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(v1.5.0.9001) more informative argument errors

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dr. M.S. (Matthijs) Berends
2021-01-14 14:41:44 +01:00
parent d014955ce0
commit bc00470dca
30 changed files with 126 additions and 74 deletions
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12
docs/reference/eucast_rules.html
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@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
<meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://eucast.org), see Source. Use eucast_dosage() to get advised dosages of a certain bug-drug combination, which is based on the dosage data set.
<meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://eucast.org), see Source. Use eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the dosage data set.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.5.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
</span>
</div>
@ -240,7 +240,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</div>
<div class="ref-description">
<p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='https://eucast.org'>https://eucast.org</a>), see <em>Source</em>. Use <code>eucast_dosage()</code> to get advised dosages of a certain bug-drug combination, which is based on the <a href='dosage.html'>dosage</a> data set.</p>
<p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='https://eucast.org'>https://eucast.org</a>), see <em>Source</em>. Use <code>eucast_dosage()</code> to get a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with advised dosages of a certain bug-drug combination, which is based on the <a href='dosage.html'>dosage</a> data set.</p>
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.</p>
</div>
@ -250,7 +250,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
rules <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_eucastrules"</span>, default <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span><span class='op'>)</span><span class='op'>)</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
version_breakpoints <span class='op'>=</span> <span class='fl'>10</span>,
version_breakpoints <span class='op'>=</span> <span class='fl'>11</span>,
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</span>,
<span class='va'>...</span>
@ -283,11 +283,11 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</tr>
<tr>
<th>version_breakpoints</th>
<td><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Currently supported: 11.0, 10.0.</p></td>
<td><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".</p></td>
</tr>
<tr>
<th>version_expertrules</th>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: 3.1, 3.2.</p></td>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".</p></td>
</tr>
<tr>
<th>ampc_cephalosporin_resistance</th>