <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co"># $ CLI <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…</span></span>
<span><span class="co"># $ AZM <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co"># $ IPM <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co"># $ MEM <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ MTR <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ CHL <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ COL <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …</span></span>
<span><span class="co"># $ MUP <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ RIF <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span></code></pre></div>
<span><span class="co"># $ PEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co"># $ OXA <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ FLC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R…</span></span>
<span><span class="co"># $ AMX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
<span><span class="co"># $ AMC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N…</span></span>
<span><span class="co"># $ AMP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
<span><span class="co"># $ TZP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ CZO <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
<span><span class="co"># $ FEP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ CXM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S…</span></span>
<span><span class="co"># $ FOX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
<span><span class="co"># $ CTX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co"># $ CAZ <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, …</span></span>
<span><span class="co"># $ CRO <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co"># $ GEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ TOB <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA…</span></span>
<span><span class="co"># $ AMK <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ KAN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ TMP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, …</span></span>
<span><span class="co"># $ SXT <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N…</span></span>
<span><span class="co"># $ NIT <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,…</span></span>
<span><span class="co"># $ FOS <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ LNZ <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
<span><span class="co"># $ CIP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S…</span></span>
<span><span class="co"># $ MFX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ VAN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, …</span></span>
<span><span class="co"># $ TEC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
<span><span class="co"># $ TCY <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, …</span></span>
<span><span class="co"># $ TGC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
<span><span class="co"># $ DOX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
<span><span class="co"># $ ERY <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co"># $ CLI <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…</span></span>
<span><span class="co"># $ AZM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co"># $ IPM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co"># $ MEM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ MTR <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ CHL <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ COL <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …</span></span>
<span><span class="co"># $ MUP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co"># $ RIF <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span></code></pre></div>
<p>Now to transform this to a data set with only resistance percentages
per taxonomic order and genus:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
@ -244,7 +244,7 @@ per taxonomic order and genus:</p>
<span> order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span>
<span> genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span></span>
<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># and genus as we do here</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># then get resistance of all drugs</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.sir</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># then get resistance of all drugs</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span></span>
<span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
<span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span>

4
articles/SPSS.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">20 January 2023</h4>
<h4 data-toc-skip class="date">21 January 2023</h4>
<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>
<div class="d-none name"><code>SPSS.Rmd</code></div>

14
articles/WHONET.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@ -212,15 +212,15 @@ recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Antimicrobial results or interpretations have to be clean and valid.
In other words, they should only contain values <code>"S"</code>,
<code>"I"</code> or <code>"R"</code>. That is exactly where the
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> function is for.</li>
</ul>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform variables</span></span>
<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">WHONET</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># get microbial ID based on given organism</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></span></code></pre></div>
<span> <span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `sir` class</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></code></pre></div>
<p>No errors or warnings, so all values are transformed succesfully.</p>
<p>We also created a package dedicated to data cleaning and checking,
called the <code>cleaner</code> package. Its <code><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq()</a></code>
@ -342,7 +342,7 @@ Longest: 40</p>
<span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>
<span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
<p>Class: factor &gt; ordered &gt; sir (numeric)<br>
Length: 500<br>
Levels: 3: S &lt; I &lt; R<br>
Available: 481 (96.2%, NA: 19 = 3.8%)<br>
@ -391,12 +391,12 @@ Drug group: Beta-lactams/penicillins<br>
<h3 id="a-first-glimpse-at-results">A first glimpse at results<a class="anchor" aria-label="anchor" href="#a-first-glimpse-at-results"></a>
</h3>
<p>An easy <code>ggplot</code> will already give a lot of information,
using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> function:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">Country</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">"ab"</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<span> <span class="fu"><a href="../reference/ggplot_sir.html">ggplot_sir</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">"ab"</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

36
articles/datasets.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@ -166,7 +166,7 @@
<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>
<h4 data-toc-skip class="date">20 January 2023</h4>
<h4 data-toc-skip class="date">21 January 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>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -174,7 +174,7 @@
<p>All reference data (about microorganisms, antibiotics, R/SI
<p>All reference data (about microorganisms, antibiotics, SIR
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, MS Excel, Apache Feather, Apache
@ -863,42 +863,42 @@ inhibitors</td>
</div>
</div>
<div class="section level2">
<h2 id="rsi_translation-interpretation-from-mic-values-disk-diameters-to-rsi">
<code>rsi_translation</code>: Interpretation from MIC values / disk
diameters to R/SI<a class="anchor" aria-label="anchor" href="#rsi_translation-interpretation-from-mic-values-disk-diameters-to-rsi"></a>
<h2 id="clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir">
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 18,308 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>,
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 October 2022 17:01:23 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 21 January 2023 22:47:20 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (42 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">tab-separated
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (1.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Microsoft
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (0.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.feather" class="external-link">Apache
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (0.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (87 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sas" class="external-link">SAS
data file</a> (3.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">IBM
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (2.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (3.4 MB)</li>
</ul>
<div class="section level3">
@ -1485,7 +1485,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 August 2022 18:49:37 UTC. Find more info
<p>It was last updated on 21 January 2023 22:47:20 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>

2
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">

12
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@ -252,15 +252,15 @@ input. We extended its function to cope with resistance predictions:</p>
right axes, error bars, titles, number of available observations and
type of model.</p>
<p>We also support the <code>ggplot2</code> package with our custom
function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing
function <code><a href="../reference/resistance_predict.html">ggplot_sir_predict()</a></code> to create more appealing
plots:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></span></code></pre></div>
<code class="sourceCode R"><span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_sir_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co"># choose for error bars instead of a ribbon</span></span>
<span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span>, ribbon <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_sir_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span>, ribbon <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
<div class="section level3">
<h3 id="choosing-the-right-model">Choosing the right model<a class="anchor" aria-label="anchor" href="#choosing-the-right-model"></a>
@ -272,7 +272,7 @@ is enormous:</p>
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<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"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_sir_predict</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>Vancomycin resistance could be 100% in ten years, but might remain
very low.</p>
@ -324,7 +324,7 @@ model might be more appropriate:</p>
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<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"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_sir_predict</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<p>The model itself is also available from the object, as an
<code>attribute</code>:</p>

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@ -195,7 +195,7 @@ treatment evaluation in any setting.</p>
<p>After installing this package, R knows ~52,000 distinct microbial
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid R/SI and MIC values. The integral
CT), and knows all about valid SIR and MIC values. The integral
breakpoint guidelines from CLSI and EUCAST are included from the last 10
years. It supports and can read any data format, including WHONET
data.</p>
@ -239,10 +239,10 @@ microorganism based on a SNOMED code</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an
antibiotic based on a LOINC code</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to
translate MIC values and disk diffusion diameters to R/SI</li>
translate MIC values and disk diffusion diameters to SIR</li>
<li>Principal component analysis for AMR</li>
</ul>
<p>All reference data sets (about microorganisms, antibiotics, R/SI
<p>All reference data sets (about microorganisms, antibiotics, SIR
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
publicly and freely available. We continually export our data sets to
formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat