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404.html
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@@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
LICENSE-text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

78
articles/AMR.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,7 +91,7 @@
website update since they are based on randomly created values and the 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 24 November 2025.</p> generated on 15 December 2025.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2025-11-24</td> <td align="center">2025-12-15</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2025-11-24</td> <td align="center">2025-12-15</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2025-11-24</td> <td align="center">2025-12-15</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>
@@ -405,7 +405,7 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span> <span><span class="co">#&gt; <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>
<span><span class="co"><span style="color: #BB0000;">#&gt; of 2</span></span></span> <span><span class="co"><span style="color: #BB0000;">#&gt; of 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">2,724 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (90.8% of total where a</span></span></span> <span><span class="co">#&gt; <span style="color: #BBBBBB;">=&gt; Found </span><span style="color: #BBBBBB; font-weight: bold;">2,730 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (91.0% of total where a</span></span></span>
<span><span class="co"><span style="color: #BBBBBB;">#&gt; microbial ID was available)</span></span></span></code></pre></div> <span><span class="co"><span style="color: #BBBBBB;">#&gt; microbial ID was available)</span></span></span></code></pre></div>
<p>So only 91% is suitable for resistance analysis! We can now filter on <p>So only 91% is suitable for resistance analysis! We can now filter on
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
@@ -417,11 +417,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 2 724 isolates for analysis. Now our data looks <p>So we end up with 2 730 isolates for analysis. Now our data looks
like:</p> like:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span></span> <code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
@@ -434,7 +434,7 @@ like:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> J3 A 2019-06-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> J3 A 2019-06-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> G6 A 2015-04-27 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> G6 A 2015-04-27 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> P4 A 2011-06-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> P4 A 2011-06-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span></code></pre></div>
<p>Time for the analysis.</p> <p>Time for the analysis.</p>
</div> </div>
</div> </div>
@@ -447,29 +447,29 @@ impression, as it comes with support for the new <code>mo</code> and
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb12"><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">our_data_1st</span><span class="op">)</span></span> <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">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; patient_id hospital date </span></span> <span><span class="co">#&gt; patient_id hospital date </span></span>
<span><span class="co">#&gt; Length:2724 Length:2724 Min. :2011-01-01 </span></span> <span><span class="co">#&gt; Length:2730 Length:2730 Min. :2011-01-01 </span></span>
<span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-04-07 </span></span> <span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-04-06 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-03 </span></span> <span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-04 </span></span>
<span><span class="co">#&gt; Mean :2015-06-09 </span></span> <span><span class="co">#&gt; Mean :2015-06-09 </span></span>
<span><span class="co">#&gt; 3rd Qu.:2017-08-11 </span></span> <span><span class="co">#&gt; 3rd Qu.:2017-08-14 </span></span>
<span><span class="co">#&gt; Max. :2019-12-27 </span></span> <span><span class="co">#&gt; Max. :2019-12-27 </span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span> <span><span class="co">#&gt; bacteria AMX AMC </span></span>
<span><span class="co">#&gt; Class :mo Class:sir Class:sir </span></span> <span><span class="co">#&gt; Class :mo Class:sir Class:sir </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %S :41.6% (n=1133) %S :52.6% (n=1432) </span></span> <span><span class="co">#&gt; &lt;NA&gt; :0 %S :40.1% (n=1071) %S :51.1% (n=1354) </span></span>
<span><span class="co">#&gt; Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span> <span><span class="co">#&gt; Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) </span></span> <span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :17.0% (n=453) %I :12.7% (n=335) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) </span></span> <span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.9% (n=1147) %R :36.2% (n=959) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span> <span><span class="co">#&gt; #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; CIP GEN first </span></span> <span><span class="co">#&gt; CIP GEN first </span></span>
<span><span class="co">#&gt; Class:sir Class:sir Mode:logical </span></span> <span><span class="co">#&gt; Class:sir Class:sir Mode:logical </span></span>
<span><span class="co">#&gt; %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 </span></span> <span><span class="co">#&gt; %S :52.2% (n=1426) %S :60.7% (n=1656) TRUE:2730 </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span> <span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 6.5% (n=176) %I : 3.0% (n=82) </span></span> <span><span class="co">#&gt; %I : 6.5% (n=178) %I : 3.0% (n=83) </span></span>
<span><span class="co">#&gt; %R :41.0% (n=1117) %R :36.0% (n=981) </span></span> <span><span class="co">#&gt; %R :41.2% (n=1126) %R :36.3% (n=991) </span></span>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span> <span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span>
<span></span> <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">our_data_1st</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">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; Rows: 2,724</span></span> <span><span class="co">#&gt; Rows: 2,730</span></span>
<span><span class="co">#&gt; Columns: 9</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"<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; $ 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; $ 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>
@@ -484,7 +484,7 @@ impression, as it comes with support for the new <code>mo</code> and
<span><span class="co"># number of unique values per column:</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> <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>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP </span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP </span></span>
<span><span class="co">#&gt; 260 3 1854 4 3 3 3 </span></span> <span><span class="co">#&gt; 260 3 1854 4 4 4 3 </span></span>
<span><span class="co">#&gt; GEN first </span></span> <span><span class="co">#&gt; GEN first </span></span>
<span><span class="co">#&gt; 3 1</span></span></code></pre></div> <span><span class="co">#&gt; 3 1</span></span></code></pre></div>
<div class="section level3"> <div class="section level3">
@@ -509,9 +509,9 @@ microorganisms:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
<span><span class="co">#&gt; `mo_name(bacteria)` n</span></span> <span><span class="co">#&gt; `mo_name(bacteria)` n</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;int&gt;</span></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;int&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>321</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>326</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 682</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 684</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 402</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 401</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 319</span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 319</span></span></code></pre></div>
</div> </div>
<div class="section level3"> <div class="section level3">
@@ -524,7 +524,7 @@ in:</p>
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 2</span></span></span>
<span><span class="co">#&gt; date GEN </span></span> <span><span class="co">#&gt; date GEN </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2012-11-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2012-11-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
@@ -537,13 +537,13 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2019-06-19 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2019-06-19 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2015-04-27 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2015-04-27 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2011-06-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2011-06-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span>
<span></span> <span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></span></span> <span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 3</span></span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span> <span><span class="co">#&gt; bacteria AMX AMC </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span></span></span>
@@ -556,11 +556,11 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span>
<span></span> <span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,730 × 5</span></span></span>
<span><span class="co">#&gt; bacteria AMX AMC CIP GEN </span></span> <span><span class="co">#&gt; bacteria AMX AMC CIP GEN </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span> <span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FFD787;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
@@ -573,13 +573,13 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span>
<span></span> <span></span>
<span><span class="co"># filtering using AB selectors is also possible:</span></span> <span><span class="co"># filtering using AB selectors is also possible:</span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`aminoglycosides()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 981 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 991 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J5 A 2017-12-25 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> J5 A 2017-12-25 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
@@ -592,13 +592,13 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 971 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 981 more rows</span></span></span>
<span></span> <span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></span></span> <span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 461 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
@@ -611,13 +611,13 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 452 more rows</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 451 more rows</span></span></span>
<span></span> <span></span>
<span><span class="co"># even works in base R (since R 3.0):</span></span> <span><span class="co"># even works in base R (since R 3.0):</span></span>
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span> <span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span> <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`betalactams()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></span></span> <span><span class="co"><span style="color: #0000BB;">#&gt; (amoxicillin/clavulanic acid)</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 461 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span> <span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
@@ -630,7 +630,7 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 452 more rows</span></span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 451 more rows</span></span></span></code></pre></div>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a> <h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a>
@@ -1283,7 +1283,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p> own:</p>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div> <span><span class="co">#&gt; [1] 0.4294272</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p> <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
@@ -1293,8 +1293,8 @@ own:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3 × 2</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3 × 2</span></span></span>
<span><span class="co">#&gt; hospital amoxicillin</span></span> <span><span class="co">#&gt; hospital amoxicillin</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;dbl&gt;</span></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;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A 0.340</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A 0.341</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B 0.551</span></span> <span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B 0.586</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div> <span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div>
</div> </div>
<div class="section level3"> <div class="section level3">

76
articles/AMR.md
View File

@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update **Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 24 November methodology remains unchanged. This page was generated on 15 December
2025. 2025.
## Introduction ## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP | | date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:| |:----------:|:----------:|:----------------:|:---:|:---:|
| 2025-11-24 | abcd | Escherichia coli | S | S | | 2025-12-15 | abcd | Escherichia coli | S | S |
| 2025-11-24 | abcd | Escherichia coli | S | R | | 2025-12-15 | abcd | Escherichia coli | S | R |
| 2025-11-24 | efgh | Escherichia coli | R | S | | 2025-12-15 | efgh | Escherichia coli | R | S |
### Needed R packages ### Needed R packages
@@ -322,7 +322,7 @@ our_data <- our_data %>%
#> ℹ Using column 'patient_id' as input for `col_patient_id`. #> ℹ Using column 'patient_id' as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold #> ℹ Basing inclusion on all antimicrobial results, using a points threshold
#> of 2 #> of 2
#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a #> => Found 2,730 'phenotype-based' first isolates (91.0% of total where a
#> microbial ID was available) #> microbial ID was available)
``` ```
@@ -342,11 +342,11 @@ our_data_1st <- our_data %>%
filter_first_isolate() filter_first_isolate()
``` ```
So we end up with 2 724 isolates for analysis. Now our data looks like: So we end up with 2 730 isolates for analysis. Now our data looks like:
``` r ``` r
our_data_1st our_data_1st
#> # A tibble: 2,724 × 9 #> # A tibble: 2,730 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first #> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl> #> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 1 J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE #> 1 J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE
@@ -359,7 +359,7 @@ our_data_1st
#> 8 J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE #> 8 J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE
#> 9 G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE #> 9 G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE
#> 10 P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE #> 10 P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE
#> # ℹ 2,714 more rows #> # ℹ 2,720 more rows
``` ```
Time for the analysis. Time for the analysis.
@@ -373,29 +373,29 @@ and `sir` classes that we now have in our data set:
``` r ``` r
summary(our_data_1st) summary(our_data_1st)
#> patient_id hospital date #> patient_id hospital date
#> Length:2724 Length:2724 Min. :2011-01-01 #> Length:2730 Length:2730 Min. :2011-01-01
#> Class :character Class :character 1st Qu.:2013-04-07 #> Class :character Class :character 1st Qu.:2013-04-06
#> Mode :character Mode :character Median :2015-06-03 #> Mode :character Mode :character Median :2015-06-04
#> Mean :2015-06-09 #> Mean :2015-06-09
#> 3rd Qu.:2017-08-11 #> 3rd Qu.:2017-08-14
#> Max. :2019-12-27 #> Max. :2019-12-27
#> bacteria AMX AMC #> bacteria AMX AMC
#> Class :mo Class:sir Class:sir #> Class :mo Class:sir Class:sir
#> <NA> :0 %S :41.6% (n=1133) %S :52.6% (n=1432) #> <NA> :0 %S :40.1% (n=1071) %S :51.1% (n=1354)
#> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) #> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) #> #1 :B_ESCHR_COLI %I :17.0% (n=453) %I :12.7% (n=335)
#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) #> #2 :B_STPHY_AURS %R :42.9% (n=1147) %R :36.2% (n=959)
#> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) #> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0)
#> CIP GEN first #> CIP GEN first
#> Class:sir Class:sir Mode:logical #> Class:sir Class:sir Mode:logical
#> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 #> %S :52.2% (n=1426) %S :60.7% (n=1656) TRUE:2730
#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) #> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> %I : 6.5% (n=176) %I : 3.0% (n=82) #> %I : 6.5% (n=178) %I : 3.0% (n=83)
#> %R :41.0% (n=1117) %R :36.0% (n=981) #> %R :41.2% (n=1126) %R :36.3% (n=991)
#> %NI : 0.0% (n=0) %NI : 0.0% (n=0) #> %NI : 0.0% (n=0) %NI : 0.0% (n=0)
glimpse(our_data_1st) glimpse(our_data_1st)
#> Rows: 2,724 #> Rows: 2,730
#> Columns: 9 #> Columns: 9
#> $ patient_id <chr> "J3", "R7", "P3", "P10", "B7", "W3", "M3", "J3", "G6", "P4"… #> $ patient_id <chr> "J3", "R7", "P3", "P10", "B7", "W3", "M3", "J3", "G6", "P4"…
#> $ hospital <chr> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",… #> $ hospital <chr> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…
@@ -410,7 +410,7 @@ glimpse(our_data_1st)
# number of unique values per column: # number of unique values per column:
sapply(our_data_1st, n_distinct) sapply(our_data_1st, n_distinct)
#> patient_id hospital date bacteria AMX AMC CIP #> patient_id hospital date bacteria AMX AMC CIP
#> 260 3 1854 4 3 3 3 #> 260 3 1854 4 4 4 3
#> GEN first #> GEN first
#> 3 1 #> 3 1
``` ```
@@ -437,9 +437,9 @@ our_data_1st %>%
#> # A tibble: 4 × 2 #> # A tibble: 4 × 2
#> `mo_name(bacteria)` n #> `mo_name(bacteria)` n
#> <chr> <int> #> <chr> <int>
#> 1 Escherichia coli 1321 #> 1 Escherichia coli 1326
#> 2 Staphylococcus aureus 682 #> 2 Staphylococcus aureus 684
#> 3 Streptococcus pneumoniae 402 #> 3 Streptococcus pneumoniae 401
#> 4 Klebsiella pneumoniae 319 #> 4 Klebsiella pneumoniae 319
``` ```
@@ -453,7 +453,7 @@ in:
our_data_1st %>% our_data_1st %>%
select(date, aminoglycosides()) select(date, aminoglycosides())
#> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin) #> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
#> # A tibble: 2,724 × 2 #> # A tibble: 2,730 × 2
#> date GEN #> date GEN
#> <date> <sir> #> <date> <sir>
#> 1 2012-11-21 S #> 1 2012-11-21 S
@@ -466,13 +466,13 @@ our_data_1st %>%
#> 8 2019-06-19 S #> 8 2019-06-19 S
#> 9 2015-04-27 S #> 9 2015-04-27 S
#> 10 2011-06-21 S #> 10 2011-06-21 S
#> # ℹ 2,714 more rows #> # ℹ 2,720 more rows
our_data_1st %>% our_data_1st %>%
select(bacteria, betalactams()) select(bacteria, betalactams())
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC' #> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> (amoxicillin/clavulanic acid) #> (amoxicillin/clavulanic acid)
#> # A tibble: 2,724 × 3 #> # A tibble: 2,730 × 3
#> bacteria AMX AMC #> bacteria AMX AMC
#> <mo> <sir> <sir> #> <mo> <sir> <sir>
#> 1 B_ESCHR_COLI R I #> 1 B_ESCHR_COLI R I
@@ -485,11 +485,11 @@ our_data_1st %>%
#> 8 B_ESCHR_COLI S S #> 8 B_ESCHR_COLI S S
#> 9 B_STPHY_AURS S S #> 9 B_STPHY_AURS S S
#> 10 B_ESCHR_COLI S S #> 10 B_ESCHR_COLI S S
#> # ℹ 2,714 more rows #> # ℹ 2,720 more rows
our_data_1st %>% our_data_1st %>%
select(bacteria, where(is.sir)) select(bacteria, where(is.sir))
#> # A tibble: 2,724 × 5 #> # A tibble: 2,730 × 5
#> bacteria AMX AMC CIP GEN #> bacteria AMX AMC CIP GEN
#> <mo> <sir> <sir> <sir> <sir> #> <mo> <sir> <sir> <sir> <sir>
#> 1 B_ESCHR_COLI R I S S #> 1 B_ESCHR_COLI R I S S
@@ -502,13 +502,13 @@ our_data_1st %>%
#> 8 B_ESCHR_COLI S S S S #> 8 B_ESCHR_COLI S S S S
#> 9 B_STPHY_AURS S S S S #> 9 B_STPHY_AURS S S S S
#> 10 B_ESCHR_COLI S S S S #> 10 B_ESCHR_COLI S S S S
#> # ℹ 2,714 more rows #> # ℹ 2,720 more rows
# filtering using AB selectors is also possible: # filtering using AB selectors is also possible:
our_data_1st %>% our_data_1st %>%
filter(any(aminoglycosides() == "R")) filter(any(aminoglycosides() == "R"))
#> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin) #> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
#> # A tibble: 981 × 9 #> # A tibble: 991 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first #> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl> #> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 1 J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE #> 1 J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE
@@ -521,13 +521,13 @@ our_data_1st %>%
#> 8 P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE #> 8 P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE
#> 9 Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE #> 9 Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE
#> 10 K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE #> 10 K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE
#> # ℹ 971 more rows #> # ℹ 981 more rows
our_data_1st %>% our_data_1st %>%
filter(all(betalactams() == "R")) filter(all(betalactams() == "R"))
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC' #> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> (amoxicillin/clavulanic acid) #> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9 #> # A tibble: 461 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first #> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl> #> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE #> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE
@@ -540,13 +540,13 @@ our_data_1st %>%
#> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE #> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE
#> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE
#> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE #> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE
#> # ℹ 452 more rows #> # ℹ 451 more rows
# even works in base R (since R 3.0): # even works in base R (since R 3.0):
our_data_1st[all(betalactams() == "R"), ] our_data_1st[all(betalactams() == "R"), ]
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC' #> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> (amoxicillin/clavulanic acid) #> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9 #> # A tibble: 461 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first #> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl> #> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE #> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE
@@ -559,7 +559,7 @@ our_data_1st[all(betalactams() == "R"), ]
#> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE #> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE
#> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE
#> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE #> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE
#> # ℹ 452 more rows #> # ℹ 451 more rows
``` ```
### Generate antibiograms ### Generate antibiograms
@@ -843,7 +843,7 @@ These functions can be used on their own:
``` r ``` r
our_data_1st %>% resistance(AMX) our_data_1st %>% resistance(AMX)
#> [1] 0.4203377 #> [1] 0.4294272
``` ```
Or can be used in conjunction with Or can be used in conjunction with
@@ -858,8 +858,8 @@ our_data_1st %>%
#> # A tibble: 3 × 2 #> # A tibble: 3 × 2
#> hospital amoxicillin #> hospital amoxicillin
#> <chr> <dbl> #> <chr> <dbl>
#> 1 A 0.340 #> 1 A 0.341
#> 2 B 0.551 #> 2 B 0.586
#> 3 C 0.370 #> 3 C 0.370
``` ```

2
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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4
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">24 November 2025</h4> <h4 data-toc-skip class="date">15 December 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div> <div class="d-none name"><code>datasets.Rmd</code></div>

2
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

15
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,11 +49,20 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9003" id="amr-3019003">AMR 3.0.1.9003<a class="anchor" aria-label="anchor" href="#amr-3019003"></a></h2> <h2 class="pkg-version" data-toc-text="3.0.1.9004" id="amr-3019004">AMR 3.0.1.9004<a class="anchor" aria-label="anchor" href="#amr-3019004"></a></h2>
<div class="section level4"> <div class="section level4">
<h4 id="changed-3-0-1-9003">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9003"></a></h4> <h4 id="changed-3-0-1-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9004"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li> <ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li> <li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>i</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Updated handling of capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>
</li>
<li>Interpretation of capped MIC values now consistently returns <code>"NI"</code> (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode</li>
<li>This results in more reliable behaviour compared to previous versions for capped MIC values</li>
<li>Removed the <code>"inverse"</code> option, which has now become redundant</li>
</ul></li>
</ul></div> </ul></div>
</div> </div>
<div class="section level2"> <div class="section level2">

21
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@@ -1,6 +1,6 @@
# Changelog # Changelog
## AMR 3.0.1.9003 ## AMR 3.0.1.9004
#### Changed #### Changed
@@ -9,6 +9,25 @@
when no antimicrobials are set when no antimicrobials are set
- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the - Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the
`antimicrobials` data set `antimicrobials` data set
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
where for numeric input the arguments `S`, `i`, and `R` would not be
considered ([\#244](https://github.com/msberends/AMR/issues/244))
- Added explaining message to
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when
interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R)
([\#244](https://github.com/msberends/AMR/issues/244))
- Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the
argument `capped_mic_handling`:
([\#243](https://github.com/msberends/AMR/issues/243))
- Introduced four clearly defined options: `"none"`, `"conservative"`
(default), `"standard"`, and `"lenient"`
- Interpretation of capped MIC values now consistently returns `"NI"`
(non-interpretable) when the true MIC could be at either side of a
breakpoint, depending on the selected handling mode
- This results in more reliable behaviour compared to previous
versions for capped MIC values
- Removed the `"inverse"` option, which has now become redundant
## AMR 3.0.1 ## AMR 3.0.1

2
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2025-11-24T10:38Z last_built: 2025-12-15T12:28Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -60,7 +60,7 @@
<ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-22) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li> <ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-22) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li>
<li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li> <li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li>
<li><p><code>AMR_capped_mic_handling</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate how capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) should be interpreted. Must be one of <code>"standard"</code>, <code>"strict"</code>, <code>"relaxed"</code>, or <code>"inverse"</code> - the default is <code>"standard"</code>.</p></li> <li><p><code>AMR_capped_mic_handling</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate how capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) should be interpreted. Must be one of <code>"none"</code>, <code>"conservative"</code>, <code>"standard"</code>, or <code>"lenient"</code> - the default is <code>"conservative"</code>.</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li> <li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li> <li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
<li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li> <li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>

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reference/AMR-options.md
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@@ -21,8 +21,8 @@ This is an overview of all the package-specific
A [character](https://rdrr.io/r/base/character.html) to use in A [character](https://rdrr.io/r/base/character.html) to use in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted.
Must be one of `"standard"`, `"strict"`, `"relaxed"`, or `"inverse"` - Must be one of `"none"`, `"conservative"`, `"standard"`, or
the default is `"standard"`. `"lenient"` - the default is `"conservative"`.
- `AMR_cleaning_regex` - `AMR_cleaning_regex`
A [regular expression](https://rdrr.io/r/base/regex.html) A [regular expression](https://rdrr.io/r/base/regex.html)

2
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/WHONET.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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reference/ab_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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22
reference/age.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.73973 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.79726 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.33151 46</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.38904 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.22740 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.28493 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.30959 13</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.36712 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.01370 67</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.07123 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.65479 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.71233 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.42192 3</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.47945 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.18904 36</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.24658 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.52603 47</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.58356 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.02740 47</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.08493 47</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
View File

@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df df
#> birth_date age age_exact age_at_y2k #> birth_date age age_exact age_at_y2k
#> 1 1980-02-27 45 45.73973 19 #> 1 1980-02-27 45 45.79726 19
#> 2 1953-07-26 72 72.33151 46 #> 2 1953-07-26 72 72.38904 46
#> 3 1949-09-02 76 76.22740 50 #> 3 1949-09-02 76 76.28493 50
#> 4 1986-08-03 39 39.30959 13 #> 4 1986-08-03 39 39.36712 13
#> 5 1932-11-19 93 93.01370 67 #> 5 1932-11-19 93 93.07123 67
#> 6 1949-03-30 76 76.65479 50 #> 6 1949-03-30 76 76.71233 50
#> 7 1996-06-23 29 29.42192 3 #> 7 1996-06-23 29 29.47945 3
#> 8 1963-09-16 62 62.18904 36 #> 8 1963-09-16 62 62.24658 36
#> 9 1952-05-16 73 73.52603 47 #> 9 1952-05-16 73 73.58356 47
#> 10 1952-11-14 73 73.02740 47 #> 10 1952-11-14 73 73.08493 47
``` ```

2
reference/age_groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.ab.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.av.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/as.disk.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/as.mic.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/as.mo.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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51
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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@@ -67,8 +67,9 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span><span class="fu">is_sir_eligible</span><span class="op">(</span><span class="va">x</span>, threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span> <span><span class="fu">is_sir_eligible</span><span class="op">(</span><span class="va">x</span>, threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="co"># Default S3 method</span></span> <span><span class="co"># Default S3 method</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>, I <span class="op">=</span> <span class="st">"^(I)+$"</span>, R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span> <span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, S <span class="op">=</span> <span class="st">"^(S|U|1)+$"</span>, I <span class="op">=</span> <span class="st">"^(I|2)+$"</span>,</span>
<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>, SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> <span> R <span class="op">=</span> <span class="st">"^(R|3)+$"</span>, NI <span class="op">=</span> <span class="st">"^(N|NI|V|4)+$"</span>, SDD <span class="op">=</span> <span class="st">"^(SDD|D|H|5)+$"</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="co"># S3 method for class 'mic'</span></span> <span><span class="co"># S3 method for class 'mic'</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> <span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
@@ -128,7 +129,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a> such as <code>as.sir(df, penicillins())</code>.</p> <dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a>, e.g. <code>as.sir(df, penicillins())</code>.</p>
<p>Otherwise: arguments passed on to methods.</p></dd> <p>Otherwise: arguments passed on to methods.</p></dd>
@@ -162,15 +163,15 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dt id="arg-capped-mic-handling">capped_mic_handling<a class="anchor" aria-label="anchor" href="#arg-capped-mic-handling"></a></dt> <dt id="arg-capped-mic-handling">capped_mic_handling<a class="anchor" aria-label="anchor" href="#arg-capped-mic-handling"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> string that controls how MIC values with a cap (i.e., starting with <code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, or <code>&gt;=</code>) are interpreted. Supports the following options:</p> <dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> string that controls how MIC values with a cap (i.e., starting with <code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, or <code>&gt;=</code>) are interpreted. Supports the following options:</p>
<p><code>"none"</code></p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> are treated as-is.</p></li> <p><code>"none"</code></p><ul><li><p><code>&lt;=</code>, <code>&lt;</code>, <code>&gt;</code> and <code>&gt;=</code> are ignored.</p></li>
<li><p><code>&lt;</code> and <code>&gt;</code> are treated as-is.</p></li> </ul><p><code>"conservative"</code> (default)</p><ul><li><p><code>&lt;=</code>, <code>&lt;</code>, <code>&gt;</code> and <code>&gt;=</code> return <code>"NI"</code> (non-interpretable) if the <em>true</em> MIC could be at either side of the breakpoint.</p></li>
</ul><p><code>"conservative"</code></p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> return <code>"NI"</code> (non-interpretable) if the MIC is within the breakpoint guideline range.</p></li> <li><p>This is the only mode that preserves uncertainty for ECOFFs.</p></li>
<li><p><code>&lt;</code> always returns <code>"S"</code>, and <code>&gt;</code> always returns <code>"R"</code>.</p></li> </ul><p><code>"standard"</code></p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> return <code>"NI"</code> (non-interpretable) if the <em>true</em> MIC could be at either side of the breakpoint.</p></li>
</ul><p><code>"standard"</code> (default)</p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> return <code>"NI"</code> (non-interpretable) if the MIC is within the breakpoint guideline range.</p></li> <li><p><code>&lt;</code> always returns <code>"S"</code>, regardless of the breakpoint.</p></li>
<li><p><code>&lt;</code> and <code>&gt;</code> are treated as-is.</p></li> <li><p><code>&gt;</code> always returns <code>"R"</code>, regardless of the breakpoint.</p></li>
</ul><p><code>"inverse"</code></p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> are treated as-is.</p></li> </ul><p><code>"lenient"</code></p><ul><li><p><code>&lt;=</code> and <code>&lt;</code> always return <code>"S"</code>, regardless of the breakpoint.</p></li>
<li><p><code>&lt;</code> always returns <code>"S"</code>, and <code>&gt;</code> always returns <code>"R"</code>.</p></li> <li><p><code>&gt;=</code> and <code>&gt;</code> always return <code>"R"</code>, regardless of the breakpoint.</p></li>
</ul><p>The default <code>"standard"</code> setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option <code><a href="AMR-options.html">AMR_capped_mic_handling</a></code>.</p></dd> </ul><p>The default <code>"conservative"</code> setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option <code><a href="AMR-options.html">AMR_capped_mic_handling</a></code>.</p></dd>
<dt id="arg-add-intrinsic-resistance">add_intrinsic_resistance<a class="anchor" aria-label="anchor" href="#arg-add-intrinsic-resistance"></a></dt> <dt id="arg-add-intrinsic-resistance">add_intrinsic_resistance<a class="anchor" aria-label="anchor" href="#arg-add-intrinsic-resistance"></a></dt>
@@ -251,7 +252,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span></span> <span></span>
<span><span class="co"># fast processing with parallel computing:</span></span> <span><span class="co"># fast processing with parallel computing:</span></span>
<span><span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">your_data</span>, <span class="va">...</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div></li> <span><span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">your_data</span>, <span class="va">...</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>capped_mic_handling = "conservative"</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>capped_mic_handling = "standard"</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li> <li><p>Operators like "&lt;=" will be considered according to the <code>capped_mic_handling</code> setting. At default, an MIC value of e.g. "&gt;2" will return "NI" (non-interpretable) if the breakpoint is 4-8; the <em>true</em> MIC could be at either side of the breakpoint. This is to prevent that capped values from raw laboratory data would not be treated conservatively.</p></li>
<li><p><strong>Note:</strong> When using CLSI as the guideline, MIC values must be log2-based doubling dilutions. Values not in this format, will be automatically rounded up to the nearest log2 level as CLSI instructs, and a warning will be thrown.</p></li> <li><p><strong>Note:</strong> When using CLSI as the guideline, MIC values must be log2-based doubling dilutions. Values not in this format, will be automatically rounded up to the nearest log2 level as CLSI instructs, and a warning will be thrown.</p></li>
</ul></li> </ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Example to apply using <code>dplyr</code>:</p> <li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Example to apply using <code>dplyr</code>:</p>
@@ -415,10 +416,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-12-15 <span style="color: #949494;">12:29:02</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-12-15 <span style="color: #949494;">12:29:02</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-12-15 <span style="color: #949494;">12:29:02</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-11-24 <span style="color: #949494;">10:38:56</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-12-15 <span style="color: #949494;">12:29:03</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -624,8 +625,20 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span> <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 1 result in index '20' truncated (100%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "&lt;= 0.002; S"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #444444;">`as.sir()`</span><span style="color: #0000BB;">: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I R</span>
<span class="r-in"><span><span class="fu">as.sir</span><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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, S <span class="op">=</span> <span class="fl">3</span>, I <span class="op">=</span> <span class="fl">2</span>, R <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #444444;">`as.sir()`</span><span style="color: #0000BB;">: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">sir_data</span> <span class="op">&lt;-</span> <span class="fu">as.sir</span><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="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">sir_data</span> <span class="op">&lt;-</span> <span class="fu">as.sir</span><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="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">is.sir</span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">is.sir</span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>

73
reference/as.sir.md
View File

@@ -24,8 +24,9 @@ is.sir(x)
is_sir_eligible(x, threshold = 0.05) is_sir_eligible(x, threshold = 0.05)
# Default S3 method # Default S3 method
as.sir(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$", as.sir(x, S = "^(S|U|1)+$", I = "^(I|2)+$",
NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = interactive(), ...) R = "^(R|3)+$", NI = "^(N|NI|V|4)+$", SDD = "^(SDD|D|H|5)+$",
info = interactive(), ...)
# S3 method for class 'mic' # S3 method for class 'mic'
as.sir(x, mo = NULL, ab = deparse(substitute(x)), as.sir(x, mo = NULL, ab = deparse(substitute(x)),
@@ -115,8 +116,8 @@ disk diffusion diameters:
language](https://tidyselect.r-lib.org/reference/starts_with.html) language](https://tidyselect.r-lib.org/reference/starts_with.html)
such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and
can thus also be [antimicrobial can thus also be [antimicrobial
selectors](https://amr-for-r.org/reference/antimicrobial_selectors.md) selectors](https://amr-for-r.org/reference/antimicrobial_selectors.md),
such as `as.sir(df, penicillins())`. e.g. `as.sir(df, penicillins())`.
Otherwise: arguments passed on to methods. Otherwise: arguments passed on to methods.
@@ -187,31 +188,31 @@ disk diffusion diameters:
`"none"` `"none"`
- `<=` and `>=` are treated as-is. - `<=`, `<`, `>` and `>=` are ignored.
- `<` and `>` are treated as-is. `"conservative"` (default)
`"conservative"` - `<=`, `<`, `>` and `>=` return `"NI"` (non-interpretable) if the
*true* MIC could be at either side of the breakpoint.
- `<=` and `>=` return `"NI"` (non-interpretable) if the MIC is within - This is the only mode that preserves uncertainty for ECOFFs.
the breakpoint guideline range.
- `<` always returns `"S"`, and `>` always returns `"R"`. `"standard"`
`"standard"` (default) - `<=` and `>=` return `"NI"` (non-interpretable) if the *true* MIC
could be at either side of the breakpoint.
- `<=` and `>=` return `"NI"` (non-interpretable) if the MIC is within - `<` always returns `"S"`, regardless of the breakpoint.
the breakpoint guideline range.
- `<` and `>` are treated as-is. - `>` always returns `"R"`, regardless of the breakpoint.
`"inverse"` `"lenient"`
- `<=` and `>=` are treated as-is. - `<=` and `<` always return `"S"`, regardless of the breakpoint.
- `<` always returns `"S"`, and `>` always returns `"R"`. - `>=` and `>` always return `"R"`, regardless of the breakpoint.
The default `"standard"` setting ensures cautious handling of The default `"conservative"` setting ensures cautious handling of
uncertain values while preserving interpretability. This option can uncertain values while preserving interpretability. This option can
also be set with the package option also be set with the package option
[`AMR_capped_mic_handling`](https://amr-for-r.org/reference/AMR-options.md). [`AMR_capped_mic_handling`](https://amr-for-r.org/reference/AMR-options.md).
@@ -397,14 +398,12 @@ The `as.sir()` function can work in four ways:
# fast processing with parallel computing: # fast processing with parallel computing:
as.sir(your_data, ..., parallel = TRUE) as.sir(your_data, ..., parallel = TRUE)
- Operators like "\<=" will be stripped before interpretation. When - Operators like "\<=" will be considered according to the
using `capped_mic_handling = "conservative"`, an MIC value of e.g. `capped_mic_handling` setting. At default, an MIC value of e.g.
"\>2" will always return "R", even if the breakpoint according to "\>2" will return "NI" (non-interpretable) if the breakpoint is
the chosen guideline is "\>=4". This is to prevent that capped 4-8; the *true* MIC could be at either side of the breakpoint.
values from raw laboratory data would not be treated This is to prevent that capped values from raw laboratory data
conservatively. The default behaviour would not be treated conservatively.
(`capped_mic_handling = "standard"`) considers "\>2" to be lower
than "\>=4" and might in this case return "S" or "I".
- **Note:** When using CLSI as the guideline, MIC values must be - **Note:** When using CLSI as the guideline, MIC values must be
log2-based doubling dilutions. Values not in this format, will be log2-based doubling dilutions. Values not in this format, will be
@@ -649,10 +648,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2025-11-24 10:38:56 1 MIC amoxicillin Escherich… human 8 #> 1 2025-12-15 12:29:02 1 MIC amoxicillin Escherich… human 8
#> 2 2025-11-24 10:38:56 1 MIC cipro Escherich… human 0.256 #> 2 2025-12-15 12:29:02 1 MIC cipro Escherich… human 0.256
#> 3 2025-11-24 10:38:56 1 DISK tobra Escherich… human 16 #> 3 2025-12-15 12:29:02 1 DISK tobra Escherich… human 16
#> 4 2025-11-24 10:38:56 1 DISK genta Escherich… human 18 #> 4 2025-12-15 12:29:03 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>
@@ -858,8 +857,20 @@ as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Class 'sir' #> Class 'sir'
#> [1] S SDD I R NI <NA> <NA> <NA> #> [1] S SDD I R NI <NA> <NA> <NA>
as.sir("<= 0.002; S") # will return "S" as.sir("<= 0.002; S") # will return "S"
#> Warning: in `as.sir()`: 1 result in index '20' truncated (100%) that were invalid
#> antimicrobial interpretations: "<= 0.002; S"
#> Class 'sir' #> Class 'sir'
#> [1] S #> [1] <NA>
as.sir(c(1, 2, 3))
#> ℹ in `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"
#> Class 'sir'
#> [1] S I R
as.sir(c(1, 2, 3), S = 3, I = 2, R = 1)
#> ℹ in `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"
#> Class 'sir'
#> [1] R I S
sir_data <- as.sir(c(rep("S", 474), rep("I", 36), rep("R", 370))) sir_data <- as.sir(c(rep("S", 474), rep("I", 36), rep("R", 370)))
is.sir(sir_data) is.sir(sir_data)
#> [1] TRUE #> [1] TRUE

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_property.html
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@@ -7,7 +7,7 @@
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2
reference/availability.html
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@@ -7,7 +7,7 @@
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2
reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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2
reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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2
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
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2
reference/dosage.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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reference/eucast_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/example_isolates.html
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@@ -7,7 +7,7 @@
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2
reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
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2
reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
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reference/first_isolate.html
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@@ -9,7 +9,7 @@
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2
reference/g.test.html
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@@ -7,7 +7,7 @@
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reference/get_episode.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/index.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/intrinsic_resistant.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/italicise_taxonomy.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/join.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/kurtosis.html
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@@ -7,7 +7,7 @@
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2
reference/like.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/mdro.html
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@@ -7,7 +7,7 @@
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2
reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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2
reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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reference/mo_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
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reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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@@ -7,7 +7,7 @@
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reference/translate.html
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@@ -7,7 +7,7 @@
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search.json
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