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fix warnings

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dr. M.S. (Matthijs) Berends
2019-01-04 09:49:42 +01:00
parent 80ea555663
commit 6652f7d82b
31 changed files with 948 additions and 762 deletions
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docs/reference/eucast_rules.html
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@ -222,22 +222,27 @@
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>amik</span> <span class='kw'>=</span> <span class='st'>"amik"</span>, <span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='st'>"ampi"</span>,
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='st'>"azit"</span>, <span class='kw'>azlo</span> <span class='kw'>=</span> <span class='st'>"azlo"</span>, <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='st'>"aztr"</span>, <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='st'>"cefa"</span>,
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='st'>"cfep"</span>, <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>, <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"cfox"</span>, <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='st'>"cfra"</span>,
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='st'>"cftr"</span>, <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='st'>"chlo"</span>,
<span class='kw'>cipr</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>clar</span> <span class='kw'>=</span> <span class='st'>"clar"</span>, <span class='kw'>clin</span> <span class='kw'>=</span> <span class='st'>"clin"</span>, <span class='kw'>clox</span> <span class='kw'>=</span> <span class='st'>"clox"</span>,
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>czol</span> <span class='kw'>=</span> <span class='st'>"czol"</span>, <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='st'>"dapt"</span>, <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='st'>"doxy"</span>,
<span class='kw'>erta</span> <span class='kw'>=</span> <span class='st'>"erta"</span>, <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>, <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='st'>"fosf"</span>, <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='st'>"fusi"</span>,
<span class='kw'>gent</span> <span class='kw'>=</span> <span class='st'>"gent"</span>, <span class='kw'>imip</span> <span class='kw'>=</span> <span class='st'>"imip"</span>, <span class='kw'>kana</span> <span class='kw'>=</span> <span class='st'>"kana"</span>, <span class='kw'>levo</span> <span class='kw'>=</span> <span class='st'>"levo"</span>,
<span class='kw'>linc</span> <span class='kw'>=</span> <span class='st'>"linc"</span>, <span class='kw'>line</span> <span class='kw'>=</span> <span class='st'>"line"</span>, <span class='kw'>mero</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>mezl</span> <span class='kw'>=</span> <span class='st'>"mezl"</span>,
<span class='kw'>mino</span> <span class='kw'>=</span> <span class='st'>"mino"</span>, <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='st'>"moxi"</span>, <span class='kw'>nali</span> <span class='kw'>=</span> <span class='st'>"nali"</span>, <span class='kw'>neom</span> <span class='kw'>=</span> <span class='st'>"neom"</span>,
<span class='kw'>neti</span> <span class='kw'>=</span> <span class='st'>"neti"</span>, <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='st'>"nitr"</span>, <span class='kw'>norf</span> <span class='kw'>=</span> <span class='st'>"norf"</span>, <span class='kw'>novo</span> <span class='kw'>=</span> <span class='st'>"novo"</span>,
<span class='kw'>oflo</span> <span class='kw'>=</span> <span class='st'>"oflo"</span>, <span class='kw'>oxac</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"peni"</span>, <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='st'>"pipe"</span>,
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='st'>"pita"</span>, <span class='kw'>poly</span> <span class='kw'>=</span> <span class='st'>"poly"</span>, <span class='kw'>pris</span> <span class='kw'>=</span> <span class='st'>"pris"</span>, <span class='kw'>qida</span> <span class='kw'>=</span> <span class='st'>"qida"</span>,
<span class='kw'>rifa</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='st'>"roxi"</span>, <span class='kw'>siso</span> <span class='kw'>=</span> <span class='st'>"siso"</span>, <span class='kw'>teic</span> <span class='kw'>=</span> <span class='st'>"teic"</span>,
<span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>tica</span> <span class='kw'>=</span> <span class='st'>"tica"</span>, <span class='kw'>tige</span> <span class='kw'>=</span> <span class='st'>"tige"</span>, <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>,
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='st'>"trim"</span>, <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>)
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>azlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>mezl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>oxac</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>pris</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>())
<span class='fu'>EUCAST_rules</span>(<span class='no'>...</span>)
@ -295,7 +300,7 @@
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
<p>To define antibiotics column names, input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab.html'>guess_ab</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>),