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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9234</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">
@ -92,7 +92,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 31 March 2025.</p>
generated on 07 April 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -148,21 +148,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-03-31</td>
<td align="center">2025-04-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-03-31</td>
<td align="center">2025-04-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-03-31</td>
<td align="center">2025-04-07</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -472,15 +472,15 @@ impression, as it comes with support for the new <code>mo</code> and
<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">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; Rows: 2,724</span></span>
<span><span class="co">#&gt; Columns: 9</span></span>
<span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3", "R7", "P3", "P10", "B7", "W3", "M3", "J3", "G6", "P4"…</span></span>
<span><span class="co">#&gt; $ hospital <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…</span></span>
<span><span class="co">#&gt; $ date <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2012-11-21, 2018-04-03, 2014-09-19, 2015-12-10, 2015-03-02…</span></span>
<span><span class="co">#&gt; $ bacteria <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> "B_ESCHR_COLI", "B_KLBSL_PNMN", "B_ESCHR_COLI", "B_ESCHR_COL…</span></span>
<span><span class="co">#&gt; $ AMX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, S, S, R, R, S, S, S, S, R, S, S, R, R, R, R, S, R,…</span></span>
<span><span class="co">#&gt; $ AMC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, S, I, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, S,…</span></span>
<span><span class="co">#&gt; $ CIP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
<span><span class="co">#&gt; $ GEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,…</span></span>
<span><span class="co">#&gt; $ first <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span>
<span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3"<span style="color: #949494;">, </span>"R7"<span style="color: #949494;">, </span>"P3"<span style="color: #949494;">, </span>"P10"<span style="color: #949494;">, </span>"B7"<span style="color: #949494;">, </span>"W3"<span style="color: #949494;">, </span>"M3"<span style="color: #949494;">, </span>"J3"<span style="color: #949494;">, </span>"G6"<span style="color: #949494;">, </span>"P4"…</span></span>
<span><span class="co">#&gt; $ hospital <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">,</span>…</span></span>
<span><span class="co">#&gt; $ date <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2012-11-21<span style="color: #949494;">, </span>2018-04-03<span style="color: #949494;">, </span>2014-09-19<span style="color: #949494;">, </span>2015-12-10<span style="color: #949494;">, </span>2015-03-02…</span></span>
<span><span class="co">#&gt; $ bacteria <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> "B_ESCHR_COLI"<span style="color: #949494;">, </span>"B_KLBSL_PNMN"<span style="color: #949494;">, </span>"B_ESCHR_COLI"<span style="color: #949494;">, </span>"B_ESCHR_COL…</span></span>
<span><span class="co">#&gt; $ AMX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">,</span>…</span></span>
<span><span class="co">#&gt; $ AMC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I<span style="color: #949494;">, </span>I<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>I<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">,</span>…</span></span>
<span><span class="co">#&gt; $ CIP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">,</span>…</span></span>
<span><span class="co">#&gt; $ GEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">,</span>…</span></span>
<span><span class="co">#&gt; $ first <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">,</span>…</span></span>
<span></span>
<span><span class="co"># number of unique values per column:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
@ -1147,9 +1147,9 @@ incidence and antimicrobial susceptibility patterns.</p>
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead>
<tbody><tr class="odd">
<td align="left">71.7% (57.5-83.6%)</td>
<td align="left">95.1% (88.9-98.6%)</td>
<td align="left">91.1% (81.4-96.9%)</td>
<td align="left">69.2% (51-85.2%)</td>
<td align="left">92.9% (84-98.5%)</td>
<td align="left">89% (76.4-96.9%)</td>
</tr></tbody>
</table>
<p>WISCA uses a <strong>Bayesian decision model</strong> to integrate
@ -1190,56 +1190,56 @@ function on a grouped <code>tibble</code>, i.e., using
<tr class="odd">
<td align="left">0-24</td>
<td align="left">F</td>
<td align="left">66.8% (13.5-98.9%)</td>
<td align="left">57.5% (7-98.4%)</td>
<td align="left">74.6% (30.6-98.9%)</td>
<td align="left">77.9% (34.5-99.1%)</td>
<td align="left">69.7% (24.5-98.5%)</td>
</tr>
<tr class="even">
<td align="left">0-24</td>
<td align="left">M</td>
<td align="left">75.4% (34-99.1%)</td>
<td align="left">59% (14.8-97.9%)</td>
<td align="left">80% (40.6-99.2%)</td>
<td align="left">76.1% (33.7-99.2%)</td>
<td align="left">60.1% (15-98.2%)</td>
</tr>
<tr class="odd">
<td align="left">25-49</td>
<td align="left">F</td>
<td align="left">88.5% (67.7-98.9%)</td>
<td align="left">65.4% (30.2-97.9%)</td>
<td align="left">91.6% (72.9-99.7%)</td>
<td align="left">82.6% (49.7-99.3%)</td>
</tr>
<tr class="even">
<td align="left">25-49</td>
<td align="left">M</td>
<td align="left">74.7% (38.4-97.5%)</td>
<td align="left">54.4% (10.9-97.3%)</td>
<td align="left">89.4% (66.7-99.7%)</td>
<td align="left">76.3% (33.1-99.1%)</td>
<td align="left">70.7% (26.9-98.6%)</td>
</tr>
<tr class="odd">
<td align="left">50-74</td>
<td align="left">F</td>
<td align="left">75.4% (61-90.6%)</td>
<td align="left">68.2% (44.6-92.6%)</td>
<td align="left">95.8% (87.6-99.5%)</td>
<td align="left">88.3% (71-97.7%)</td>
</tr>
<tr class="even">
<td align="left">50-74</td>
<td align="left">M</td>
<td align="left">66.9% (46.2-85.6%)</td>
<td align="left">65.8% (43.7-86.2%)</td>
<td align="left">95.3% (86-99.6%)</td>
<td align="left">83.7% (62.9-97%)</td>
</tr>
<tr class="odd">
<td align="left">75+</td>
<td align="left">F</td>
<td align="left">73.3% (51.3-91.6%)</td>
<td align="left">71.8% (48-92%)</td>
<td align="left">96.6% (90-99.7%)</td>
<td align="left">90.8% (76.5-98.8%)</td>
</tr>
<tr class="even">
<td align="left">75+</td>
<td align="left">M</td>
<td align="left">73.9% (55.7-89.4%)</td>
<td align="left">72.9% (53.7-89.7%)</td>
<td align="left">96.7% (89.9-99.7%)</td>
<td align="left">92.5% (80.3-98.9%)</td>
</tr>