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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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10
docs/reference/as.ab.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">1.5.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
</span>
</div>
@ -347,6 +347,14 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='co'># they use as.ab() internally:</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01FA01"</span><span class='op'>)</span> <span class='co'># "Erythromycin"</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"eryt"</span><span class='op'>)</span> <span class='co'># "Erythromycin"</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># you can quickly rename &lt;rsi&gt; columns using dplyr &gt;= 1.0.0:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/rename.html'>rename_with</a></span><span class='op'>(</span><span class='va'>as.ab</span>, <span class='fu'>where</span><span class='op'>(</span><span class='va'>is.rsi</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

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docs/reference/as.rsi.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">1.5.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
</span>
</div>
@ -363,7 +363,7 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported guidelines</h3>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020", "EUCAST 2021".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After interpretation</h3>
@ -374,7 +374,7 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine readable interpretation guidelines</h3>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 20,486 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>

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docs/reference/dosage.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">1.5.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
</span>
</div>
@ -252,7 +252,7 @@
<li><p><code>name</code><br /> Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>type</code><br /> Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"</p></li>
<li><p><code>dose</code><br /> Dose, such as "2 g" or "25 mg/kg"</p></li>
<li><p><code>dose_times</code><br /> Dose, such as "2 g" or "25 mg/kg"</p></li>
<li><p><code>dose_times</code><br /> Number of times a dose must be administered</p></li>
<li><p><code>administration</code><br /> Route of administration, either "im", "iv" or "oral"</p></li>
<li><p><code>notes</code><br /> Additional dosage notes</p></li>
<li><p><code>original_txt</code><br /> Original text in the PDF file of EUCAST</p></li>

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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>

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docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.5.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
</span>
</div>

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docs/reference/rsi_translation.html
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@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Data set for R/SI interpretation — rsi_translation" />
<meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
<meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
<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">1.5.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
</span>
</div>
@ -239,7 +239,7 @@
</div>
<div class="ref-description">
<p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
<p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<pre class="usage"><span class='va'>rsi_translation</span></pre>
@ -247,7 +247,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 18,650 observations and 10 variables:</p><ul>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 20,486 observations and 10 variables:</p><ul>
<li><p><code>guideline</code><br /> Name of the guideline</p></li>
<li><p><code>method</code><br /> Either "MIC" or "DISK"</p></li>
<li><p><code>site</code><br /> Body site, e.g. "Oral" or "Respiratory"</p></li>