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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">2.1.1.9233</small>
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@ -194,14 +194,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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>
<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>
<li><p><strong>R = Resistant</strong><br>
A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p><ul><li><p><em>Exposure</em> is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
</ul></li>
</ul><p>This AMR package honours this insight. Use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
<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 (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>).</p>
<p>This AMR package follows insight; use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@ -263,16 +257,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu">proportion_S</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4022222</span>
<span class="r-in"><span><span class="fu">proportion_SI</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Note that </span><span style="color: #0000BB; background-color: #EEEEEE;">proportion_SI()</span><span style="color: #0000BB;"> will also include dose-dependent</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">susceptibility, 'SDD'. This note will be shown once for this session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4044444</span>
<span class="r-in"><span><span class="fu">proportion_I</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Note that </span><span style="color: #0000BB; background-color: #EEEEEE;">proportion_I()</span><span style="color: #0000BB;"> will also include dose-dependent susceptibility,</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'SDD'. This note will be shown once for this session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002222222</span>
<span class="r-in"><span><span class="fu">proportion_IR</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Note that </span><span style="color: #0000BB; background-color: #EEEEEE;">proportion_IR()</span><span style="color: #0000BB;"> will also include dose-dependent</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">susceptibility, 'SDD'. This note will be shown once for this session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5977778</span>
<span class="r-in"><span><span class="fu">proportion_R</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5955556</span>