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(v0.9.0.9023) EUCAST 2020 guidelines

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dr. M.S. (Matthijs) Berends
2020-02-14 19:54:13 +01:00
parent 5a98e6b777
commit 9b8b02960e
43 changed files with 16588 additions and 14564 deletions
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15
docs/reference/as.rsi.html
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@ -85,7 +85,7 @@
</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">0.9.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
</span>
</div>
@ -273,7 +273,7 @@
</tr>
<tr>
<th>guideline</th>
<td><p>defaults to the latest included EUCAST guideline, run <code><a href='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for all options</p></td>
<td><p>defaults to the latest included EUCAST guideline, run <code><a href='https://rdrr.io/r/base/unique.html'>unique(rsi_translation$guideline)</a></code> for all options</p></td>
</tr>
<tr>
<th>col_mo</th>
@ -290,7 +290,7 @@
<p>Ordered factor with new class <code>rsi</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Run <code><a href='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines. The repository of this package contains <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>this machine readable version</a> of these guidelines.</p>
<p>Run <code><a href='https://rdrr.io/r/base/unique.html'>unique(rsi_translation$guideline)</a></code> for a list of all supported guidelines. The repository of this package contains <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>this machine readable version</a> of these guidelines.</p>
<p>These guidelines are machine readable, since <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'></a>.</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>
@ -335,11 +335,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># interpret MIC values</span>
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMP"</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>4</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>

4
docs/reference/filter_ab_class.html
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@ -85,7 +85,7 @@
</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">0.9.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
</span>
</div>
@ -272,7 +272,7 @@
</tr>
<tr>
<th>ab_class</th>
<td><p>an antimicrobial class, like <code>"carbapenems"</code>, as can be found in <code><a href='antibiotics.html'>AMR::antibiotics$group</a></code></p></td>
<td><p>an antimicrobial class, like <code>"carbapenems"</code>, as can be found in <code><a href='antibiotics.html'>antibiotics$group</a></code></p></td>
</tr>
<tr>
<th>result</th>

2
docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
</span>
</div>

8
docs/reference/like.html
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@ -85,7 +85,7 @@
</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">0.9.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
</span>
</div>
@ -296,15 +296,15 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># also supports multiple patterns, length must be equal to x</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span>)
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( <span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='co'>#&gt; TRUE TRUE TRUE</span>
<span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='no'>mo</span>))</pre>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>))</pre>
</div>
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<h2>Contents</h2>