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articles/AMR.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -721,9 +721,9 @@ Carlo simulation:</p>
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead>
<tbody><tr class="odd">
<td align="left">70.2% (64.8-75.2%)</td>
<td align="left">93.6% (92.2-95%)</td>
<td align="left">89.9% (87-92.3%)</td>
<td align="left">70% (64.4-75.3%)</td>
<td align="left">93.6% (92.1-95%)</td>
<td align="left">89.8% (87-92.3%)</td>
</tr></tbody>
</table>
<p>The output tells you: <em>“given the species distribution in your
@@ -764,51 +764,51 @@ accepts any column or expression:</p>
<tr class="odd">
<td align="left">0-24</td>
<td align="left">F</td>
<td align="left">56.8% (29.9-81.3%)</td>
<td align="left">70.7% (45.2-89%)</td>
<td align="left">65.9% (42.3-86.6%)</td>
<td align="left">57% (29.7-81.3%)</td>
<td align="left">70.8% (45.2-88.9%)</td>
<td align="left">66.1% (43-86.8%)</td>
</tr>
<tr class="even">
<td align="left">0-24</td>
<td align="left">M</td>
<td align="left">59.5% (31.2-85.5%)</td>
<td align="left">76.1% (56.5-92%)</td>
<td align="left">59.6% (31.7-85.1%)</td>
<td align="left">59.7% (31.2-85.9%)</td>
<td align="left">76.1% (57.1-91.7%)</td>
<td align="left">59.5% (31.7-85.1%)</td>
</tr>
<tr class="odd">
<td align="left">25-49</td>
<td align="left">F</td>
<td align="left">67.7% (43.9-89.7%)</td>
<td align="left">67.9% (44.6-89.7%)</td>
<td align="left">93.8% (87.4-98.1%)</td>
<td align="left">87% (70.1-97%)</td>
<td align="left">87% (70-97%)</td>
</tr>
<tr class="even">
<td align="left">25-49</td>
<td align="left">M</td>
<td align="left">56.9% (26.6-86.2%)</td>
<td align="left">91% (82-97.2%)</td>
<td align="left">76.6% (51.4-93.5%)</td>
<td align="left">91.1% (82-97.2%)</td>
<td align="left">76.5% (51.4-93.5%)</td>
</tr>
<tr class="odd">
<td align="left">50-74</td>
<td align="left">F</td>
<td align="left">68% (54.1-81.8%)</td>
<td align="left">96.9% (94.6-98.5%)</td>
<td align="left">90.2% (82-96.2%)</td>
<td align="left">90.3% (82-96.2%)</td>
</tr>
<tr class="even">
<td align="left">50-74</td>
<td align="left">M</td>
<td align="left">67% (56-78.5%)</td>
<td align="left">96.7% (94.1-98.5%)</td>
<td align="left">86.7% (77.3-94.4%)</td>
<td align="left">96.7% (94-98.5%)</td>
<td align="left">86.7% (77.3-94.5%)</td>
</tr>
<tr class="odd">
<td align="left">75+</td>
<td align="left">F</td>
<td align="left">73.1% (61.8-84.1%)</td>
<td align="left">73.2% (61.9-84.2%)</td>
<td align="left">97.7% (95.9-99%)</td>
<td align="left">92.8% (85.7-97.2%)</td>
<td align="left">92.7% (85.6-97.2%)</td>
</tr>
<tr class="even">
<td align="left">75+</td>
@@ -1424,7 +1424,7 @@ values:</p>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
<div class="pkgdown-footer-right">

16
articles/AMR.md
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@@ -656,7 +656,7 @@ wisca_result
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|
| 70.2% (64.8-75.2%) | 93.6% (92.2-95%) | 89.9% (87-92.3%) |
| 70% (64.4-75.3%) | 93.6% (92.1-95%) | 89.8% (87-92.3%) |
The output tells you: *“given the species distribution in your data,
there is an estimated X% probability that this regimen covers the
@@ -683,13 +683,13 @@ wisca_out
| age_group | gender | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|:---|
| 0-24 | F | 56.8% (29.9-81.3%) | 70.7% (45.2-89%) | 65.9% (42.3-86.6%) |
| 0-24 | M | 59.5% (31.2-85.5%) | 76.1% (56.5-92%) | 59.6% (31.7-85.1%) |
| 25-49 | F | 67.7% (43.9-89.7%) | 93.8% (87.4-98.1%) | 87% (70.1-97%) |
| 25-49 | M | 56.9% (26.6-86.2%) | 91% (82-97.2%) | 76.6% (51.4-93.5%) |
| 50-74 | F | 68% (54.1-81.8%) | 96.9% (94.6-98.5%) | 90.2% (82-96.2%) |
| 50-74 | M | 67% (56-78.5%) | 96.7% (94.1-98.5%) | 86.7% (77.3-94.4%) |
| 75+ | F | 73.1% (61.8-84.1%) | 97.7% (95.9-99%) | 92.8% (85.7-97.2%) |
| 0-24 | F | 57% (29.7-81.3%) | 70.8% (45.2-88.9%) | 66.1% (43-86.8%) |
| 0-24 | M | 59.7% (31.2-85.9%) | 76.1% (57.1-91.7%) | 59.5% (31.7-85.1%) |
| 25-49 | F | 67.9% (44.6-89.7%) | 93.8% (87.4-98.1%) | 87% (70-97%) |
| 25-49 | M | 56.9% (26.6-86.2%) | 91.1% (82-97.2%) | 76.5% (51.4-93.5%) |
| 50-74 | F | 68% (54.1-81.8%) | 96.9% (94.6-98.5%) | 90.3% (82-96.2%) |
| 50-74 | M | 67% (56-78.5%) | 96.7% (94-98.5%) | 86.7% (77.3-94.5%) |
| 75+ | F | 73.2% (61.9-84.2%) | 97.7% (95.9-99%) | 92.7% (85.6-97.2%) |
| 75+ | M | 74% (63.6-82.6%) | 97.9% (96-99%) | 94.7% (89.3-97.9%) |
Keep in mind that more granular stratification produces more relevant

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articles/AMR_for_Python.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -642,7 +642,7 @@ Python.</p>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
<div class="pkgdown-footer-right">

4
articles/AMR_with_tidymodels.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -998,7 +998,7 @@ settings.</p>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
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4
articles/EUCAST.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -319,7 +319,7 @@ reading</em>, and is basically a form of imputation:</p>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
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4
articles/PCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -236,7 +236,7 @@ automatically adds the right labels and even groups:</p>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
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4
articles/WHONET.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -325,7 +325,7 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
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109
articles/WISCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -341,7 +341,11 @@ traditional antibiogram remains fit for purpose.</p>
<span><span class="co">#&gt; <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span></span>
<span></span>
<span><span class="co"># Add a synthetic syndrome column for demonstration</span></span>
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"Non-UTI"</span><span class="op">)</span></span></code></pre></div>
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"Non-UTI"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Keep only 10 most common microorganisms</span></span>
<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/top_n_microorganisms.html">top_n_microorganisms</a></span><span class="op">(</span><span class="va">data</span>, n <span class="op">=</span> <span class="fl">10</span>, property <span class="op">=</span> <span class="st">"species"</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `col_mo`.</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="basic-wisca">Basic WISCA<a class="anchor" aria-label="anchor" href="#basic-wisca"></a>
@@ -357,9 +361,9 @@ traditional antibiogram remains fit for purpose.</p>
<th align="left">Gentamicin</th>
</tr></thead>
<tbody><tr class="odd">
<td align="left">74.2% (72.1-76.1%)</td>
<td align="left">78.4% (75.6-81.1%)</td>
<td align="left">72.5% (70.4-74.6%)</td>
<td align="left">76.8% (74.7-79.1%)</td>
<td align="left">81.5% (78.9-84.1%)</td>
<td align="left">82.9% (81-84.8%)</td>
</tr></tbody>
</table>
</div>
@@ -385,9 +389,9 @@ covers the pathogen:</p>
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
</tr></thead>
<tbody><tr class="odd">
<td align="left">74.2% (72.2-76.1%)</td>
<td align="left">88.8% (87.2-90.4%)</td>
<td align="left">90.8% (89.4-92.2%)</td>
<td align="left">76.8% (74.6-78.9%)</td>
<td align="left">89.6% (88-91.1%)</td>
<td align="left">93.7% (92.5-94.9%)</td>
</tr></tbody>
</table>
</div>
@@ -397,10 +401,11 @@ covers the pathogen:</p>
<p>Use <code>syndromic_group</code> to produce separate WISCA estimates
per clinical stratum. You can pass a column name or any expression:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<code class="sourceCode R"><span><span class="va">wisca_out</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span></span>
<span><span class="op">)</span></span></code></pre></div>
<span><span class="op">)</span></span>
<span><span class="va">wisca_out</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="12%">
@@ -417,15 +422,15 @@ per clinical stratum. You can pass a column name or any expression:</p>
<tbody>
<tr class="odd">
<td align="left">Non-UTI</td>
<td align="left">70.3% (67.9-72.7%)</td>
<td align="left">86.8% (84.9-88.7%)</td>
<td align="left">88.4% (86.4-90.2%)</td>
<td align="left">72.5% (69.9-75.1%)</td>
<td align="left">86.9% (84.8-89%)</td>
<td align="left">91.4% (89.5-93%)</td>
</tr>
<tr class="even">
<td align="left">UTI</td>
<td align="left">80.3% (77-83.3%)</td>
<td align="left">88.4% (85.7-90.8%)</td>
<td align="left">91% (88.3-93.3%)</td>
<td align="left">86% (82.5-89%)</td>
<td align="left">94.8% (92.5-96.6%)</td>
<td align="left">97.9% (96.3-99%)</td>
</tr>
</tbody>
</table>
@@ -453,15 +458,15 @@ all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></c
<tbody>
<tr class="odd">
<td align="left">Non-UCI</td>
<td align="left">70.4% (68-72.8%)</td>
<td align="left">86.7% (84.6-88.7%)</td>
<td align="left">88.5% (86.5-90.2%)</td>
<td align="left">72.6% (69.9-75.3%)</td>
<td align="left">87% (84.9-89.1%)</td>
<td align="left">91.4% (89.7-92.9%)</td>
</tr>
<tr class="even">
<td align="left">UCI</td>
<td align="left">80.3% (77.2-83.5%)</td>
<td align="left">88.4% (85.5-90.8%)</td>
<td align="left">91% (88.4-93.1%)</td>
<td align="left">86% (82.7-89%)</td>
<td align="left">94.8% (92.7-96.4%)</td>
<td align="left">97.9% (96.5-99%)</td>
</tr>
</tbody>
</table>
@@ -482,6 +487,62 @@ preferred on stewardship grounds.</li>
clinically meaningful difference in coverage.</li>
</ul>
</div>
<div class="section level3">
<h3 id="plotting">Plotting<a class="anchor" aria-label="anchor" href="#plotting"></a>
</h3>
<p>WISCA results can be visualised in several ways. All plot functions
work on the output of <code><a href="../reference/antibiogram.html">wisca()</a></code> (or
<code>antibiogram(..., wisca = TRUE)</code>).</p>
<p>Below we use the <code>wisca_out</code> object that was generated
above.</p>
<div class="section level4">
<h4 id="coverage-with-credible-intervals">Coverage with credible intervals<a class="anchor" aria-label="anchor" href="#coverage-with-credible-intervals"></a>
</h4>
<p>The extended <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> method from the
<code>ggplot2()</code> package produces a point-and-interval plot
showing the coverage estimate and 95% credible interval for each
regimen, grouped by syndromic stratum. This is the most direct way to
compare regimens: overlapping intervals suggest clinical
non-inferiority, non-overlapping intervals indicate a meaningful
difference.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">wisca_out</span><span class="op">)</span></span></code></pre></div>
<p><img src="WISCA_files/figure-html/unnamed-chunk-6-1.png" class="r-plt" alt="" width="720"></p>
</div>
<div class="section level4">
<h4 id="susceptibility-vs--incidence-weight">Susceptibility vs. incidence weight<a class="anchor" aria-label="anchor" href="#susceptibility-vs--incidence-weight"></a>
</h4>
<p><code><a href="../reference/antibiogram.html">wisca_plot()</a></code> produces a scatter plot of the Monte Carlo
simulation draws, showing each pathogen’s susceptibility (x-axis)
against its incidence weight (y-axis) for each regimen. Each dot
represents one of 1,000 simulated draws, so the spread reflects
posterior uncertainty. This plot reveals <em>why</em> a regimen achieves
its coverage: you can see which pathogens dominate the syndrome (high on
the y-axis), how susceptible they are (position on the x-axis), and how
uncertain both estimates are (spread of the cloud). The dashed vertical
lines denote the point estimates, i.e., the coverage percentages. The
ribbon behind the dashed lines denote the credible interval, which is
95% at default.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca_plot</a></span><span class="op">(</span><span class="va">wisca_out</span><span class="op">)</span></span></code></pre></div>
<p><img src="WISCA_files/figure-html/unnamed-chunk-7-1.png" class="r-plt" alt="" width="720"></p>
</div>
<div class="section level4">
<h4 id="posterior-coverage-distributions">Posterior coverage distributions<a class="anchor" aria-label="anchor" href="#posterior-coverage-distributions"></a>
</h4>
<p>Setting <code>wisca_plot_type = "posterior_coverage"</code> shows the
full posterior distribution of coverage for each regimen as a density
curve. This is the most complete representation of what the Bayesian
model produces: each curve shows the relative likelihood of each
coverage value across all 1,000 simulations. Narrow, tall peaks indicate
high certainty; wide, flat curves indicate greater uncertainty. Where
two curves overlap, the regimens cannot be confidently
distinguished.</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca_plot</a></span><span class="op">(</span><span class="va">wisca_out</span>, wisca_plot_type <span class="op">=</span> <span class="st">"posterior_coverage"</span><span class="op">)</span></span></code></pre></div>
<p><img src="WISCA_files/figure-html/unnamed-chunk-8-1.png" class="r-plt" alt="" width="720"></p>
</div>
</div>
</div>
<div class="section level2">
<h2 id="sensible-defaults-which-can-be-customised">Sensible defaults, which can be customised<a class="anchor" aria-label="anchor" href="#sensible-defaults-which-can-be-customised"></a>
@@ -554,7 +615,7 @@ by any clinical variable</li>
intervals that honestly communicate uncertainty</li>
</ul>
<p>It is available in the <code>AMR</code> package via either:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">...</span>, wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@@ -593,7 +654,7 @@ of weighted-incidence syndromic combination antibiograms (WISCA).
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
<div class="pkgdown-footer-right">

88
articles/WISCA.md
View File

@@ -214,6 +214,10 @@ data
# Add a synthetic syndrome column for demonstration
data$syndrome <- ifelse(data$mo %like% "coli", "UTI", "Non-UTI")
# Keep only 10 most common microorganisms
data <- top_n_microorganisms(data, n = 10, property = "species")
#> ℹ Using column mo as input for `col_mo`.
```
### Basic WISCA
@@ -225,9 +229,9 @@ wisca(data,
)
```
| Amoxicillin/clavulanic acid | Ciprofloxacin | Gentamicin |
|:----------------------------|:-------------------|:-------------------|
| 74.2% (72.1-76.1%) | 78.4% (75.6-81.1%) | 72.5% (70.4-74.6%) |
| Amoxicillin/clavulanic acid | Ciprofloxacin | Gentamicin |
|:----------------------------|:-------------------|:-----------------|
| 76.8% (74.7-79.1%) | 81.5% (78.9-84.1%) | 82.9% (81-84.8%) |
### Use combination regimens
@@ -243,7 +247,7 @@ wisca(data,
| Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin |
|:---|:---|:---|
| 74.2% (72.2-76.1%) | 88.8% (87.2-90.4%) | 90.8% (89.4-92.2%) |
| 76.8% (74.6-78.9%) | 89.6% (88-91.1%) | 93.7% (92.5-94.9%) |
### Stratify by syndrome
@@ -252,16 +256,17 @@ stratum. You can pass a column name or any expression:
``` r
wisca(data,
wisca_out <- wisca(data,
antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
syndromic_group = "syndrome"
)
wisca_out
```
| Syndromic Group | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin |
|:---|:---|:---|:---|
| Non-UTI | 70.3% (67.9-72.7%) | 86.8% (84.9-88.7%) | 88.4% (86.4-90.2%) |
| UTI | 80.3% (77-83.3%) | 88.4% (85.7-90.8%) | 91% (88.3-93.3%) |
| Non-UTI | 72.5% (69.9-75.1%) | 86.9% (84.8-89%) | 91.4% (89.5-93%) |
| UTI | 86% (82.5-89%) | 94.8% (92.5-96.6%) | 97.9% (96.3-99%) |
The `AMR` package is available in 28 languages, which can all be used
for the [`wisca()`](https://amr-for-r.org/reference/antibiogram.md)
@@ -278,8 +283,8 @@ wisca(data,
| Grupo sindrómico | Amoxicilina/ácido clavulánico | Amoxicilina/ácido clavulánico + Ciprofloxacina | Amoxicilina/ácido clavulánico + Gentamicina |
|:---|:---|:---|:---|
| Non-UCI | 70.4% (68-72.8%) | 86.7% (84.6-88.7%) | 88.5% (86.5-90.2%) |
| UCI | 80.3% (77.2-83.5%) | 88.4% (85.5-90.8%) | 91% (88.4-93.1%) |
| Non-UCI | 72.6% (69.9-75.3%) | 87% (84.9-89.1%) | 91.4% (89.7-92.9%) |
| UCI | 86% (82.7-89%) | 94.8% (92.7-96.4%) | 97.9% (96.5-99%) |
### Interpreting the output
@@ -293,6 +298,71 @@ Each row shows the estimated empirical coverage for a regimen, with a
- **Non-overlapping credible intervals** indicate a clinically
meaningful difference in coverage.
### Plotting
WISCA results can be visualised in several ways. All plot functions work
on the output of
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md) (or
`antibiogram(..., wisca = TRUE)`).
Below we use the `wisca_out` object that was generated above.
#### Coverage with credible intervals
The extended
[`autoplot()`](https://ggplot2.tidyverse.org/reference/autoplot.html)
method from the `ggplot2()` package produces a point-and-interval plot
showing the coverage estimate and 95% credible interval for each
regimen, grouped by syndromic stratum. This is the most direct way to
compare regimens: overlapping intervals suggest clinical
non-inferiority, non-overlapping intervals indicate a meaningful
difference.
``` r
ggplot2::autoplot(wisca_out)
```
![](WISCA_files/figure-html/unnamed-chunk-6-1.png)
#### Susceptibility vs. incidence weight
[`wisca_plot()`](https://amr-for-r.org/reference/antibiogram.md)
produces a scatter plot of the Monte Carlo simulation draws, showing
each pathogen’s susceptibility (x-axis) against its incidence weight
(y-axis) for each regimen. Each dot represents one of 1,000 simulated
draws, so the spread reflects posterior uncertainty. This plot reveals
*why* a regimen achieves its coverage: you can see which pathogens
dominate the syndrome (high on the y-axis), how susceptible they are
(position on the x-axis), and how uncertain both estimates are (spread
of the cloud). The dashed vertical lines denote the point estimates,
i.e., the coverage percentages. The ribbon behind the dashed lines
denote the credible interval, which is 95% at default.
``` r
wisca_plot(wisca_out)
```
![](WISCA_files/figure-html/unnamed-chunk-7-1.png)
#### Posterior coverage distributions
Setting `wisca_plot_type = "posterior_coverage"` shows the full
posterior distribution of coverage for each regimen as a density curve.
This is the most complete representation of what the Bayesian model
produces: each curve shows the relative likelihood of each coverage
value across all 1,000 simulations. Narrow, tall peaks indicate high
certainty; wide, flat curves indicate greater uncertainty. Where two
curves overlap, the regimens cannot be confidently distinguished.
``` r
wisca_plot(wisca_out, wisca_plot_type = "posterior_coverage")
```
![](WISCA_files/figure-html/unnamed-chunk-8-1.png)
## Sensible defaults, which can be customised
- `simulations = 1000`: number of Monte Carlo draws

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6
articles/datasets.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -1327,7 +1327,7 @@ 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 9 February 2026 12:16:36 UTC. Find more info
<p>It was last updated on 24 June 2026 16:36:47 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set
here</a>.</p>
<p><strong>Example content</strong></p>
@@ -2052,7 +2052,7 @@ inhibitors</td>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
<div class="pkgdown-footer-right">

4
articles/datasets.md
View File

@@ -418,8 +418,8 @@ column names:
This data set is in R available as `example_isolates`, after you load
the `AMR` package.
It was last updated on 9 February 2026 12:16:36 UTC. Find more info
about the contents, (scientific) source, and structure of this [data set
It was last updated on 24 June 2026 16:36:47 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/example_isolates.html).
**Example content**

4
articles/index.html
View File

@@ -7,7 +7,7 @@
<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="">3.0.1.9063</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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">
@@ -72,7 +72,7 @@
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div>
<div class="pkgdown-footer-right">