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(v0.7.1.9035) cephalosporins and unit tests

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dr. M.S. (Matthijs) Berends
2019-08-11 19:07:26 +02:00
parent 3f5828e74a
commit 1d423cca89
38 changed files with 382 additions and 361 deletions
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8
docs/reference/as.rsi.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>
@ -267,7 +267,7 @@
</tr>
<tr>
<th>ab</th>
<td><p>an antibiotic code, generated with <code><a href='as.ab.html'>as.ab</a></code></p></td>
<td><p>an antimicrobial code, generated with <code><a href='as.ab.html'>as.ab</a></code></p></td>
</tr>
<tr>
<th>guideline</th>
@ -279,7 +279,7 @@
</tr>
<tr>
<th>threshold</th>
<td><p>maximum fraction of <code>x</code> that is allowed to fail transformation, see Examples</p></td>
<td><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see Examples</p></td>
</tr>
</table>
@ -290,7 +290,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Run <code><a href='https://www.rdocumentation.org/packages/base/topics/unique'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines.</p>
<p>After using <code>as.rsi</code>, you can use <code><a href='eucast_rules.html'>eucast_rules</a></code> to (1) apply inferred susceptibility and resistance based on results of other antibiotics and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>After using <code>as.rsi</code>, you can use <code><a href='eucast_rules.html'>eucast_rules</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>

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docs/reference/catalogue_of_life.html
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@ -80,7 +80,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>

4
docs/reference/like.html
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@ -80,7 +80,7 @@
</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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>
@ -261,7 +261,7 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/master/R/like.R'><code>like</code> function from the <code>data.table</code> package</a>, but made it case insensitive at default and let it support multiple patterns.</p>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/master/R/like.R'><code>like</code> function from the <code>data.table</code> package</a>, but made it case insensitive at default and let it support multiple patterns. Also, if the regex fails the first time, it tries again with <code>perl = TRUE</code>.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

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docs/reference/microorganisms.codes.html
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@ -80,7 +80,7 @@
</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">0.7.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>

2
docs/reference/microorganisms.html
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@ -80,7 +80,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>

2
docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>

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docs/reference/translate.html
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@ -47,7 +47,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Translate strings from AMR package — translate" />
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_fullname and mo_type." />
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_name, mo_type and ab_name." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
</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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9035</span>
</span>
</div>
@ -230,7 +230,7 @@
<div class="ref-description">
<p>For language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_fullname</a></code> and <code><a href='mo_property.html'>mo_type</a></code>.</p>
<p>For language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_name</a></code>, <code><a href='mo_property.html'>mo_type</a></code> and <code><a href='ab_property.html'>ab_name</a></code>.</p>
</div>
@ -239,9 +239,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
<p>Currently supported languages can be found if running: <code><a href='https://www.rdocumentation.org/packages/base/topics/unique'>unique(AMR:::translations_file$lang)</a></code>.</p>
<p>Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.).</p>
<p>The system language will be used at default, if supported, using <code>get_locale</code>. The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</p>
<p>The system language will be used at default, if that language is supported. The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -256,27 +257,27 @@
<span class='co'># with get_locale()</span>
<span class='co'># English</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"en"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"en"</span>)
<span class='co'>#&gt; "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class='co'># German</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)
<span class='co'>#&gt; "Koagulase-negative Staphylococcus (KNS)"</span>
<span class='co'># Dutch</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
<span class='co'>#&gt; "Coagulase-negatieve Staphylococcus (CNS)"</span>
<span class='co'># Spanish</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>)
<span class='co'>#&gt; "Staphylococcus coagulasa negativo (SCN)"</span>
<span class='co'># Italian</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"it"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"it"</span>)
<span class='co'>#&gt; "Staphylococcus negativo coagulasi (CoNS)"</span>
<span class='co'># Portuguese</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"pt"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"pt"</span>)
<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span>
<span class='co'># }</span></pre>
</div>