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(v1.7.1.9022) rely on vctrs for ab selectors

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dr. M.S. (Matthijs) Berends
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@ -56,6 +56,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -67,9 +69,15 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -83,7 +91,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -91,14 +99,14 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -107,77 +115,77 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -186,14 +194,14 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -216,7 +224,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -244,7 +252,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
</div>
<pre class="usage"><span class='fu'>resistance</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>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>resistance</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 class='fu'>susceptibility</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>
@ -276,7 +284,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -335,7 +343,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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>susceptibility()</code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
<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>susceptibility()</code> works to calculate the %SI:</p><pre><code>--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
@ -351,15 +359,15 @@ resistance() should be used to calculate resistance, susceptibility() should be
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</pre>
</code></pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@ -393,7 +401,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<div class='dont-index'><p><code><a href='count.html'>count()</a></code> to count resistant and susceptible isolates.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># example_isolates is a data set available in the AMR package.</span>
<span class='op'>?</span><span class='va'>example_isolates</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 class='co'># determines %R</span>
@ -466,7 +474,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>proportion_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
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@ -478,11 +486,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@ -491,6 +499,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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