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Generate Antibiogram (Trad./Syndromic/WISCA)
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<img src="../logo.svg" class="logo" alt=""><h1>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/antibiogram.R" class="external-link"><code>R/antibiogram.R</code></a></small>
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<div class="d-none name"><code>antibiogram.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker <em>et al.</em> and Barbieri <em>et al.</em> (see <em>Source</em>), and allow reporting in e.g. R Markdown and Quarto as well.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">antibiogram</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> antibiotics <span class="op">=</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>
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<span> mo_transform <span class="op">=</span> <span class="st">"shortname"</span>,</span>
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<span> ab_transform <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> syndromic_group <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> add_total_n <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> digits <span class="op">=</span> <span class="fl">0</span>,</span>
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<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<span> minimum <span class="op">=</span> <span class="fl">30</span>,</span>
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<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> sep <span class="op">=</span> <span class="st">" + "</span>,</span>
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<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for antibiogram</span></span>
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<span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for antibiogram</span></span>
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<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for antibiogram</span></span>
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<span><span class="fu">knit_print</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> italicise <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> na <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"knitr.kable.NA"</span>, default <span class="op">=</span> <span class="st">""</span><span class="op">)</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<ul><li><p>Klinker KP <em>et al.</em> (2021). <strong>Antimicrobial stewardship and antibiograms: importance of moving beyond traditional antibiograms</strong>. <em>Therapeutic Advances in Infectious Disease</em>, May 5;8:20499361211011373; <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a></p></li>
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<li><p>Barbieri E <em>et al.</em> (2021). <strong>Development of a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) to guide the choice of the empiric antibiotic treatment for urinary tract infection in paediatric patients: a Bayesian approach</strong> <em>Antimicrobial Resistance & Infection Control</em> May 1;10(1):74; <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">doi:10.1186/s13756-021-00939-2</a></p></li>
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<li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
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<dt>antibiotics</dt>
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<dd><p>vector of any antibiotic name or code (will be evaluated with <code><a href="as.ab.html">as.ab()</a></code>, column name of <code>x</code>, or (any combinations of) <a href="antibiotic_class_selectors.html">antibiotic selectors</a> such as <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> or <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be set to values separated with <code>"+"</code>, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in <code>x</code>. See <em>Examples</em>.</p></dd>
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<dt>mo_transform</dt>
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<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
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<dt>ab_transform</dt>
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<dd><p>a character to transform antibiotic input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set: "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
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<dt>syndromic_group</dt>
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<dd><p>a column name of <code>x</code>, or values calculated to split rows of <code>x</code>, e.g. by using <code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> or <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code>. See <em>Examples</em>.</p></dd>
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<dt>add_total_n</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether total available numbers per pathogen should be added to the table (default is <code>TRUE</code>). This will add the lowest and highest number of available isolate per antibiotic (e.g, if for <em>E. coli</em> 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").</p></dd>
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<dt>only_all_tested</dt>
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<dd><p>(for combination antibiograms): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antibiotics, see <em>Details</em></p></dd>
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<dt>digits</dt>
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<dd><p>number of digits to use for rounding</p></dd>
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<dt>col_mo</dt>
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<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
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<dt>language</dt>
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<dd><p>language to translate text, which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
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<dt>minimum</dt>
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<dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
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|
||
<dt>combine_SI</dt>
|
||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (default is <code>TRUE</code>)</p></dd>
|
||
|
||
|
||
<dt>sep</dt>
|
||
<dd><p>a separating character for antibiotic columns in combination antibiograms</p></dd>
|
||
|
||
|
||
<dt>info</dt>
|
||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
|
||
|
||
|
||
<dt>...</dt>
|
||
<dd><p>when used in <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">R Markdown or Quarto</a>: arguments passed on to <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> (otherwise, has no use)</p></dd>
|
||
|
||
|
||
<dt>object</dt>
|
||
<dd><p>an <code>antibiogram()</code> object</p></dd>
|
||
|
||
|
||
<dt>italicise</dt>
|
||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr</a> table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>.</p></dd>
|
||
|
||
|
||
<dt>na</dt>
|
||
<dd><p>character to use for showing <code>NA</code> values</p></dd>
|
||
|
||
</dl></div>
|
||
<div class="section level2">
|
||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||
<p>This function returns a table with values between 0 and 100 for <em>susceptibility</em>, not resistance.</p>
|
||
<p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
|
||
<p>All types of antibiograms as listed below can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>). The <code>antibiogram</code> object can also be used directly in R Markdown / Quarto (i.e., <code>knitr</code>) for reports. In this case, <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> will be applied automatically and microorganism names will even be printed in italics at default (see argument <code>italicise</code>). You can also use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. with <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p><div class="section">
|
||
<h3 id="antibiogram-types">Antibiogram Types<a class="anchor" aria-label="anchor" href="#antibiogram-types"></a></h3>
|
||
|
||
|
||
<p>There are four antibiogram types, as proposed by Klinker <em>et al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a>
|
||
), and they are all supported by <code>antibiogram()</code>:</p><ol><li><p><strong>Traditional Antibiogram</strong></p>
|
||
<p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to piperacillin/tazobactam (TZP)</p>
|
||
<p>Code example:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
|
||
<span> antibiotics <span class="op">=</span> <span class="st">"TZP"</span><span class="op">)</span></span></code></pre><p></p></div></li>
|
||
<li><p><strong>Combination Antibiogram</strong></p>
|
||
<p>Case example: Additional susceptibility of <em>Pseudomonas aeruginosa</em> to TZP + tobramycin versus TZP alone</p>
|
||
<p>Code example:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
|
||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
|
||
<li><p><strong>Syndromic Antibiogram</strong></p>
|
||
<p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to TZP among respiratory specimens (obtained among ICU patients only)</p>
|
||
<p>Code example:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
|
||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></code></pre><p></p></div></li>
|
||
<li><p><strong>Weighted-Incidence Syndromic Combination Antibiogram (WISCA)</strong></p>
|
||
<p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to TZP among respiratory specimens (obtained among ICU patients only) for male patients age >=65 years with heart failure</p>
|
||
<p>Code example:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
|
||
<span><span class="va">your_data</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="va">ward</span> <span class="op">==</span> <span class="st">"ICU"</span> <span class="op">&</span> <span class="va">specimen_type</span> <span class="op">==</span> <span class="st">"Respiratory"</span><span class="op">)</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="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span>antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
|
||
<span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">.</span><span class="op">$</span><span class="va">age</span> <span class="op">>=</span> <span class="fl">65</span> <span class="op">&</span></span>
|
||
<span> <span class="va">.</span><span class="op">$</span><span class="va">gender</span> <span class="op">==</span> <span class="st">"Male"</span> <span class="op">&</span></span>
|
||
<span> <span class="va">.</span><span class="op">$</span><span class="va">condition</span> <span class="op">==</span> <span class="st">"Heart Disease"</span>,</span>
|
||
<span> <span class="st">"Study Group"</span>, <span class="st">"Control Group"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
|
||
</ol><p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (default is <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
|
||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
|
||
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
|
||
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>
|
||
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> Drug A Drug B include as include as include as include as</span>
|
||
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> numerator denominator numerator denominator</span>
|
||
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="sc">--------</span> <span class="sc">--------</span> <span class="sc">----------</span> <span class="sc">-----------</span> <span class="sc">----------</span> <span class="sc">-----------</span></span>
|
||
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> S or I S or I X X X X</span>
|
||
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a> R S or I X X X X</span>
|
||
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> S or I X X <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a> S or I R X X X X</span>
|
||
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a> R R <span class="sc">-</span> X <span class="sc">-</span> X</span>
|
||
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> R <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a> S or I <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> X X <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a> R <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span></code></pre><p></p></div>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># example_isolates is a data set available in the AMR package.</span></span></span>
|
||
<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
|
||
<span class="r-in"><span><span class="va">example_isolates</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <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;"><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 class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,990 more rows</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||
<span class="r-in"><span><span class="co"># Traditional antibiogram ----------------------------------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 10 × 7</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> CoNS (43-309) 0 86 52 0 52 22</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E. coli (0-462) 100 98 100 <span style="color: #BB0000;">NA</span> 100 97</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E. faecalis (0-39) 0 0 100 0 <span style="color: #BB0000;">NA</span> 0</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae (0-58) <span style="color: #BB0000;">NA</span> 90 100 <span style="color: #BB0000;">NA</span> 100 90</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa (17-30) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 100</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis (0-34) <span style="color: #BB0000;">NA</span> 94 94 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> S. aureus (2-233) <span style="color: #BB0000;">NA</span> 99 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 98</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis (8-163) 0 79 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 51</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> S. hominis (3-80) <span style="color: #BB0000;">NA</span> 92 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> S. pneumoniae (11-117) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
|
||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` J01GB01 J01GB03 J01GB04 J01GB06</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (35-686) 96 96 0 98</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (436-1170) 34 63 0 0</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
|
||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 3</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` Imipenem Meropenem</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) (48-48) 52 52</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis (0-38) 100 <span style="color: #BB0000;">NA</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Escherichia coli (418-422) 100 100</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae (51-53) 100 100</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis (27-32) 94 <span style="color: #BB0000;">NA</span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Combined antibiogram -------------------------------------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># combined antibiotics yield higher empiric coverage</span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` TZP `TZP + GEN` `TZP + TOB`</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 99 98</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 98 95</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># names of antibiotics do not need to resemble columns exactly:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Cipro"</span>, <span class="st">"cipro + genta"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
|
||
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
|
||
<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" & "</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` Ciprofloxacin `Ciprofloxacin & Gentamicin`</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (684-694) 91 99</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (724-847) 77 93</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Syndromic antibiogram ------------------------------------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># the data set could contain a filter for e.g. respiratory specimens</span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 14 × 8</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical CoNS (23-205) <span style="color: #BB0000;">NA</span> 89 57 <span style="color: #BB0000;">NA</span> 57 26</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU CoNS (10-73) <span style="color: #BB0000;">NA</span> 79 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Outpatient CoNS (3-31) <span style="color: #BB0000;">NA</span> 84 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical E. coli (0-299) 100 98 100 <span style="color: #BB0000;">NA</span> 100 98</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU E. coli (0-137) 100 99 100 <span style="color: #BB0000;">NA</span> 100 96</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical K. pneumoniae (0-51) <span style="color: #BB0000;">NA</span> 92 100 <span style="color: #BB0000;">NA</span> 100 92</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical P. mirabilis (0-30) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 100</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical S. aureus (2-150) <span style="color: #BB0000;">NA</span> 99 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 97</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU S. aureus (0-66) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical S. epidermidis (4-79) <span style="color: #BB0000;">NA</span> 82 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 55</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> ICU S. epidermidis (4-75) <span style="color: #BB0000;">NA</span> 72 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 41</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis (1-45) <span style="color: #BB0000;">NA</span> 96 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumoniae (5-78) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> ICU S. pneumoniae (5-30) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># now define a data set with only E. coli</span></span></span>
|
||
<span class="r-in"><span><span class="va">ex1</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Escherichia"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># with a custom language, though this will be determined automatically</span></span></span>
|
||
<span class="r-in"><span><span class="co"># (i.e., this table will be in Spanish on Spanish systems)</span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">ex1</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
|
||
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">ex1</span><span class="op">$</span><span class="va">ward</span> <span class="op">==</span> <span class="st">"ICU"</span>,</span></span>
|
||
<span class="r-in"><span> <span class="st">"UCI"</span>, <span class="st">"No UCI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> No UCI E. coli (0-325) 100 98 98</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> UCI E. coli (0-137) 100 99 96</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Weighted-incidence syndromic combination antibiogram (WISCA) ---------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># the data set could contain a filter for e.g. respiratory specimens/ICU</span></span></span>
|
||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC+CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
|
||
<span class="r-in"><span> minimum <span class="op">=</span> <span class="fl">10</span>, <span class="co"># this should be >=30, but now just as example</span></span></span>
|
||
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">age</span> <span class="op">>=</span> <span class="fl">65</span> <span class="op">&</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span><span class="op">$</span><span class="va">gender</span> <span class="op">==</span> <span class="st">"M"</span>,</span></span>
|
||
<span class="r-in"><span> <span class="st">"WISCA Group 1"</span>, <span class="st">"WISCA Group 2"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 6</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Pathogen (N min-max)` AMC `AMC + CIP` TZP `TZP + TOB`</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="va">ureido</span> <span class="op"><-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For ureidopenicillins() using column 'TZP' (piperacillin/tazobactam)</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># in an Rmd file, you would just need to return `ureido` in a chunk,</span></span></span>
|
||
<span class="r-in"><span><span class="co"># but to be explicit here:</span></span></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"knitr"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/cat.html" class="external-link">cat</a></span><span class="op">(</span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/knit_print.html" class="external-link">knit_print</a></span><span class="op">(</span><span class="va">ureido</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> |Pathogen (N) | Piperacillin/tazobactam|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> |:---------------------|-----------------------:|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> |CoNS (33) | 30|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> |*E. coli* (416) | 94|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> |*K. pneumoniae* (53) | 89|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> |*S. pneumoniae* (112) | 100|</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="va">ab1</span> <span class="op"><-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="va">ab2</span> <span class="op"><-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
|
||
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-plt img"><img src="antibiogram-1.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">ab2</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-plt img"><img src="antibiogram-2.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>
|
||
<span class="r-plt img"><img src="antibiogram-3.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab2</span><span class="op">)</span></span></span>
|
||
<span class="r-plt img"><img src="antibiogram-4.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
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|
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