<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><metaname="description"content="Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker et al. and Barbieri et al. (see Source), and allow reporting in e.g. R Markdown and Quarto as well."><title>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.2.2/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><linkhref="../deps/Fira_Code-0.4.5/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- bootstrap-toc --><scriptsrc="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js"integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram"><metaproperty="og:description"content="Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker et al. and Barbieri et al. (see Source), and allow reporting in e.g. R Markdown and Quarto as well.">
<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>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> info <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/interactive.html"class="external-link">interactive</a></span><spanclass="op">(</span><spanclass="op">)</span></span>
<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; <ahref="https://doi.org/10.1177/20499361211011373"class="external-link">doi:10.1177/20499361211011373</a></p></li>
<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; <ahref="https://doi.org/10.1186/s13756-021-00939-2"class="external-link">doi:10.1186/s13756-021-00939-2</a></p></li>
<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>. <ahref="https://clsi.org/standards/products/microbiology/documents/m39/"class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<dd><p>a <ahref="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><ahref="as.sir.html">as.sir()</a></code>)</p></dd>
<dt>antibiotics</dt>
<dd><p>vector of column names, or (any combinations of) <ahref="antibiotic_class_selectors.html">antibiotic selectors</a> such as <code><ahref="antibiotic_class_selectors.html">aminoglycosides()</a></code> or <code><ahref="antibiotic_class_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be column names separated with <code>"+"</code>, such as "TZP+TOB" given that the data set contains columns "TZP" and "TOB". See <em>Examples</em>.</p></dd>
<dt>mo_transform</dt>
<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <ahref="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "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>
<dt>ab_transform</dt>
<dd><p>a character to transform antibiotic input - must be one of the column names of the <ahref="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>
<dt>syndromic_group</dt>
<dd><p>a column name of <code>x</code>, or values calculated to split rows of <code>x</code>, e.g. by using <code><ahref="https://rdrr.io/r/base/ifelse.html"class="external-link">ifelse()</a></code> or <code><ahref="https://dplyr.tidyverse.org/reference/case_when.html"class="external-link">case_when()</a></code>. See <em>Examples</em>.</p></dd>
<dt>add_total_n</dt>
<dd><p>a <ahref="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 (defaults to <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>
<dt>only_all_tested</dt>
<dd><p>(for combination antibiograms): a <ahref="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>
<dt>digits</dt>
<dd><p>number of digits to use for rounding</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><ahref="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><ahref="as.mo.html">mo</a></code>. Values will be coerced using <code><ahref="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>language</dt>
<dd><p>language to translate text, which defaults to the system language (see <code><ahref="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dt>minimum</dt>
<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>
<dt>combine_SI</dt>
<dd><p>a <ahref="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 (defaults to <code>TRUE</code>)</p></dd>
<dt>sep</dt>
<dd><p>a separating character for antibiotic columns in combination antibiograms</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>when used in <code><ahref="https://rdrr.io/r/base/print.html"class="external-link">print()</a></code>: arguments passed on to <code><ahref="https://rdrr.io/pkg/knitr/man/kable.html"class="external-link">knitr::kable()</a></code> (otherwise, has no use)</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether the printing should be done using <code><ahref="https://rdrr.io/pkg/knitr/man/kable.html"class="external-link">knitr::kable()</a></code> (which is the default in non-interactive sessions)</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether the microorganism names in the output table should be made italic, using <code><ahref="italicise_taxonomy.html">italicise_taxonomy()</a></code>. This only works when the output format is markdown, such as in HTML output.</p></dd>
<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><ahref="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
<p>There are four antibiogram types, as proposed by Klinker <em>et al.</em> (2021, <ahref="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>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>
</ol><p>All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using <code><ahref="https://ggplot2.tidyverse.org/reference/autoplot.html"class="external-link">ggplot2::autoplot()</a></code> or base <spanstyle="R">R</span><code><ahref="plot.html">plot()</a></code>/<code><ahref="https://rdrr.io/r/graphics/barplot.html"class="external-link">barplot()</a></code>) or printed into R Markdown / Quarto formats for reports using <code><ahref="https://rdrr.io/r/base/print.html"class="external-link">print()</a></code>. Use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p>
<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 (defaults to <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>
<spanid="cb1-7"><ahref="#cb1-7"aria-hidden="true"tabindex="-1"></a> S or I S or I X X X X</span>
<spanid="cb1-8"><ahref="#cb1-8"aria-hidden="true"tabindex="-1"></a> R S or I X X X X</span>
<spanid="cb1-9"><ahref="#cb1-9"aria-hidden="true"tabindex="-1"></a><spanclass="sc"><</span><spanclass="cn">NA</span><spanclass="sc">></span> S or I X X <spanclass="sc">-</span><spanclass="sc">-</span></span>
<spanid="cb1-10"><ahref="#cb1-10"aria-hidden="true"tabindex="-1"></a> S or I R X X X X</span>
<spanid="cb1-11"><ahref="#cb1-11"aria-hidden="true"tabindex="-1"></a> R R <spanclass="sc">-</span> X <spanclass="sc">-</span> X</span>
<spanid="cb1-12"><ahref="#cb1-12"aria-hidden="true"tabindex="-1"></a><spanclass="sc"><</span><spanclass="cn">NA</span><spanclass="sc">></span> R <spanclass="sc">-</span><spanclass="sc">-</span><spanclass="sc">-</span><spanclass="sc">-</span></span>
<spanid="cb1-13"><ahref="#cb1-13"aria-hidden="true"tabindex="-1"></a> S or I <spanclass="sc"><</span><spanclass="cn">NA</span><spanclass="sc">></span> X X <spanclass="sc">-</span><spanclass="sc">-</span></span>
<spanid="cb1-14"><ahref="#cb1-14"aria-hidden="true"tabindex="-1"></a> R <spanclass="sc"><</span><spanclass="cn">NA</span><spanclass="sc">></span><spanclass="sc">-</span><spanclass="sc">-</span><spanclass="sc">-</span><spanclass="sc">-</span></span>
<p>Printing the antibiogram in non-interactive sessions will be done by <code><ahref="https://rdrr.io/pkg/knitr/man/kable.html"class="external-link">knitr::kable()</a></code>, with support for <ahref="https://rdrr.io/pkg/knitr/man/kable.html"class="external-link">all their implemented formats</a>, such as "markdown". The knitr format will be automatically determined if printed inside a knitr document (LaTeX, HTML, etc.).</p>
<divclass="sourceCode"><preclass="sourceCode r"><code><spanclass="r-in"><span><spanclass="co"># example_isolates is a data set available in the AMR package.</span></span></span>
<spanclass="r-in"><span><spanclass="co"># run ?example_isolates for more info.</span></span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>,</span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #949494;"># … with abbreviated variable name ¹`Piperacillin/tazobactam & Tobramycin`</span></span>
<spanclass="r-in"><span> minimum <spanclass="op">=</span><spanclass="fl">10</span>, <spanclass="co"># this should be >=30, but now just as example</span></span></span>
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