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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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11
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">1.3.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9035</span>
</span>
</div>
@ -282,7 +282,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></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>) {
<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>,
@ -290,8 +290,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.disk</span>)
<span class='kw'>df</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='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>),
@ -300,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>df</span>)
}
<span class='co'># }</span>
</pre>
</div>
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