<metaproperty="og:description"content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples."/>
<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><ahref='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publicable/printable format, see <em>Examples</em>.</p>
<td><p>column name of the IDs 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></td>
<td><p>the function to call on the <code>mo</code> column to transform the microorganism IDs, defaults to <code><ahref='mo_property.html'>mo_shortname()</a></code></p></td>
<td><p>a <ahref='https://rdrr.io/r/base/character.html'>character</a> of length 1 containing column names of the <ahref='antibiotics.html'>antibiotics</a> data set</p></td>
<td><p>language of the returned text, defaults to system language (see <code><ahref='translate.html'>get_locale()</a></code>) and can also be set with <code><ahref='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>
<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 <em>Source</em>.</p></td>
<td><p>a <ahref='https://rdrr.io/r/base/logical.html'>logical</a> 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 argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
<td><p>a <ahref='https://rdrr.io/r/base/logical.html'>logical</a> to indicate where the group of the antimicrobials must be included as a first column</p></td>
<td><p><ahref='https://rdrr.io/r/base/logical.html'>logical</a> to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table</p></td>
<p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <ahref='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
<p>The function <code>bug_drug_combinations()</code> returns a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with columns "mo", "ab", "S", "I", "R" and "total".</p>
<p>The function <code><ahref='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>
The <ahref='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first 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>
<p>On our website <ahref='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <ahref='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <ahref='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <ahref='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
FUN <spanclass='op'>=</span><spanclass='kw'>function</span><spanclass='op'>(</span><spanclass='va'>x</span><spanclass='op'>)</span><spanclass='fu'><ahref='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><spanclass='op'>(</span><spanclass='va'>x</span><spanclass='op'>==</span><spanclass='fu'><ahref='as.mo.html'>as.mo</a></span><spanclass='op'>(</span><spanclass='st'>"E. coli"</span><spanclass='op'>)</span>,
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <ahref='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
