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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -162,7 +162,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
<span> as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> confidence_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
<span> side <span class="op">=</span> <span class="st">"both"</span></span>
<span> side <span class="op">=</span> <span class="st">"both"</span>,</span>
<span> collapse <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">proportion_R</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
@ -230,6 +231,10 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dd><p>the side of the confidence interval to return. The default is <code>"both"</code> for a length 2 vector, but can also be (abbreviated as) <code>"min"</code>/<code>"left"</code>/<code>"lower"</code>/<code>"less"</code> or <code>"max"</code>/<code>"right"</code>/<code>"higher"</code>/<code>"greater"</code>.</p></dd>
<dt>collapse</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing</p></dd>
<dt>data</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
@ -339,11 +344,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu">resistance</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5955556</span>
<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5688204 0.6218738</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.569 0.622</span>
<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5650148 0.6255670</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.565 0.626</span>
<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</span>,</span></span>
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">", "</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> [1] "0.565, 0.626"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># determines %S+I:</span></span></span>
<span class="r-in"><span><span class="fu">susceptibility</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
@ -351,7 +361,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
<span class="r-in"><span> ab_result <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</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> [1] 0.3781262 0.4311796</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.378 0.431</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># be more specific</span></span></span>
<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>
@ -393,9 +403,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward cipro_R ci_min ci_max</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 0.147 0.124 0.173</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 0.190 0.155 0.230</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.161 0.093<span style="text-decoration: underline;">2</span> 0.252</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 0.147 0.124 0.173</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 0.190 0.155 0.23 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.161 0.093 0.252</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>
<span class="r-in"><span> <span class="co"># scoped dplyr verbs with antibiotic selectors</span></span></span>
<span class="r-in"><span> <span class="co"># (you could also use across() of course)</span></span></span>