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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9139</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9140</small>
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@@ -153,7 +153,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
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<p>For a more automated and comprehensive analysis, consider using <code><a href="antibiogram.html">antibiogram()</a></code> or <code><a href="antibiogram.html">wisca()</a></code>, which streamline many aspects of susceptibility reporting and, importantly, also support WISCA. The functions described here offer a more hands-on, manual approach for greater customisation.</p>
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<p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
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<p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>. Since AMR v3.0, <code>proportion_SI()</code> and <code>proportion_I()</code> include dose-dependent susceptibility ('SDD').</p>
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<p>Use <code>sir_confidence_interval()</code> to calculate the confidence interval, which relies on <code><a href="https://rdrr.io/r/stats/binom.test.html" class="external-link">binom.test()</a></code>, i.e., the Clopper-Pearson method. This function returns a vector of length 2 at default for antimicrobial <em>resistance</em>. Change the <code>side</code> argument to "left"/"min" or "right"/"max" to return a single value, and change the <code>ab_result</code> argument to e.g. <code>c("S", "I")</code> to test for antimicrobial <em>susceptibility</em>, see Examples.</p>
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<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href="count.html">count_*()</a></code> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code><a href="count.html">count_susceptible()</a></code><code>/</code><code><a href="count.html">count_all()</a></code>. <em>Low counts can influence the outcome - the <code>proportion_*()</code> functions may camouflage this, since they only return the proportion (albeit dependent on the <code>minimum</code> argument).</em></p>
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@@ -167,18 +168,18 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
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<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
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<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>
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<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> Drug A Drug B include as include as include as include as</span>
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<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> numerator denominator numerator denominator</span>
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<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="sc">--------</span> <span class="sc">--------</span> <span class="sc">----------</span> <span class="sc">-----------</span> <span class="sc">----------</span> <span class="sc">-----------</span></span>
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<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> S or I S or I X X X X</span>
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<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a> R S or I X X X X</span>
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<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> S or I X X <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a> S or I R X X X X</span>
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<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a> R R <span class="sc">-</span> X <span class="sc">-</span> X</span>
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<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> R <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a> S or I <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> X X <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a> R <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> Drug A Drug B considered considered considered considered</span>
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<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> susceptible tested susceptible tested</span>
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<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="sc">--------</span> <span class="sc">--------</span> <span class="sc">-----------</span> <span class="sc">----------</span> <span class="sc">-----------</span> <span class="sc">----------</span></span>
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<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> S or I S or I X X X X</span>
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<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a> R S or I X X X X</span>
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<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> S or I X X <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a> S or I R X X X X</span>
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<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a> R R <span class="sc">-</span> X <span class="sc">-</span> X</span>
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<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> R <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a> S or I <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> X X <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a> R <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
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<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span></code></pre><p></p></div>
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<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p>
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<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">count_S</span>() <span class="sc">+</span> <span class="fu">count_I</span>() <span class="sc">+</span> <span class="fu">count_R</span>() <span class="ot">=</span> <span class="fu">count_all</span>()</span>
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