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<img src="../logo.svg" class="logo" alt=""><h1>Determine Multidrug-Resistant Organisms (MDRO)</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mdro.R" class="external-link"><code>R/mdro.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/mdro.R" class="external-link"><code>R/mdro.R</code></a></small>
<div class="d-none name"><code>mdro.Rd</code></div>
</div>
@@ -196,49 +90,50 @@
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be left blank for automatic determination.</p></dd>
<dt>guideline</dt>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>a specific guideline to follow, see sections <em>Supported international / national guidelines</em> and <em>Using Custom Guidelines</em> below. When left empty, the publication by Magiorakos <em>et al.</em> (see below) will be followed.</p></dd>
<dt>col_mo</dt>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
<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>
<dt>info</dt>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions</p></dd>
<dt>pct_required_classes</dt>
<dt id="arg-pct-required-classes">pct_required_classes<a class="anchor" aria-label="anchor" href="#arg-pct-required-classes"></a></dt>
<dd><p>minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for <em>S. aureus</em>. Setting this <code>pct_required_classes</code> argument to <code>0.5</code> (default) means that for every <em>S. aureus</em> isolate at least 8 different classes must be available. Any lower number of available classes will return <code>NA</code> for that isolate.</p></dd>
<dt>combine_SI</dt>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the <code>mdro()</code> function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using <code>combine_SI = FALSE</code>, resistance is considered when isolates are R or I.</p></dd>
<dt>verbose</dt>
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></dd>
<dt>only_sir_columns</dt>
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>in case of <code>custom_mdro_guideline()</code>: a set of rules, see section <em>Using Custom Guidelines</em> below. Otherwise: column name of an antibiotic, see section <em>Antibiotics</em> below.</p></dd>
<dt>as_factor</dt>
<dt id="arg-as-factor">as_factor<a class="anchor" aria-label="anchor" href="#arg-as-factor"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the returned value should be an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> (<code>TRUE</code>, default), or otherwise a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<ul><li><p>CMI 2012 paper - function <code>mdr_cmi2012()</code> or <code>mdro()</code>:<br>
Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Multi-drug-resistant (MDR)</code> &lt; <code>Extensively drug-resistant (XDR)</code> &lt; <code>Pandrug-resistant (PDR)</code></p></li>
@@ -257,7 +152,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
</div>
<div class="section level2">
<h2 id="supported-international-national-guidelines">Supported International / National Guidelines<a class="anchor" aria-label="anchor" href="#supported-international-national-guidelines"></a></h2>
<p>Currently supported guidelines are (case-insensitive):</p><ul><li><p><code>guideline = "CMI2012"</code> (default)</p>
@@ -279,7 +174,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
</div>
<div class="section level2">
<h2 id="using-custom-guidelines">Using Custom Guidelines<a class="anchor" aria-label="anchor" href="#using-custom-guidelines"></a></h2>
<p>Custom guidelines can be set with the <code>custom_mdro_guideline()</code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
@@ -312,7 +207,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
</div>
<div class="section level2">
<h2 id="antibiotics">Antibiotics<a class="anchor" aria-label="anchor" href="#antibiotics"></a></h2>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href="guess_ab_col.html">guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are eligible for the functions <code><a href="eucast_rules.html">eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href="https://atcddd.fhi.no/atc/structure_and_principles/" class="external-link">ATC code</a>)', sorted alphabetically:</p>
@@ -320,7 +215,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
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<div class="section level2">
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
@@ -380,7 +275,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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@@ -394,9 +289,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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