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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>
<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">

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

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>
<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">
@@ -91,7 +91,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 24 November 2025.</p>
generated on 15 December 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<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">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<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">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<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">Escherichia coli</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: #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">#&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>
<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
@@ -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">
<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>
<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>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<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; <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>
@@ -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;"> 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: #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>
</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">
<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; Length:2724 Length:2724 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; Mode :character Mode :character Median :2015-06-03 </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.:2013-04-06 </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; 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; bacteria AMX AMC </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; #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) </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; #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 :42.9% (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; CIP GEN first </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; %I : 6.5% (n=176) %I : 3.0% (n=82) </span></span>
<span><span class="co">#&gt; %R :41.0% (n=1117) %R :36.0% (n=981) </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 :41.2% (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>
<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; $ 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>
@@ -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="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; 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; 3 1</span></span></code></pre></div>
<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; `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: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>321</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;">3</span> Streptococcus pneumoniae 402</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 684</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>
</div>
<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>
<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: #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; <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>
@@ -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;"> 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: #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 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="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">#&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; <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>
@@ -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;"> 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: #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 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="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; <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>
@@ -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;"> 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: #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 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="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: #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; <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>
@@ -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;"> 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: #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 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="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">#&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; <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>
@@ -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;"> 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: #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 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="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">#&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; <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>
@@ -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;"> 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: #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 class="section level3">
<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>
<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>
<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
<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">
@@ -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; 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: #BCBCBC;">1</span> A 0.340</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;">1</span> A 0.341</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>
</div>
<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
since they are based on randomly created values and the page was written
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.
## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2025-11-24 | abcd | Escherichia coli | S | S |
| 2025-11-24 | abcd | Escherichia coli | S | R |
| 2025-11-24 | efgh | Escherichia coli | R | S |
| 2025-12-15 | abcd | Escherichia coli | S | S |
| 2025-12-15 | abcd | Escherichia coli | S | R |
| 2025-12-15 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -322,7 +322,7 @@ our_data <- our_data %>%
#> ℹ Using column 'patient_id' as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
#> 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)
```
@@ -342,11 +342,11 @@ our_data_1st <- our_data %>%
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
our_data_1st
#> # A tibble: 2,724 × 9
#> # A tibble: 2,730 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 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
#> 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
#> # ℹ 2,714 more rows
#> # ℹ 2,720 more rows
```
Time for the analysis.
@@ -373,29 +373,29 @@ and `sir` classes that we now have in our data set:
``` r
summary(our_data_1st)
#> patient_id hospital date
#> Length:2724 Length:2724 Min. :2011-01-01
#> Class :character Class :character 1st Qu.:2013-04-07
#> Mode :character Mode :character Median :2015-06-03
#> Length:2730 Length:2730 Min. :2011-01-01
#> Class :character Class :character 1st Qu.:2013-04-06
#> Mode :character Mode :character Median :2015-06-04
#> Mean :2015-06-09
#> 3rd Qu.:2017-08-11
#> 3rd Qu.:2017-08-14
#> Max. :2019-12-27
#> bacteria AMX AMC
#> 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)
#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333)
#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959)
#> #1 :B_ESCHR_COLI %I :17.0% (n=453) %I :12.7% (n=335)
#> #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)
#> CIP GEN first
#> 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)
#> %I : 6.5% (n=176) %I : 3.0% (n=82)
#> %R :41.0% (n=1117) %R :36.0% (n=981)
#> %I : 6.5% (n=178) %I : 3.0% (n=83)
#> %R :41.2% (n=1126) %R :36.3% (n=991)
#> %NI : 0.0% (n=0) %NI : 0.0% (n=0)
glimpse(our_data_1st)
#> Rows: 2,724
#> Rows: 2,730
#> Columns: 9
#> $ 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",…
@@ -410,7 +410,7 @@ glimpse(our_data_1st)
# number of unique values per column:
sapply(our_data_1st, n_distinct)
#> patient_id hospital date bacteria AMX AMC CIP
#> 260 3 1854 4 3 3 3
#> 260 3 1854 4 4 4 3
#> GEN first
#> 3 1
```
@@ -437,9 +437,9 @@ our_data_1st %>%
#> # A tibble: 4 × 2
#> `mo_name(bacteria)` n
#> <chr> <int>
#> 1 Escherichia coli 1321
#> 2 Staphylococcus aureus 682
#> 3 Streptococcus pneumoniae 402
#> 1 Escherichia coli 1326
#> 2 Staphylococcus aureus 684
#> 3 Streptococcus pneumoniae 401
#> 4 Klebsiella pneumoniae 319
```
@@ -453,7 +453,7 @@ in:
our_data_1st %>%
select(date, aminoglycosides())
#> ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)
#> # A tibble: 2,724 × 2
#> # A tibble: 2,730 × 2
#> date GEN
#> <date> <sir>
#> 1 2012-11-21 S
@@ -466,13 +466,13 @@ our_data_1st %>%
#> 8 2019-06-19 S
#> 9 2015-04-27 S
#> 10 2011-06-21 S
#> # ℹ 2,714 more rows
#> # ℹ 2,720 more rows
our_data_1st %>%
select(bacteria, betalactams())
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> (amoxicillin/clavulanic acid)
#> # A tibble: 2,724 × 3
#> # A tibble: 2,730 × 3
#> bacteria AMX AMC
#> <mo> <sir> <sir>
#> 1 B_ESCHR_COLI R I
@@ -485,11 +485,11 @@ our_data_1st %>%
#> 8 B_ESCHR_COLI S S
#> 9 B_STPHY_AURS S S
#> 10 B_ESCHR_COLI S S
#> # ℹ 2,714 more rows
#> # ℹ 2,720 more rows
our_data_1st %>%
select(bacteria, where(is.sir))
#> # A tibble: 2,724 × 5
#> # A tibble: 2,730 × 5
#> bacteria AMX AMC CIP GEN
#> <mo> <sir> <sir> <sir> <sir>
#> 1 B_ESCHR_COLI R I S S
@@ -502,13 +502,13 @@ our_data_1st %>%
#> 8 B_ESCHR_COLI S S S S
#> 9 B_STPHY_AURS 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:
our_data_1st %>%
filter(any(aminoglycosides() == "R"))
#> 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
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 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
#> 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
#> # ℹ 971 more rows
#> # ℹ 981 more rows
our_data_1st %>%
filter(all(betalactams() == "R"))
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9
#> # A tibble: 461 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 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
#> 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
#> # ℹ 452 more rows
#> # ℹ 451 more rows
# even works in base R (since R 3.0):
our_data_1st[all(betalactams() == "R"), ]
#> ℹ For `betalactams()` using columns 'AMX' (amoxicillin) and 'AMC'
#> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9
#> # A tibble: 461 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
#> <chr> <chr> <date> <mo> <sir> <sir> <sir> <sir> <lgl>
#> 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
#> 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
#> # ℹ 452 more rows
#> # ℹ 451 more rows
```
### Generate antibiograms
@@ -843,7 +843,7 @@ These functions can be used on their own:
``` r
our_data_1st %>% resistance(AMX)
#> [1] 0.4203377
#> [1] 0.4294272
```
Or can be used in conjunction with
@@ -858,8 +858,8 @@ our_data_1st %>%
#> # A tibble: 3 × 2
#> hospital amoxicillin
#> <chr> <dbl>
#> 1 A 0.340
#> 2 B 0.551
#> 1 A 0.341
#> 2 B 0.586
#> 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>
<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">

2
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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
articles/PCA.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

2
articles/WHONET.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

2
articles/WISCA.html
View File

@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

4
articles/datasets.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">
@@ -80,7 +80,7 @@
<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>
<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>
<div class="d-none name"><code>datasets.Rmd</code></div>

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

2
authors.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

2
index.html
View File

@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

15
news/index.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">
@@ -49,11 +49,20 @@
</div>
<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">
<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>
<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>
</div>
<div class="section level2">

21
news/index.md
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@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9003
## AMR 3.0.1.9004
#### Changed
@@ -9,6 +9,25 @@
when no antimicrobials are set
- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the
`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

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

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

4
reference/AMR-options.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">
@@ -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>
<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_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>

4
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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
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted.
Must be one of `"standard"`, `"strict"`, `"relaxed"`, or `"inverse"` -
the default is `"standard"`.
Must be one of `"none"`, `"conservative"`, `"standard"`, or
`"lenient"` - the default is `"conservative"`.
- `AMR_cleaning_regex`
A [regular expression](https://rdrr.io/r/base/regex.html)

2
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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>
<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">

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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<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 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> 1 1980-02-27 45 45.73973 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> 3 1949-09-02 76 76.22740 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> 5 1932-11-19 93 93.01370 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> 7 1996-06-23 29 29.42192 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> 9 1952-05-16 73 73.52603 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> 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 72.38904 46</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 39.36712 13</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 76.71233 50</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 62.24658 36</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 73.08493 47</span>
</code></pre></div>
</div>
</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
#> birth_date age age_exact age_at_y2k
#> 1 1980-02-27 45 45.73973 19
#> 2 1953-07-26 72 72.33151 46
#> 3 1949-09-02 76 76.22740 50
#> 4 1986-08-03 39 39.30959 13
#> 5 1932-11-19 93 93.01370 67
#> 6 1949-03-30 76 76.65479 50
#> 7 1996-06-23 29 29.42192 3
#> 8 1963-09-16 62 62.18904 36
#> 9 1952-05-16 73 73.52603 47
#> 10 1952-11-14 73 73.02740 47
#> 1 1980-02-27 45 45.79726 19
#> 2 1953-07-26 72 72.38904 46
#> 3 1949-09-02 76 76.28493 50
#> 4 1986-08-03 39 39.36712 13
#> 5 1932-11-19 93 93.07123 67
#> 6 1949-03-30 76 76.71233 50
#> 7 1996-06-23 29 29.47945 3
#> 8 1963-09-16 62 62.24658 36
#> 9 1952-05-16 73 73.58356 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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/antibiogram.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/antimicrobial_selectors.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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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>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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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>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/as.mo.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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">

51
reference/as.sir.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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>
<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)+$"</span>,</span>
<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>, SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, S <span class="op">=</span> <span class="st">"^(S|U|1)+$"</span>, I <span class="op">=</span> <span class="st">"^(I|2)+$"</span>,</span>
<span> R <span class="op">=</span> <span class="st">"^(R|3)+$"</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 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>
@@ -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>
<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>
@@ -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>
<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>
<li><p><code>&lt;</code> and <code>&gt;</code> are treated as-is.</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><code>&lt;</code> always returns <code>"S"</code>, and <code>&gt;</code> always returns <code>"R"</code>.</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> and <code>&gt;</code> are treated as-is.</p></li>
</ul><p><code>"inverse"</code></p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> are treated as-is.</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>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>
<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>
</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>
<li><p>This is the only mode that preserves uncertainty for ECOFFs.</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>
<li><p><code>&lt;</code> always returns <code>"S"</code>, regardless of the breakpoint.</p></li>
<li><p><code>&gt;</code> always returns <code>"R"</code>, regardless of the breakpoint.</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>&gt;=</code> and <code>&gt;</code> always return <code>"R"</code>, regardless of the breakpoint.</p></li>
</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>
@@ -251,7 +252,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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>
<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>
</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>
@@ -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> 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: #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;">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;">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;">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;">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> 2025-12-15 <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> 2025-12-15 <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> 2025-12-15 <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;"># 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>
@@ -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> [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-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> [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="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>

73
reference/as.sir.md
View File

@@ -24,8 +24,9 @@ is.sir(x)
is_sir_eligible(x, threshold = 0.05)
# Default S3 method
as.sir(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$",
NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = interactive(), ...)
as.sir(x, S = "^(S|U|1)+$", I = "^(I|2)+$",
R = "^(R|3)+$", NI = "^(N|NI|V|4)+$", SDD = "^(SDD|D|H|5)+$",
info = interactive(), ...)
# S3 method for class 'mic'
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)
such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and
can thus also be [antimicrobial
selectors](https://amr-for-r.org/reference/antimicrobial_selectors.md)
such as `as.sir(df, penicillins())`.
selectors](https://amr-for-r.org/reference/antimicrobial_selectors.md),
e.g. `as.sir(df, penicillins())`.
Otherwise: arguments passed on to methods.
@@ -187,31 +188,31 @@ disk diffusion diameters:
`"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
the breakpoint guideline range.
- This is the only mode that preserves uncertainty for ECOFFs.
- `<` 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
the breakpoint guideline range.
- `<` always returns `"S"`, regardless of the breakpoint.
- `<` 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
also be set with the package option
[`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:
as.sir(your_data, ..., parallel = TRUE)
- Operators like "\<=" will be stripped before interpretation. When
using `capped_mic_handling = "conservative"`, an MIC value of e.g.
"\>2" will always return "R", even if the breakpoint according to
the chosen guideline is "\>=4". This is to prevent that capped
values from raw laboratory data would not be treated
conservatively. The default behaviour
(`capped_mic_handling = "standard"`) considers "\>2" to be lower
than "\>=4" and might in this case return "S" or "I".
- Operators like "\<=" will be considered according to the
`capped_mic_handling` setting. At default, an MIC value of e.g.
"\>2" will return "NI" (non-interpretable) if the breakpoint is
4-8; the *true* 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.
- **Note:** When using CLSI as the guideline, MIC values must be
log2-based doubling dilutions. Values not in this format, will be
@@ -649,10 +648,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2025-11-24 10:38:56 1 MIC amoxicillin Escherich… human 8
#> 2 2025-11-24 10:38:56 1 MIC cipro Escherich… human 0.256
#> 3 2025-11-24 10:38:56 1 DISK tobra Escherich… human 16
#> 4 2025-11-24 10:38:56 1 DISK genta Escherich… human 18
#> 1 2025-12-15 12:29:02 1 MIC amoxicillin Escherich… human 8
#> 2 2025-12-15 12:29:02 1 MIC cipro Escherich… human 0.256
#> 3 2025-12-15 12:29:02 1 DISK tobra Escherich… human 16
#> 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>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>
@@ -858,8 +857,20 @@ as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Class 'sir'
#> [1] S SDD I R NI <NA> <NA> <NA>
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'
#> [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)))
is.sir(sir_data)
#> [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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/av_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/availability.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/clinical_breakpoints.html
View File

@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<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>
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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(
<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>
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2
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
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2
reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</small>
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2
reference/example_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
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2
reference/first_isolate.html
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@@ -9,7 +9,7 @@
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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 @@
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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>
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<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/ggplot_sir.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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/guess_ab_col.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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>
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<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>
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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>
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<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>
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<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/kurtosis.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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/like.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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/mdro.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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/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>
<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/microorganisms.codes.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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/microorganisms.groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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>
<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_matching_score.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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/pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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/random.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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/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
<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/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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/top_n_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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/translate.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<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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search.json
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