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<h1>Determine bug-drug combinations</h1>
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<div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
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<div class="ref-description">
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<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code>format</code> on the result to prettify it to a publicable/printable format, see Examples.</p>
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<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_shortname</span>, <span class='no'>...</span>)
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<span class='co'># S3 method for bug_drug_combinations</span>
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<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>,
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<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name (ab, atc)"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>remove_intrinsic_resistant</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>==</span>
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<span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>), <span class='no'>...</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
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</tr>
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<tr>
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<th>col_mo</th>
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<td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
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</tr>
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<tr>
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<th>FUN</th>
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<td><p>the function to call on the <code>mo</code> column to transform the microorganism IDs, defaults to <code><a href='mo_property.html'>mo_shortname</a></code></p></td>
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</tr>
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<tr>
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<th>...</th>
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<td><p>arguments passed on to <code>FUN</code></p></td>
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</tr>
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<tr>
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<th>translate_ab</th>
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<td><p>a character of length 1 containing column names of the <code><a href='antibiotics.html'>antibiotics</a></code> data set</p></td>
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</tr>
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<tr>
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<th>language</th>
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<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
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</tr>
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<tr>
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<th>minimum</th>
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<td><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 Source.</p></td>
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</tr>
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<tr>
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<th>combine_SI</th>
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<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
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</tr>
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<tr>
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<th>combine_IR</th>
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<td><p>logical to indicate whether values R and I should be summed</p></td>
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</tr>
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<tr>
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<th>add_ab_group</th>
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<td><p>logical to indicate where the group of the antimicrobials must be included as a first column</p></td>
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</tr>
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<tr>
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<th>remove_intrinsic_resistant</th>
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<td><p>logical to indicate that rows with 100% resistance for all tested antimicrobials must be removed from the table</p></td>
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</tr>
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<tr>
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<th>decimal.mark</th>
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<td><p>the character to be used to indicate the numeric
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decimal point.</p></td>
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</tr>
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<tr>
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<th>big.mark</th>
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<td><p>character; if not empty used as mark between every
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<code>big.interval</code> decimals <em>before</em> (hence <code>big</code>) the
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decimal point.</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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<p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>The function <code>bug_drug_combinations</code> returns a <code>data.frame</code> with columns "mo", "ab", "S", "I", "R" and "total".</p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>The function <code>format</code> calculates the resistance per bug-drug combination. Use <code>combine_IR = FALSE</code> (default) to test R vs. S+I and <code>combine_IR = TRUE</code> to test R+I vs. S.</p>
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<p>The language of the output can be overwritten with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale)</a></code>, please see <a href='translate.html'>translate</a>.</p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># \donttest{</span>
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<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>)
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<span class='no'>x</span>
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<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name (atc)"</span>)
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<span class='co'># Use FUN to change to transformation of microorganism codes</span>
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<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>,
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<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_gramstain</span>)
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<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>,
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<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>x</span> <span class='kw'>==</span> <span class='st'>"B_ESCHR_COLI"</span>,
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<span class='st'>"E. coli"</span>,
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<span class='st'>"Others"</span>))
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<span class='co'># }</span></pre>
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#source">Source</a></li>
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<li><a href="#value">Value</a></li>
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<li><a href="#details">Details</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#examples">Examples</a></li>
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</ul>
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