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(v1.4.0.9000) more extensive unit tests

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dr. M.S. (Matthijs) Berends
2020-10-15 09:46:41 +02:00
parent 28e77680c5
commit 833a1be36d
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32
docs/reference/as.disk.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
</span>
</div>
@ -242,9 +242,9 @@
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<pre class="usage"><span class='fu'>as.disk</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>is.disk</span>(<span class='kw'>x</span>)</pre>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -284,23 +284,23 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='co'># transform existing disk zones to the `disk` class</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(microorganism = <span class='st'>"E. coli"</span>,
AMP = <span class='fl'>20</span>,
CIP = <span class='fl'>14</span>,
GEN = <span class='fl'>18</span>,
TOB = <span class='fl'>16</span>)
<span class='kw'>df</span>[, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span>] <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='kw'>df</span>[, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span>], <span class='kw'>as.disk</span>)
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://dplyr.tidyverse.org'>dplyr</a></span><span class='op'>)</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
AMP <span class='op'>=</span> <span class='fl'>20</span>,
CIP <span class='op'>=</span> <span class='fl'>14</span>,
GEN <span class='op'>=</span> <span class='fl'>18</span>,
TOB <span class='op'>=</span> <span class='fl'>16</span><span class='op'>)</span>
<span class='va'>df</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span>, <span class='va'>as.disk</span><span class='op'>)</span>
<span class='co'># same with dplyr:</span>
<span class='co'># df %&gt;% mutate(across(AMP:TOB, as.disk))</span>
<span class='co'># interpret disk values, see ?as.rsi</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(x = <span class='fu'>as.disk</span>(<span class='fl'>18</span>),
mo = <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
ab = <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.disk</span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
mo <span class='op'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
ab <span class='op'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>df</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
</div>
@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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