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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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14
docs/reference/antibiotic_class_selectors.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Antibiotic class selectors — antibiotic_class_selectors" />
<meta property="og:description" content="Use these selection helpers inside any function that allows Tidyverse selection helpers, like dplyr::select() or tidyr::pivot_longer(). They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -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">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9035</span>
</span>
</div>
@ -298,8 +298,7 @@
<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</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>)
<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
@ -322,11 +321,12 @@
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>()
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(irrelevant = <span class='st'>"value"</span>,
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(some_column = <span class='st'>"some_value"</span>,
J01CA01 = <span class='st'>"S"</span>) <span class='op'>%&gt;%</span> <span class='co'># ATC code of ampicillin</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>()) <span class='co'># the 'J01CA01' column will be selected</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>()) <span class='co'># only the 'J01CA01' column will be selected</span>
}</pre>
}
</pre>
</div>
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