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(v1.8.1.9011) update prevalence of some genera

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dr. M.S. (Matthijs) Berends
2022-06-03 12:43:25 +02:00
parent 70a07bad39
commit 1b84564d36
35 changed files with 278 additions and 429 deletions
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docs/reference/count.html
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@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
</span>
</div>
@ -243,30 +243,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<h2>Combination Therapy</h2>
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p><div class="sourceCode"><pre><code>--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
numerator denominator numerator denominator
-------- -------- ---------- ----------- ---------- -----------
S or I S or I X X X X
R S or I X X X X
&lt;NA&gt; S or I X X - -
S or I R X X X X
R R - X - X
&lt;NA&gt; R - - - -
S or I &lt;NA&gt; X X - -
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</code></pre></div>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/count.html">count_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/count.html">count_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/count.html">count_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="../reference/count.html">count_all</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu"><a href="../reference/proportion.html">proportion_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">=</span> <span class="fl">1</span></code></pre></div>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><div class="sourceCode"><pre><code><span class="fu"><a href="../reference/count.html">count_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/count.html">count_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/count.html">count_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&gt;=</span> <span class="fu"><a href="../reference/count.html">count_all</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu"><a href="../reference/proportion.html">proportion_S</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_I</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="../reference/proportion.html">proportion_R</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&gt;=</span> <span class="fl">1</span></code></pre></div>
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p>
<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p>
<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
</div>
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