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@@ -30,7 +30,7 @@
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<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="">3.0.1.9003</small>
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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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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -91,7 +91,7 @@
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 24 November 2025.</p>
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generated on 15 December 2025.</p>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">2025-11-24</td>
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<td align="center">2025-12-15</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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<tr class="even">
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<td align="center">2025-11-24</td>
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<td align="center">2025-12-15</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">R</td>
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</tr>
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<tr class="odd">
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<td align="center">2025-11-24</td>
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<td align="center">2025-12-15</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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@@ -405,7 +405,7 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
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<span><span class="co">#> <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>
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<span><span class="co">#> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>
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<span><span class="co"><span style="color: #BB0000;">#> of 2</span></span></span>
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<span><span class="co">#> <span style="color: #BBBBBB;">=> 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>
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<span><span class="co">#> <span style="color: #BBBBBB;">=> 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>
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<span><span class="co"><span style="color: #BBBBBB;">#> microbial ID was available)</span></span></span></code></pre></div>
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<p>So only 91% is suitable for resistance analysis! We can now filter on
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it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
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@@ -417,11 +417,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
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<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
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<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>
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<p>So we end up with 2 724 isolates for analysis. Now our data looks
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<p>So we end up with 2 730 isolates for analysis. Now our data looks
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like:</p>
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<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 9</span></span></span>
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<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
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<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
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||||
<span><span class="co">#> <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>
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@@ -434,7 +434,7 @@ like:</p>
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||||
<span><span class="co">#> <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>
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||||
<span><span class="co">#> <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>
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||||
<span><span class="co">#> <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>
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||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
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||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,720 more rows</span></span></span></code></pre></div>
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||||
<p>Time for the analysis.</p>
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||||
</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>
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||||
<span><span class="co">#> patient_id hospital date </span></span>
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||||
<span><span class="co">#> Length:2724 Length:2724 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-07 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-03 </span></span>
|
||||
<span><span class="co">#> Length:2730 Length:2730 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-06 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-04 </span></span>
|
||||
<span><span class="co">#> Mean :2015-06-09 </span></span>
|
||||
<span><span class="co">#> 3rd Qu.:2017-08-11 </span></span>
|
||||
<span><span class="co">#> 3rd Qu.:2017-08-14 </span></span>
|
||||
<span><span class="co">#> Max. :2019-12-27 </span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
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||||
<span><span class="co">#> Class :mo Class:sir Class:sir </span></span>
|
||||
<span><span class="co">#> <NA> :0 %S :41.6% (n=1133) %S :52.6% (n=1432) </span></span>
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||||
<span><span class="co">#> <NA> :0 %S :40.1% (n=1071) %S :51.1% (n=1354) </span></span>
|
||||
<span><span class="co">#> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI %I :17.0% (n=453) %I :12.7% (n=335) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS %R :42.9% (n=1147) %R :36.2% (n=959) </span></span>
|
||||
<span><span class="co">#> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> CIP GEN first </span></span>
|
||||
<span><span class="co">#> Class:sir Class:sir Mode:logical </span></span>
|
||||
<span><span class="co">#> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 </span></span>
|
||||
<span><span class="co">#> %S :52.2% (n=1426) %S :60.7% (n=1656) TRUE:2730 </span></span>
|
||||
<span><span class="co">#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> %I : 6.5% (n=176) %I : 3.0% (n=82) </span></span>
|
||||
<span><span class="co">#> %R :41.0% (n=1117) %R :36.0% (n=981) </span></span>
|
||||
<span><span class="co">#> %I : 6.5% (n=178) %I : 3.0% (n=83) </span></span>
|
||||
<span><span class="co">#> %R :41.2% (n=1126) %R :36.3% (n=991) </span></span>
|
||||
<span><span class="co">#> %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">#> Rows: 2,724</span></span>
|
||||
<span><span class="co">#> Rows: 2,730</span></span>
|
||||
<span><span class="co">#> Columns: 9</span></span>
|
||||
<span><span class="co">#> $ patient_id <span style="color: #949494; font-style: italic;"><chr></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">#> $ hospital <span style="color: #949494; font-style: italic;"><chr></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">#> patient_id hospital date bacteria AMX AMC CIP </span></span>
|
||||
<span><span class="co">#> 260 3 1854 4 3 3 3 </span></span>
|
||||
<span><span class="co">#> 260 3 1854 4 4 4 3 </span></span>
|
||||
<span><span class="co">#> GEN first </span></span>
|
||||
<span><span class="co">#> 3 1</span></span></code></pre></div>
|
||||
<div class="section level3">
|
||||
@@ -509,9 +509,9 @@ microorganisms:</p>
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||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||||
<span><span class="co">#> `mo_name(bacteria)` n</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>321</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 682</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 402</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>326</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 684</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 401</span></span>
|
||||
<span><span class="co">#> <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">%>%</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">#> <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">#> <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 2</span></span></span>
|
||||
<span><span class="co">#> date GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <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">#> <span style="color: #BCBCBC;"> 8</span> 2019-06-19 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2015-04-27 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2011-06-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <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">%>%</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">#> <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;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 3</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <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">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <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">%>%</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">#> <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,730 × 5</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC CIP GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <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">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <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">%>%</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">#> <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">#> <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 991 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <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">#> <span style="color: #949494;"># ℹ 971 more rows</span></span></span>
|
||||
<span><span class="co">#> <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">%>%</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">#> <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;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 461 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <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">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span>
|
||||
<span><span class="co">#> <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">#> <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;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 461 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <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">#> <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">#> <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">#> <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">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <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">%>%</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">#> [1] 0.4203377</span></span></code></pre></div>
|
||||
<span><span class="co">#> [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">#> <span style="color: #949494;"># A tibble: 3 × 2</span></span></span>
|
||||
<span><span class="co">#> hospital amoxicillin</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> A 0.340</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> B 0.551</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> A 0.341</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> B 0.586</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
|
||||
+38
-38
@@ -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
|
||||
```
|
||||
|
||||
|
||||
@@ -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">
|
||||
|
||||
@@ -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">
|
||||
|
||||
@@ -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">
|
||||
|
||||
+1
-1
@@ -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">
|
||||
|
||||
@@ -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">
|
||||
|
||||
+1
-1
@@ -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">
|
||||
|
||||
@@ -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>
|
||||
|
||||
+1
-1
@@ -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">
|
||||
|
||||
Reference in new issue
Block a user