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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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docs/news/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">1.3.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span>
</span>
</div>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309021" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9021">
<a href="#amr-1309021" class="anchor"></a>AMR 1.3.0.9021<small> Unreleased </small>
<div id="amr-1309022" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9022">
<a href="#amr-1309022" class="anchor"></a>AMR 1.3.0.9022<small> Unreleased </small>
</h1>
<div id="last-updated-14-september-2020" class="section level2">
<div id="last-updated-18-september-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-14-september-2020" class="anchor"></a><small>Last updated: 14 September 2020</small>
<a href="#last-updated-18-september-2020" class="anchor"></a><small>Last updated: 18 September 2020</small>
</h2>
<p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
<div id="new" class="section level3">
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<span class="co">#&gt; [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span>
</pre></div>
</li>
<li><p>Support for veterinary ATC codes</p></li>
</ul>
</div>
<div id="changed" class="section level3">
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</li>
<li><p>Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.</p></li>
<li><p>Added parameter ‘add_intrinsic_resistance’ (defaults to <code>FALSE</code>), that considers intrinsic resistance according to EUCAST</p></li>
<li><p>Fixed a bug where in EUCAST rules the breakpoint for R would be interpreted as “&gt;=” while this should have been “&lt;”</p></li>
</ul>
</li>
<li>
@ -299,7 +301,7 @@
<li>
<p>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</p>
<ul>
<li>Any user input value that could mean more than one taxonomic entry is now considered ‘uncertain’. Instead of a warning, a message will be thrown and the accompanying <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> has been changed completely; it now prints all possible candidates with their matching score.</li>
<li>A completely new matching score for ambiguous user input, using <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code>. Any user input value that could mean more than one taxonomic entry is now considered ‘uncertain’. Instead of a warning, a message will be thrown and the accompanying <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> has been changed completely; it now prints all possible candidates with their matching score.</li>
<li>Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using <code>mo_*</code> functions like <code><a href="../reference/mo_property.html">mo_name()</a></code> on microoganism IDs.</li>
<li>Added parameter <code>ignore_pattern</code> to <code><a href="../reference/as.mo.html">as.mo()</a></code> which can also be given to <code>mo_*</code> functions like <code><a href="../reference/mo_property.html">mo_name()</a></code>, to exclude known non-relevant input from analysing. This can also be set with the option <code>AMR_ignore_pattern</code>.</li>
</ul>
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<li><p>Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: <code>tibble</code> printing support for classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and <code>&lt;mo&gt;</code>. When using <code>tibble</code>s containing antimicrobial columns (class <code>&lt;rsi&gt;</code>), “S” will print in green, “I” will print in yellow and “R” will print in red. Microbial IDs (class <code>&lt;mo&gt;</code>) will emphasise on the genus and species, not on the kingdom.</p></li>
<li><p>Names of antiviral agents in data set <code>antivirals</code> now have a starting capital letter, like it is the case in the <code>antibiotics</code> data set</p></li>
<li><p>Updated the documentation of the <code>WHONET</code> data set to clarify that all patient names are fictitious</p></li>
<li><p>Small <code><a href="../reference/as.ab.html">as.ab()</a></code> algorithm improvements</p></li>
<li><p>Fix for combining MIC values with raw numbers, i.e. <code><a href="https://rdrr.io/r/base/c.html">c(as.mic(2), 2)</a></code> previously failed but now returns a valid MIC class</p></li>
<li><p><code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> and <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code> gained parameters <code>minimum</code> and <code>language</code>, to influence the internal use of <code><a href="../reference/proportion.html">rsi_df()</a></code></p></li>
<li><p>Added abbreviation “piptazo” to piperacillin/tazobactam (TZP)</p></li>
</ul>
</div>
<div id="other" class="section level3">