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<h1>Determine bug-drug combinations</h1>
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<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
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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><a href='https://rdrr.io/r/base/format.html'>format()</a></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>(
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<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>,
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<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>,
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<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<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>,
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<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>),
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<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> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>),
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<span class='no'>...</span>
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)</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><a href='as.mo.html'>mo</a></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 <a href='antibiotics.html'>antibiotics</a> 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("AMR_locale")</a></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><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></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><a href='https://rdrr.io/r/base/format.html'>format()</a></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="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
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<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
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The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
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<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</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 comprehensive 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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</div>
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