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@@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</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">
@@ -95,7 +95,7 @@
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 September 2024.</p>
generated on 29 September 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -151,21 +151,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-09-24</td>
<td align="center">2024-09-29</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">2024-09-24</td>
<td align="center">2024-09-29</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">2024-09-24</td>
<td align="center">2024-09-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -279,37 +279,35 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
<span><span class="co">#&gt; Also matched: Escherichia coli coli (0.643), Escherichia coli</span></span>
<span><span class="co">#&gt; expressing (0.611), Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
<span><span class="co">#&gt; (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span></span>
<span><span class="co">#&gt; (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span></span>
<span><span class="co">#&gt; (0.583), Enterococcus casseliflavus (0.577), and Enterobacter cloacae</span></span>
<span><span class="co">#&gt; cloacae (0.571)</span></span>
<span><span class="co">#&gt; Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
<span><span class="co">#&gt; (0.643), Escherichia coli expressing (0.611), Erwinia coffeiphila</span></span>
<span><span class="co">#&gt; (0.605), Eubacterium coprostanoligenes (0.603), Enterobacter cowanii</span></span>
<span><span class="co">#&gt; (0.600), Eubacterium combesii (0.600), Enterococcus columbae (0.595),</span></span>
<span><span class="co">#&gt; Eggerthia catenaformis (0.591), and Enterococcus camelliae (0.591)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
<span><span class="co">#&gt; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
<span><span class="co">#&gt; pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span></span>
<span><span class="co">#&gt; (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span></span>
<span><span class="co">#&gt; Kingella potus (0.400), Kluyveromyces pseudotropicale (0.386),</span></span>
<span><span class="co">#&gt; Kluyveromyces pseudotropicalis (0.363), Kosakonia pseudosacchari</span></span>
<span><span class="co">#&gt; (0.361), and Kluyveromyces pseudotropicalis pseudotropicalis (0.361)</span></span>
<span><span class="co">#&gt; (0.658), Kosakonia pseudosacchari (0.542), Kaistella palustris (0.500),</span></span>
<span><span class="co">#&gt; Kaistella polysaccharea (0.500), Kingella potus (0.500), Kingella</span></span>
<span><span class="co">#&gt; pumchi (0.500), Klebsiella pasteurii (0.500), and Klebsiella planticola</span></span>
<span><span class="co">#&gt; (0.500)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
<span><span class="co">#&gt; Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
<span><span class="co">#&gt; argenteus (0.625), Staphylococcus aureus anaerobius (0.625), Salmonella</span></span>
<span><span class="co">#&gt; Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella Amounderness</span></span>
<span><span class="co">#&gt; (0.587), Selenomonas artemidis (0.571), Salmonella choleraesuis</span></span>
<span><span class="co">#&gt; arizonae (0.562), Streptococcus anginosus anginosus (0.561), and</span></span>
<span><span class="co">#&gt; Salmonella Abaetetuba (0.548)</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; Streptomyces aureus (B_SMYCS_AURS, 0.711)</span></span>
<span><span class="co">#&gt; Also matched: Streptomyces azureus (0.700), Staphylococcus aureus</span></span>
<span><span class="co">#&gt; (0.690), Streptomyces aureorectus (0.667), Streptomyces albipurpureus</span></span>
<span><span class="co">#&gt; (0.654), Streptomyces auratus (0.650), Staphylococcus aureus aureus</span></span>
<span><span class="co">#&gt; (0.643), Streptomyces aurantiogriseus (0.643), Streptomyces</span></span>
<span><span class="co">#&gt; aureocirculatus (0.643), Streptomyces aureoverticillatus (0.629), and</span></span>
<span><span class="co">#&gt; Staphylococcus argenteus (0.625)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. pneumoniae" -&gt; Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
<span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Serratia</span></span>
<span><span class="co">#&gt; proteamaculans quinovora (0.545), Streptococcus pseudoporcinus (0.536),</span></span>
<span><span class="co">#&gt; Staphylococcus pseudintermedius (0.532), Serratia proteamaculans</span></span>
<span><span class="co">#&gt; proteamaculans (0.526), Salmonella Portanigra (0.524), Sphingomonas</span></span>
<span><span class="co">#&gt; paucimobilis (0.520), Streptococcus pluranimalium (0.519),</span></span>
<span><span class="co">#&gt; Streptococcus constellatus pharyngis (0.514), and Salmonella Pakistan</span></span>
<span><span class="co">#&gt; (0.500)</span></span>
<span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Sphingomonas</span></span>
<span><span class="co">#&gt; piscinae (0.619), Sphingomonas paeninsulae (0.604), Streptomyces</span></span>
<span><span class="co">#&gt; pseudovenezuelae (0.603), Sphingomonas panaciterrae (0.600),</span></span>
<span><span class="co">#&gt; Sphingobacterium pakistanense (0.586), Shewanella pneumatophori</span></span>
<span><span class="co">#&gt; (0.583), Sphingobacterium pakistanensis (0.583), Sphingomonas palmae</span></span>
<span><span class="co">#&gt; (0.579), and Sphingomonas pseudosanguinis (0.571)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Only the first 10 other matches of each record are shown. Run</span></span>
<span><span class="co">#&gt; print(mo_uncertainties(), n = ...) to view more entries, or save</span></span>
@@ -348,11 +346,11 @@ dplyr:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_STPHY_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_SMYCS_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 B_STPHY_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 B_SMYCS_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
<p>This is basically it for the cleaning, time to start the data
inclusion.</p>
@@ -406,9 +404,9 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<span><span class="co">#&gt; ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
<span><span class="co">#&gt; ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
<span><span class="co">#&gt; of 2</span></span>
<span><span class="co">#&gt; =&gt; Found 2,712 'phenotype-based' first isolates (90.4% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 2,724 'phenotype-based' first isolates (90.8% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 90% is suitable for resistance analysis! We can now filter on
<p>So only 91% is suitable for resistance analysis! We can now filter on
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -418,24 +416,24 @@ 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 2 712 isolates for analysis. Now our data looks
<p>So we end up with 2 724 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: 2,712 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 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 B_ESCHR_COLI R I S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 B_KLBSL_PNMN R I S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> W3 A 2018-03-31 B_SMYCS_AURS R S R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> G6 A 2015-04-27 B_SMYCS_AURS S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Z1 A 2014-09-05 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
<p>Time for the analysis.</p>
</div>
</div>
@@ -448,29 +446,29 @@ 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:2712 Length:2712 Min. :2011-01-01 </span></span>
<span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-05-03 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-16 </span></span>
<span><span class="co">#&gt; Mean :2015-06-21 </span></span>
<span><span class="co">#&gt; 3rd Qu.:2017-08-24 </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.:2013-04-26 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-14 </span></span>
<span><span class="co">#&gt; Mean :2015-06-18 </span></span>
<span><span class="co">#&gt; 3rd Qu.:2017-08-21 </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 :41.0% (n=1112) %S :52.0% (n=1409) </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 :16.1% (n=437) %I :12.0% (n=325) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.9% (n=1163) %R :36.1% (n=978) </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %S :41.4% (n=1127) %S :52.2% (n=1421) </span></span>
<span><span class="co">#&gt; Unique:5 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.1% (n=438) %I :12.1% (n=329) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.5% (n=1159) %R :35.8% (n=974) </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 :51.5% (n=1396) %S :59.6% (n=1616) TRUE:2712 </span></span>
<span><span class="co">#&gt; %S :51.7% (n=1407) %S :59.9% (n=1632) TRUE:2724 </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 : 6.6% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1138) %R :37.3% (n=1011) </span></span>
<span><span class="co">#&gt; %I : 6.5% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :41.8% (n=1139) %R :37.0% (n=1007) </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: 2,712</span></span>
<span><span class="co">#&gt; Rows: 2,724</span></span>
<span><span class="co">#&gt; Columns: 9</span></span>
<span><span class="co">#&gt; $ patient_id <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "J3", "R7", "P10", "B7", "W3", "M3", "J3", "G6", "P4", "Z1"…</span></span>
<span><span class="co">#&gt; $ hospital <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…</span></span>
@@ -485,7 +483,7 @@ 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 1852 4 3 3 3 </span></span>
<span><span class="co">#&gt; 260 3 1853 5 3 3 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">
@@ -497,23 +495,25 @@ microorganisms:</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 5 × 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>518</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 730</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 483</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 426</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Streptomyces aureus 247</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="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 5 × 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>319</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 676</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 456</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 400</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 317</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 317</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Streptomyces aureus 232</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="select-and-filter-with-antibiotic-selectors">Select and filter with antibiotic selectors<a class="anchor" aria-label="anchor" href="#select-and-filter-with-antibiotic-selectors"></a>
@@ -525,7 +525,7 @@ 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/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 2</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; 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 S </span></span>
@@ -538,100 +538,100 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2015-04-27 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2011-06-21 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2014-09-05 S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 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/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 3</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; 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> B_ESCHR_COLI R I </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI S I </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_SMYCS_AURS R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ESCHR_COLI R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_SMYCS_AURS S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 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: 2,712 × 5</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 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> B_ESCHR_COLI R I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI S I S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B_SMYCS_AURS R S R S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> B_ESCHR_COLI R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_SMYCS_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 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/antibiotic_class_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; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1,011 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1,007 × 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 B_STRPT_PNMN R S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> X1 A 2017-07-04 B_STPHY_AURS R S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> X1 A 2017-07-04 B_SMYCS_AURS R S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> B3 A 2016-07-24 B_ESCHR_COLI S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> V7 A 2012-04-03 B_ESCHR_COLI S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> C9 A 2017-03-23 B_ESCHR_COLI S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> R1 A 2018-06-10 B_STPHY_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> R1 A 2018-06-10 B_SMYCS_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> S2 A 2013-07-19 B_STRPT_PNMN S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_SMYCS_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_SMYCS_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,001 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 997 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/antibiotic_class_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; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 483 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 479 × 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 B_STRPT_PNMN R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 469 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/antibiotic_class_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; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 483 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 479 × 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 B_STRPT_PNMN R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_SMYCS_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 more rows</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 469 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>
@@ -1230,7 +1230,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb22"><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] 0.4288348</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.4254772</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="cb23"><pre class="downlit sourceCode r">
@@ -1240,9 +1240,9 @@ 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 0.342</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> A 0.336</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B 0.564</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.372</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div>
<hr>
<p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
</div>