P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 14:27:53 +02:00
Code Releases Activity

Built site for AMR: 2.0.0.9021@766db4e

Browse Source
This commit is contained in:
github-actions
2023-05-26 17:31:22 +00:00
parent e0222b5d61
commit 19c2925a0a
90 changed files with 325 additions and 323 deletions
Download Patch File Download Diff File Expand all files Collapse all files

136
articles/AMR.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9021</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">
@ -388,35 +388,37 @@ 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: Eubacterium alactolyticum (0.620), Erwinia herbicola</span></span>
<span><span class="co">#&gt; (0.618), Campylobacter coli (0.611), Enterobacter cowanii (0.600),</span></span>
<span><span class="co">#&gt; Eubacterium combesii (0.600), Enterococcus faecalis (0.595), Eggerthia</span></span>
<span><span class="co">#&gt; catenaformis (0.591), Enterocloster aldensis (0.591), Eubacterium</span></span>
<span><span class="co">#&gt; callanderi (0.591), and Rhodococcus corallinus (0.591)</span></span>
<span><span class="co">#&gt; Also matched: 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), Enterobacter cloacae</span></span>
<span><span class="co">#&gt; cloacae (0.571), Ehrlichia canis (0.567), and Enterobacter cloacae</span></span>
<span><span class="co">#&gt; dissolvens (0.565)</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: Nocardia pneumoniae (0.763), Chlamydia pneumoniae</span></span>
<span><span class="co">#&gt; (0.750), Mycoplasma pneumoniae (0.738), Klebsiella quasipneumoniae</span></span>
<span><span class="co">#&gt; (0.731), Chlamydophila pneumoniae (0.708), Streptococcus pneumoniae</span></span>
<span><span class="co">#&gt; (0.708), Klebsiella pneumoniae ozaenae (0.707), Mycoplasmoides</span></span>
<span><span class="co">#&gt; pneumoniae (0.700), Klebsiella pneumoniae pneumoniae (0.688), and</span></span>
<span><span class="co">#&gt; Haemophilus pleuropneumoniae (0.679)</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), Kosakonia pseudosacchari (0.361), Kaistella</span></span>
<span><span class="co">#&gt; palustris (0.333), Kocuria palustris (0.333), and Kocuria pelophila</span></span>
<span><span class="co">#&gt; (0.333)</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),</span></span>
<span><span class="co">#&gt; Staphylococcus capitis urealyticus (0.618), Staphylococcus capitis</span></span>
<span><span class="co">#&gt; ureolyticus (0.618), Staphylococcus intermedius (0.615), Salmonella</span></span>
<span><span class="co">#&gt; choleraesuis choleraesuis (0.611), Staphylococcus sciuri lentus</span></span>
<span><span class="co">#&gt; (0.607), Salmonella Reubeuss (0.605), and Schaalia turicensis (0.605)</span></span>
<span><span class="co">#&gt; Streptomyces argenteolus (0.483), Streptomyces aureus (0.474),</span></span>
<span><span class="co">#&gt; Streptomyces azureus (0.467), Streptomyces aureorectus (0.444),</span></span>
<span><span class="co">#&gt; Streptomyces auratus (0.433), Streptomyces aurantiogriseus (0.429), and</span></span>
<span><span class="co">#&gt; Streptomyces aureocirculatus (0.429)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. pneumoniae" -&gt; Nocardia pneumoniae (B_NOCRD_PNMN, 0.763)</span></span>
<span><span class="co">#&gt; Also matched: Chlamydia pneumoniae (0.750), Streptococcus pneumoniae</span></span>
<span><span class="co">#&gt; (0.750), Klebsiella pneumoniae (0.738), Mycoplasma pneumoniae (0.738),</span></span>
<span><span class="co">#&gt; Chlamydophila pneumoniae (0.708), Mycoplasmoides pneumoniae (0.700),</span></span>
<span><span class="co">#&gt; Streptococcus pseudopneumoniae (0.700), Haemophilus pleuropneumoniae</span></span>
<span><span class="co">#&gt; (0.679), Klebsiella pneumoniae ozaenae (0.672), and Actinobacillus</span></span>
<span><span class="co">#&gt; pleuropneumoniae (0.661)</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; </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>
@ -513,8 +515,8 @@ 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 2,637 'phenotype-based' first isolates (87.9% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<span><span class="co">#&gt; =&gt; Found 2,626 'phenotype-based' first isolates (87.6% within scope and</span></span>
<span><span class="co">#&gt; 87.5% of total where a microbial ID was available)</span></span></code></pre></div>
<p>So only 88% 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>
@ -525,11 +527,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 2 637 isolates for analysis. Now our data looks
<p>So we end up with 2 626 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: 2,637 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,626 × 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>
@ -542,7 +544,7 @@ like:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</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;"> 9</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;">10</span> P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,627 more rows</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span></code></pre></div>
<p>Time for the analysis.</p>
</div>
</div>
@ -555,29 +557,29 @@ 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:2637 Length:2637 Min. :2011-01-01 </span></span>
<span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-04-13 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-04 </span></span>
<span><span class="co">#&gt; Mean :2015-06-14 </span></span>
<span><span class="co">#&gt; Length:2626 Length:2626 Min. :2011-01-01 </span></span>
<span><span class="co">#&gt; Class :character Class :character 1st Qu.:2013-04-14 </span></span>
<span><span class="co">#&gt; Mode :character Mode :character Median :2015-06-05 </span></span>
<span><span class="co">#&gt; Mean :2015-06-15 </span></span>
<span><span class="co">#&gt; 3rd Qu.:2017-08-23 </span></span>
<span><span class="co">#&gt; Max. :2020-01-01 </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 %R :43.2% (n=1140) %R :35.9% (n=948) </span></span>
<span><span class="co">#&gt; Unique:5 %SI :56.8% (n=1497) %SI :64.1% (n=1689) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI - %S :41.1% (n=1085) - %S :52.7% (n=1391) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS - %I :15.6% (n=412) - %I :11.3% (n=298) </span></span>
<span><span class="co">#&gt; #3 :B_KLBSL_PNMN </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %R :43.2% (n=1134) %R :36.1% (n=947) </span></span>
<span><span class="co">#&gt; Unique:4 %SI :56.8% (n=1492) %SI :63.9% (n=1679) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI - %S :41.1% (n=1080) - %S :52.7% (n=1383) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS - %I :15.7% (n=412) - %I :11.3% (n=296) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN </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; %R :41.9% (n=1105) %R :36.9% (n=972) TRUE:2637 </span></span>
<span><span class="co">#&gt; %SI :58.1% (n=1532) %SI :63.1% (n=1665) </span></span>
<span><span class="co">#&gt; - %S :52.0% (n=1370) - %S :60.1% (n=1584) </span></span>
<span><span class="co">#&gt; - %I : 6.1% (n=162) - %I : 3.1% (n=81) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1102) %R :37.0% (n=971) TRUE:2626 </span></span>
<span><span class="co">#&gt; %SI :58.0% (n=1524) %SI :63.0% (n=1655) </span></span>
<span><span class="co">#&gt; - %S :51.9% (n=1362) - %S :59.9% (n=1574) </span></span>
<span><span class="co">#&gt; - %I : 6.2% (n=162) - %I : 3.1% (n=81) </span></span>
<span><span class="co">#&gt; </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: 2,637</span></span>
<span><span class="co">#&gt; Rows: 2,626</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", "J8", "M3", "J3", "G6", "P4"…</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>
@ -592,7 +594,7 @@ 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 1814 5 3 3 3 </span></span>
<span><span class="co">#&gt; 260 3 1808 4 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">
@ -604,25 +606,23 @@ 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: 5 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
<span><span class="co">#&gt; `mo_name(bacteria)` n</span></span>
<span><span class="co">#&gt; <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;">3</span> Klebsiella pneumoniae 326</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 275</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Nocardia pneumoniae 151</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>
<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: 5 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
<span><span class="co">#&gt; `mo_name(bacteria)` n</span></span>
<span><span class="co">#&gt; <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>250</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 661</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Klebsiella pneumoniae 316</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 267</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> Nocardia pneumoniae 143</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 399</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 316</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>
@ -634,7 +634,7 @@ 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: 2,637 × 2</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,626 × 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>
@ -647,13 +647,13 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2019-06-19 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2015-04-27 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2011-06-21 S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,627 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 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: 2,637 × 3</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,626 × 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>
@ -666,11 +666,11 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS 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 2,627 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 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: 2,637 × 5</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,626 × 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>
@ -683,26 +683,26 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS 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 2,627 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,616 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: 972 × 9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 971 × 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_NOCRD_PNMN R S S R TRUE </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;"> 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;"> 7</span> S2 A 2013-07-19 B_NOCRD_PNMN 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;">10</span> K5 A 2013-03-15 B_NOCRD_PNMN S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 962 more rows</span></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 961 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>
@ -711,12 +711,12 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 471 × 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_NOCRD_PNMN R R S S TRUE </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;"> 5</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;"> 6</span> N3 A 2014-12-29 B_NOCRD_PNMN R R R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</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;"> 7</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;"> 8</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;"> 9</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
@ -730,12 +730,12 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 471 × 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_NOCRD_PNMN R R S S TRUE </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;"> 5</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;"> 6</span> N3 A 2014-12-29 B_NOCRD_PNMN R R R S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</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;"> 7</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;"> 8</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;"> 9</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
@ -1352,7 +1352,7 @@ 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] 0.4323094</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.4318355</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">
@ -1364,7 +1364,7 @@ own:</p>
<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 0.343</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> B 0.569</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.378</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C 0.375</span></span></code></pre></div>
<hr>
<p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
</div>