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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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">
@ -228,14 +228,14 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
<span> ampicillin <span class="op">=</span> <span class="st">"S"</span></span>
<span><span class="op">)</span></span>
<span><span class="va">oops</span></span>
<span><span class="co"># mo ampicillin</span></span>
<span><span class="co"># 1 Klebsiella S</span></span>
<span><span class="co"># 2 Escherichia S</span></span>
<span><span class="co">#&gt; mo ampicillin</span></span>
<span><span class="co">#&gt; 1 Klebsiella S</span></span>
<span><span class="co">#&gt; 2 Escherichia S</span></span>
<span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co"># mo ampicillin</span></span>
<span><span class="co"># 1 Klebsiella R</span></span>
<span><span class="co"># 2 Escherichia S</span></span></code></pre></div>
<span><span class="co">#&gt; mo ampicillin</span></span>
<span><span class="co">#&gt; 1 Klebsiella R</span></span>
<span><span class="co">#&gt; 2 Escherichia S</span></span></code></pre></div>
<p>A more convenient function is
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline,
but allows to check for one or more specific microorganisms or
@ -245,13 +245,13 @@ antibiotics:</p>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
<span> <span class="st">"ampicillin"</span></span>
<span><span class="op">)</span></span>
<span><span class="co"># [1] TRUE FALSE</span></span>
<span><span class="co">#&gt; [1] TRUE FALSE</span></span>
<span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
<span> <span class="st">"Klebsiella"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="co"># [1] TRUE FALSE</span></span></code></pre></div>
<span><span class="co">#&gt; [1] TRUE FALSE</span></span></code></pre></div>
<p>EUCAST rules can not only be used for correction, they can also be
used for filling in known resistance and susceptibility based on results
of other antimicrobials drugs. This process is called <em>interpretive

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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">
@ -268,21 +268,21 @@ maximum number of rules is unlimited.</p>
will help reading it if your console supports colours.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">custom</span></span>
<span><span class="co"># A set of custom MDRO rules:</span></span>
<span><span class="co"># 1. If CIP is "R" and age is higher than 60 then: Elderly Type A</span></span>
<span><span class="co"># 2. If ERY is "R" and age is higher than 60 then: Elderly Type B</span></span>
<span><span class="co"># 3. Otherwise: Negative</span></span>
<span><span class="co"># </span></span>
<span><span class="co"># Unmatched rows will return NA.</span></span>
<span><span class="co"># Results will be of class 'factor', with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></span></code></pre></div>
<span><span class="co">#&gt; A set of custom MDRO rules:</span></span>
<span><span class="co">#&gt; 1. If CIP is "R" and age is higher than 60 then: Elderly Type A</span></span>
<span><span class="co">#&gt; 2. If ERY is "R" and age is higher than 60 then: Elderly Type B</span></span>
<span><span class="co">#&gt; 3. Otherwise: Negative</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Unmatched rows will return NA.</span></span>
<span><span class="co">#&gt; Results will be of class 'factor', with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></span></code></pre></div>
<p>The outcome of the function can be used for the
<code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
<span><span class="co"># x</span></span>
<span><span class="co"># Negative Elderly Type A Elderly Type B </span></span>
<span><span class="co"># 1070 198 732</span></span></code></pre></div>
<span><span class="co">#&gt; x</span></span>
<span><span class="co">#&gt; Negative Elderly Type A Elderly Type B </span></span>
<span><span class="co">#&gt; 1070 198 732</span></span></code></pre></div>
<p>The rules set (the <code>custom</code> object in this case) could be
exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you
collaborate with multiple users. The custom rules set could then be
@ -309,8 +309,8 @@ on this data set, we get:</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="../reference/mdro.html">mdro</a></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="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span></span>
<span><span class="co"># Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
<span><span class="co"># antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
<span><span class="co">#&gt; Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
<span><span class="co">#&gt; antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
<p>(16 isolates had no test results)</p>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
@ -384,20 +384,20 @@ names or codes, this would have worked exactly the same way:</p>
<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 S S S R I I</span></span>
<span><span class="co"># 2 S I R R I R</span></span>
<span><span class="co"># 3 I S R S S S</span></span>
<span><span class="co"># 4 R I R S S S</span></span>
<span><span class="co"># 5 R I I R R S</span></span>
<span><span class="co"># 6 I S R S R R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R R R S I R</span></span>
<span><span class="co">#&gt; 2 R R I I S R</span></span>
<span><span class="co">#&gt; 3 I S S S S S</span></span>
<span><span class="co">#&gt; 4 S I I S I S</span></span>
<span><span class="co">#&gt; 5 R R I S I I</span></span>
<span><span class="co">#&gt; 6 R S I R S R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 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">
@ -405,8 +405,8 @@ use:</p>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># ℹ No column found as input for col_mo, assuming all rows contain</span></span>
<span><span class="co"># Mycobacterium tuberculosis.</span></span></code></pre></div>
<span><span class="co">#&gt; ℹ No column found as input for col_mo, assuming all rows contain</span></span>
<span><span class="co">#&gt; Mycobacterium tuberculosis.</span></span></code></pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></span></code></pre></div>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3208</td>
<td align="right">64.16%</td>
<td align="right">3208</td>
<td align="right">64.16%</td>
<td align="right">3244</td>
<td align="right">64.88%</td>
<td align="right">3244</td>
<td align="right">64.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1018</td>
<td align="right">20.36%</td>
<td align="right">4226</td>
<td align="right">84.52%</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4237</td>
<td align="right">84.74%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">447</td>
<td align="right">8.94%</td>
<td align="right">4673</td>
<td align="right">93.46%</td>
<td align="right">4684</td>
<td align="right">93.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">229</td>
<td align="right">4.58%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">214</td>
<td align="right">4.28%</td>
<td align="right">4898</td>
<td align="right">97.96%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">102</td>
<td align="right">2.04%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

140
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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">
@ -198,54 +198,54 @@ is currently being developed.</strong></p>
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span>
<span><span class="co"># Rows: 2,000</span></span>
<span><span class="co"># Columns: 46</span></span>
<span><span class="co"># $ date <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2…</span></span>
<span><span class="co"># $ patient <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A77334", "A77334", "067927", "067927", "067927", "067927", "4…</span></span>
<span><span class="co"># $ age <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50…</span></span>
<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;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>
<span><span class="co">#&gt; Rows: 2,000</span></span>
<span><span class="co">#&gt; Columns: 46</span></span>
<span><span class="co">#&gt; $ date <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2…</span></span>
<span><span class="co">#&gt; $ patient <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A77334", "A77334", "067927", "067927", "067927", "067927", "4…</span></span>
<span><span class="co">#&gt; $ age <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50…</span></span>
<span><span class="co">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">#&gt; $ 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">
@ -261,16 +261,16 @@ per taxonomic order and genus:</p>
<span> <span class="op">)</span> <span class="co"># and select only relevant columns</span></span>
<span></span>
<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">resistance_data</span><span class="op">)</span></span>
<span><span class="co"># <span style="color: #949494;"># A tibble: 6 × 10</span></span></span>
<span><span class="co"># <span style="color: #949494;"># Groups: order [5]</span></span></span>
<span><span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span></span>
<span><span class="co"># <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;">1</span> (unknown order) (unknown ge… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;">2</span> Actinomycetales Schaalia <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;">3</span> Bacteroidales Bacteroides <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;">4</span> Campylobacterales Campylobact… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;">5</span> Caryophanales Gemella <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;">6</span> Caryophanales Listeria <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 6 × 10</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># Groups: order [5]</span></span></span>
<span><span class="co">#&gt; order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> (unknown order) (unknown ge… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Actinomycetales Schaalia <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Bacteroidales Bacteroides <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Campylobacterales Campylobact… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Caryophanales Gemella <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">6</span> Caryophanales Listeria <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
@ -280,21 +280,21 @@ that contain numeric values in all selected variables, so we now only
need to do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span>
<span><span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span></span>
<span><span class="co"># and "TOB". Total observations available: 7.</span></span></code></pre></div>
<span><span class="co">#&gt; ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span></span>
<span><span class="co">#&gt; and "TOB". Total observations available: 7.</span></span></code></pre></div>
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>
function:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span>
<span><span class="co"># Groups (n=4, named as 'order'):</span></span>
<span><span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co"># Importance of components:</span></span>
<span><span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co"># Groups (n=4, named as 'order'):</span></span>
<span><span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span></code></pre>
<span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span></code></pre>
<p>Good news. The first two components explain a total of 93.3% of the
variance (see the PC1 and PC2 values of the <em>Proportion of
Variance</em>. We can create a so-called biplot with the base R

34
articles/SPSS.html
View File

@ -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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">17 February 2023</h4>
<h4 data-toc-skip class="date">18 February 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>
@ -324,15 +324,15 @@ would be of any better use than R.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># not all values are valid MIC values:</span></span>
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.125</span><span class="op">)</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.125</span></span>
<span><span class="co">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 0.125</span></span>
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="st">"testvalue"</span><span class="op">)</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] &lt;NA&gt;</span></span>
<span><span class="co">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] &lt;NA&gt;</span></span>
<span></span>
<span><span class="co"># the Gram stain is available for all bacteria:</span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span>
<span><span class="co"># [1] "Gram-negative"</span></span>
<span><span class="co">#&gt; [1] "Gram-negative"</span></span>
<span></span>
<span><span class="co"># Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST:</span></span>
<span><span class="va">klebsiella_test</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>
@ -341,22 +341,22 @@ would be of any better use than R.</p>
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span>
<span><span class="va">klebsiella_test</span> <span class="co"># (our original data)</span></span>
<span><span class="co"># mo amox</span></span>
<span><span class="co"># 1 klebsiella S</span></span>
<span><span class="co">#&gt; mo amox</span></span>
<span><span class="co">#&gt; 1 klebsiella S</span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">klebsiella_test</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="co"># (the edited data by EUCAST rules)</span></span>
<span><span class="co"># mo amox</span></span>
<span><span class="co"># 1 klebsiella R</span></span>
<span><span class="co">#&gt; mo amox</span></span>
<span><span class="co">#&gt; 1 klebsiella R</span></span>
<span></span>
<span><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "Flucloxacillin"</span></span>
<span><span class="co">#&gt; [1] "Flucloxacillin"</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "culpen" "floxacillin" "floxacillin sodium" </span></span>
<span><span class="co"># [4] "floxapen" "floxapen sodium salt" "fluclox" </span></span>
<span><span class="co"># [7] "flucloxacilina" "flucloxacillin" "flucloxacilline" </span></span>
<span><span class="co"># [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex"</span></span>
<span><span class="co">#&gt; [1] "culpen" "floxacillin" "floxacillin sodium" </span></span>
<span><span class="co">#&gt; [4] "floxapen" "floxapen sodium salt" "fluclox" </span></span>
<span><span class="co">#&gt; [7] "flucloxacilina" "flucloxacillin" "flucloxacilline" </span></span>
<span><span class="co">#&gt; [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex"</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "J01CF05"</span></span></code></pre></div>
<span><span class="co">#&gt; [1] "J01CF05"</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="import-data-from-spsssasstata">Import data from SPSS/SAS/Stata<a class="anchor" aria-label="anchor" href="#import-data-from-spsssasstata"></a>

2
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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">

4
articles/datasets.html
View File

@ -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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">
@ -176,7 +176,7 @@
<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">17 February 2023</h4>
<h4 data-toc-skip class="date">18 February 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>

2
articles/index.html
View File

@ -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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">

42
articles/resistance_predict.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="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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">
@ -238,20 +238,20 @@ number of observations, the actual observed resistance, the estimated
resistance and the standard error below and above the estimation:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">predict_TZP</span></span>
<span><span class="co"># <span style="color: #949494;"># A tibble: 32 × 7</span></span></span>
<span><span class="co"># year value se_min se_max observations observed estimated</span></span>
<span><span class="co"># <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 1</span> <span style="text-decoration: underline;">2</span>002 0.2 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 15 0.2 0.056<span style="text-decoration: underline;">2</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 2</span> <span style="text-decoration: underline;">2</span>003 0.062<span style="text-decoration: underline;">5</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 32 0.062<span style="text-decoration: underline;">5</span> 0.061<span style="text-decoration: underline;">6</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 3</span> <span style="text-decoration: underline;">2</span>004 0.085<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 82 0.085<span style="text-decoration: underline;">4</span> 0.067<span style="text-decoration: underline;">6</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 4</span> <span style="text-decoration: underline;">2</span>005 0.05 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 60 0.05 0.074<span style="text-decoration: underline;">1</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 5</span> <span style="text-decoration: underline;">2</span>006 0.050<span style="text-decoration: underline;">8</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 59 0.050<span style="text-decoration: underline;">8</span> 0.081<span style="text-decoration: underline;">2</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 6</span> <span style="text-decoration: underline;">2</span>007 0.121 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 66 0.121 0.088<span style="text-decoration: underline;">9</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 7</span> <span style="text-decoration: underline;">2</span>008 0.041<span style="text-decoration: underline;">7</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 72 0.041<span style="text-decoration: underline;">7</span> 0.097<span style="text-decoration: underline;">2</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 8</span> <span style="text-decoration: underline;">2</span>009 0.016<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 61 0.016<span style="text-decoration: underline;">4</span> 0.106 </span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 9</span> <span style="text-decoration: underline;">2</span>010 0.056<span style="text-decoration: underline;">6</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 53 0.056<span style="text-decoration: underline;">6</span> 0.116 </span></span>
<span><span class="co"># <span style="color: #BCBCBC;">10</span> <span style="text-decoration: underline;">2</span>011 0.183 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 93 0.183 0.127 </span></span>
<span><span class="co"># <span style="color: #949494;"># … with 22 more rows</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 32 × 7</span></span></span>
<span><span class="co">#&gt; year value se_min se_max observations observed estimated</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="text-decoration: underline;">2</span>002 0.2 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 15 0.2 0.056<span style="text-decoration: underline;">2</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> <span style="text-decoration: underline;">2</span>003 0.062<span style="text-decoration: underline;">5</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 32 0.062<span style="text-decoration: underline;">5</span> 0.061<span style="text-decoration: underline;">6</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> <span style="text-decoration: underline;">2</span>004 0.085<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 82 0.085<span style="text-decoration: underline;">4</span> 0.067<span style="text-decoration: underline;">6</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> <span style="text-decoration: underline;">2</span>005 0.05 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 60 0.05 0.074<span style="text-decoration: underline;">1</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> <span style="text-decoration: underline;">2</span>006 0.050<span style="text-decoration: underline;">8</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 59 0.050<span style="text-decoration: underline;">8</span> 0.081<span style="text-decoration: underline;">2</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> <span style="text-decoration: underline;">2</span>007 0.121 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 66 0.121 0.088<span style="text-decoration: underline;">9</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> <span style="text-decoration: underline;">2</span>008 0.041<span style="text-decoration: underline;">7</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 72 0.041<span style="text-decoration: underline;">7</span> 0.097<span style="text-decoration: underline;">2</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="text-decoration: underline;">2</span>009 0.016<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 61 0.016<span style="text-decoration: underline;">4</span> 0.106 </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="text-decoration: underline;">2</span>010 0.056<span style="text-decoration: underline;">6</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 53 0.056<span style="text-decoration: underline;">6</span> 0.116 </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="text-decoration: underline;">2</span>011 0.183 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 93 0.183 0.127 </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with 22 more rows</span></span></span></code></pre></div>
<p>The function <code>plot</code> is available in base R, and can be
extended by other packages to depend the output based on the type of
input. We extended its function to cope with resistance predictions:</p>
@ -342,14 +342,14 @@ model might be more appropriate:</p>
<code class="sourceCode R"><span><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span></span>
<span><span class="co"># </span></span>
<span><span class="co"># Family: binomial </span></span>
<span><span class="co"># Link function: logit</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Family: binomial </span></span>
<span><span class="co">#&gt; Link function: logit</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span></span>
<span><span class="co"># Estimate Std. Error z value Pr(&gt;|z|)</span></span>
<span><span class="co"># (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span></span>
<span><span class="co"># year 0.09883005 0.02295317 4.305725 1.664395e-05</span></span></code></pre></div>
<span><span class="co">#&gt; Estimate Std. Error z value Pr(&gt;|z|)</span></span>
<span><span class="co">#&gt; (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span></span>
<span><span class="co">#&gt; year 0.09883005 0.02295317 4.305725 1.664395e-05</span></span></code></pre></div>
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