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(v1.7.1.9000) ab_class update, unit tests

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dr. M.S. (Matthijs) Berends
2021-06-04 21:07:55 +02:00
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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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
</span>
</div>
@ -236,9 +236,26 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719000" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9000">
<a href="#amr-1719000" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9000</h1>
<div id="last-updated-4-june-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-4-june-2021" class="anchor"></a><small>Last updated: 4 June 2021</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Added more antibiotic class selectors, such as <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>
</li>
</ul>
</div>
</div>
</div>
<div id="amr-171" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1">
<a href="#amr-171" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1</h1>
<a href="#amr-171" class="anchor"></a><small> 2021-06-03 </small><code>AMR</code> 1.7.1</h1>
<div id="breaking-change" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking-change" class="anchor"></a>Breaking change</h3>
@ -289,9 +306,9 @@
</li>
</ul>
</div>
<div id="changed" class="section level3">
<div id="changed-1" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<a href="#changed-1" class="anchor"></a>Changed</h3>
<ul>
<li>
<code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now supports grouping using the <code>dplyr</code> package</li>
@ -427,9 +444,9 @@
</li>
</ul>
</div>
<div id="changed-1" class="section level3">
<div id="changed-2" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h3>
<a href="#changed-2" class="anchor"></a>Changed</h3>
<ul>
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LPSN</a>)
<ul>
@ -506,9 +523,9 @@
<li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
</ul>
</div>
<div id="changed-2" class="section level3">
<div id="changed-3" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-2" class="anchor"></a>Changed</h3>
<a href="#changed-3" class="anchor"></a>Changed</h3>
<ul>
<li><p>New argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to correct for AmpC de-repressed cephalosporin-resistant mutants</p></li>
<li>
@ -623,9 +640,9 @@
<li><p>Support for skimming classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;mo&gt;</code> with the <code>skimr</code> package</p></li>
</ul>
</div>
<div id="changed-3" class="section level3">
<div id="changed-4" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-3" class="anchor"></a>Changed</h3>
<a href="#changed-4" class="anchor"></a>Changed</h3>
<ul>
<li><p>Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.</p></li>
<li>
@ -728,9 +745,9 @@
<li><p>Added argument <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
</ul>
</div>
<div id="changed-4" class="section level3">
<div id="changed-5" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-4" class="anchor"></a>Changed</h3>
<a href="#changed-5" class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
@ -803,9 +820,9 @@
</li>
</ul>
</div>
<div id="changed-5" class="section level3">
<div id="changed-6" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-5" class="anchor"></a>Changed</h3>
<a href="#changed-6" class="anchor"></a>Changed</h3>
<ul>
<li>Taxonomy:
<ul>
@ -857,9 +874,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
</ul>
</div>
<div id="changed-6" class="section level3">
<div id="changed-7" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-6" class="anchor"></a>Changed</h3>
<a href="#changed-7" class="anchor"></a>Changed</h3>
<ul>
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
<ul>
@ -890,9 +907,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-101" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1">
<a href="#amr-101" class="anchor"></a><small> 2020-02-23 </small><code>AMR</code> 1.0.1</h1>
<div id="changed-7" class="section level3">
<div id="changed-8" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-7" class="anchor"></a>Changed</h3>
<a href="#changed-8" class="anchor"></a>Changed</h3>
<ul>
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
@ -1198,9 +1215,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="changed-8" class="section level3">
<div id="changed-9" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-8" class="anchor"></a>Changed</h3>
<a href="#changed-9" class="anchor"></a>Changed</h3>
<ul>
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
<ul>
@ -1310,9 +1327,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
</ul>
</div>
<div id="changed-9" class="section level4">
<div id="changed-10" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-9" class="anchor"></a>Changed</h4>
<a href="#changed-10" class="anchor"></a>Changed</h4>
<ul>
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li>
@ -1358,9 +1375,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
</ul>
</div>
<div id="changed-10" class="section level4">
<div id="changed-11" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-10" class="anchor"></a>Changed</h4>
<a href="#changed-11" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
@ -1444,9 +1461,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-061" class="section level1">
<h1 class="page-header" data-toc-text="0.6.1">
<a href="#amr-061" class="anchor"></a><small> 2019-03-29 </small><code>AMR</code> 0.6.1</h1>
<div id="changed-11" class="section level4">
<div id="changed-12" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-11" class="anchor"></a>Changed</h4>
<a href="#changed-12" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
</li>
@ -1563,9 +1580,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul>
</div>
<div id="changed-12" class="section level4">
<div id="changed-13" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-12" class="anchor"></a>Changed</h4>
<a href="#changed-13" class="anchor"></a>Changed</h4>
<ul>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
@ -1721,9 +1738,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
</ul>
</div>
<div id="changed-13" class="section level4">
<div id="changed-14" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-13" class="anchor"></a>Changed</h4>
<a href="#changed-14" class="anchor"></a>Changed</h4>
<ul>
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
@ -1911,9 +1928,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
</ul>
</div>
<div id="changed-14" class="section level4">
<div id="changed-15" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-14" class="anchor"></a>Changed</h4>
<a href="#changed-15" class="anchor"></a>Changed</h4>
<ul>
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
@ -2052,9 +2069,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="changed-15" class="section level4">
<div id="changed-16" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-15" class="anchor"></a>Changed</h4>
<a href="#changed-16" class="anchor"></a>Changed</h4>
<ul>
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
<li>More antibiotics added as arguments for EUCAST rules</li>
@ -2137,9 +2154,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
</ul>
</div>
<div id="changed-16" class="section level4">
<div id="changed-17" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-16" class="anchor"></a>Changed</h4>
<a href="#changed-17" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>