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reference/mdro.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9028</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -321,7 +321,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<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>
<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>
<li><p><strong>I - Susceptible, increased exposure</strong> <em><br>
A microorganism is categorised as "Susceptible, Increased exposure</em>" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
@ -334,13 +334,11 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (16 isolates had no test results)</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Ord.factor w/ 3 levels "Negative"&lt;"Positive, unconfirmed"&lt;..: 1 1 1 1 1 1 1 1 1 1 ...</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'out' not found</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> out</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Positive, unconfirmed Positive </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1978 0 6 </span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'out' not found</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu">custom_mdro_guideline</span><span class="op">(</span></span></span>
@ -348,10 +346,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> <span class="va">VAN</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 2"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> out</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Custom MDRO 1 Custom MDRO 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 870 804 326 </span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'out' not found</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -365,20 +362,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">MDRO</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (16 isolates had no test results)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in mdro(): NA introduced for isolates where the available percentage of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with pct_required_classes)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (16 isolates had no test results)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `MDRO = mdro()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in mdro(): NA introduced for isolates where the available percentage of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with pct_required_classes)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Multi-drug-resistant (MDR) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1601 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Extensively drug-resistant (XDR) Pandrug-resistant (PDR) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 </span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>