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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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16
docs/reference/bug_drug_combinations.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">1.3.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9035</span>
</span>
</div>
@ -304,7 +304,7 @@
</tr>
<tr>
<th>remove_intrinsic_resistant</th>
<td><p>logical to indicate that rows with 100% resistance for all tested antimicrobials must be removed from the table</p></td>
<td><p>logical to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table</p></td>
</tr>
<tr>
<th>decimal.mark</th>
@ -348,13 +348,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='kw'>x</span>, translate_ab = <span class='st'>"name (atc)"</span>)
<span class='co'># Use FUN to change to transformation of microorganism codes</span>
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='kw'>mo_gramstain</span>)
<span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='kw'>mo_gramstain</span>)
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>),
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span>))
<span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>),
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span>))
<span class='co'># }</span>
</pre>
</div>