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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9056</span>
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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Get properties of an antibiotic
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<h1 data-toc-skip>Changelog <small></small></h1>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<div id="amr-1719056" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9056">
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<a href="#amr-1719056" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9056</h1>
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<div id="last-updated-29-november-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-29-november-2021" class="anchor"></a><small>Last updated: 29 November 2021</small>
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</h2>
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<div id="breaking-changes" class="section level3">
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<h3 class="hasAnchor">
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<a href="#breaking-changes" class="anchor"></a>Breaking changes</h3>
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<ul>
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<li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
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<li>Removed the <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> functions, which were deprecated and superseded by <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><a href="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code>
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</li>
|
||
<li>Removed all previously implemented <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot2::ggplot()</a></code> generics for classes <code><mic></code>, <code><disk></code>, <code><rsi></code> and <code><resistance_predict></code> as they did not follow the <code>ggplot2</code> logic. They were replaced with <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">ggplot2::autoplot()</a></code> generics.</li>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li>Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function. This is now the default guideline (all other guidelines are still available).</li>
|
||
<li>Function <code><a href="../reference/ab_property.html">set_ab_names()</a></code> to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc.</li>
|
||
<li>Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese</li>
|
||
</ul>
|
||
</div>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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||
<a href="#changed" class="anchor"></a>Changed</h3>
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||
<ul>
|
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<li>Updated the bacterial taxonomy to 5 October 2021 (according to <a href="https://lpsn.dsmz.de">LPSN</a>), including all 11 new staphylococcal species named since 1 January last year</li>
|
||
<li>The <code>antibiotics</code> data set now contains <strong>all ATC codes</strong> that are available through the <a href="https://www.whocc.no">WHOCC website</a>, regardless of drugs being present in more than one ATC group. This means that:
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<ul>
|
||
<li>Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)</li>
|
||
<li>
|
||
<code>antibiotics$atc</code> is now a <code>list</code> containing <code>character</code> vectors, and this <code>atc</code> column was moved to the 5th position of the <code>antibiotics</code> data set</li>
|
||
<li>
|
||
<code><a href="../reference/ab_property.html">ab_atc()</a></code> does not always return a character vector of length 1, and returns a <code>list</code> if the input is larger than length 1</li>
|
||
<li>
|
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<code><a href="../reference/ab_property.html">ab_info()</a></code> has a slightly different output</li>
|
||
<li>Some DDDs (daily defined doses) were added or updated according to newly included ATC codes</li>
|
||
</ul>
|
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</li>
|
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<li>Antibiotic selectors
|
||
<ul>
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<li><p>They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package</p></li>
|
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<li><p>Added more selectors for antibiotic classes: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">antifungals()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">antimycobacterials()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">trimethoprims()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code></p></li>
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<li>
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||
<p>Added specific selectors for certain types for treatment: <code><a href="../reference/antibiotic_class_selectors.html">administrable_per_os()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">administrable_iv()</a></code>, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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||
<code class="sourceCode R">
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<span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">administrable_per_os</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span> <span class="co"># base R</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">administrable_per_os</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
|
||
</li>
|
||
<li>
|
||
<p>Added the selector <code><a href="../reference/antibiotic_class_selectors.html">ab_selector()</a></code>, which accepts a filter to be used internally on the <code>antibiotics</code> data set, yielding great flexibility on drug properties, such as selecting antibiotic columns with an oral DDD of at least 1 gram:</p>
|
||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">ab_selector</a></span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">></span> <span class="fl">1</span> <span class="op">&</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span> <span class="co"># base R</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">ab_selector</a></span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">></span> <span class="fl">1</span> <span class="op">&</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
|
||
</li>
|
||
<li><p>Fix for using selectors multiple times in one call (e.g., using them in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>)</p></li>
|
||
<li><p>Added argument <code>only_treatable</code>, which defaults to <code>TRUE</code> and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)</p></li>
|
||
</ul>
|
||
</li>
|
||
<li>Fixed the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as <em>Negativicoccus</em> and <em>Veillonella</em>.</li>
|
||
<li>Dramatic speed improvement for <code><a href="../reference/first_isolate.html">first_isolate()</a></code>
|
||
</li>
|
||
<li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
|
||
<li>Added more informative error messages when any of the <code>proportion_*()</code> and <code>count_*()</code> functions fail</li>
|
||
<li>When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using <code><a href="../reference/as.mo.html">as.mo()</a></code>
|
||
</li>
|
||
<li>Improved automatic column selector when <code>col_*</code> arguments are left blank, e.g. in <code><a href="../reference/first_isolate.html">first_isolate()</a></code>
|
||
</li>
|
||
<li>The right input types for <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> are now enforced</li>
|
||
<li>
|
||
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> has an improved algorithm and can now also correct for textual input (such as “Susceptible”, “Resistant”) in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish</li>
|
||
<li>
|
||
<code><a href="../reference/as.mic.html">as.mic()</a></code> has an improved algorithm</li>
|
||
<li>When warnings are thrown because of too few isolates in any <code>count_*()</code>, <code>proportion_*()</code> function (or <code>resistant()</code> or <code>susceptible()</code>), the <code>dplyr</code> group will be shown, if available</li>
|
||
<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)</li>
|
||
<li>Fix for minor translation errors</li>
|
||
<li>Fix for the MIC interpretation of <em>Morganellaceae</em> (such as <em>Morganella</em> and <em>Proteus</em>) when using the EUCAST 2021 guideline</li>
|
||
<li>Improved algorithm for generating random MICs with <code><a href="../reference/random.html">random_mic()</a></code>
|
||
</li>
|
||
<li>Improved plot legends for MICs and disk diffusion values</li>
|
||
<li>Improved speed of <code><a href="../reference/as.ab.html">as.ab()</a></code> and all <code>ab_*()</code> functions</li>
|
||
<li>Added <code>fortify()</code> extensions for plotting methods</li>
|
||
<li>
|
||
<code>NA</code> values of the classes <code><mic></code>, <code><disk></code> and <code><rsi></code> are now exported objects of this package, e.g. <code>NA_mic_</code> is an <code>NA</code> of class <code>mic</code> (just like the base R <code>NA_character_</code> is an <code>NA</code> of class <code>character</code>)</li>
|
||
<li>The <code><a href="../reference/proportion.html">proportion_df()</a></code>, <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/proportion.html">rsi_df()</a></code> functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packages</li>
|
||
<li>The <code><a href="../reference/mdro.html">mdro()</a></code> function now returns <code>NA</code> for all rows that have no test results</li>
|
||
<li>The <code>species_id</code> column in the <code>microorganisms</code> data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and <code><a href="../reference/mo_property.html">mo_url()</a></code> has been updated to reflect this change.</li>
|
||
<li>Fixed a small bug in the functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="other" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.</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>AMR 1.7.1<small> 2021-06-03 </small>
|
||
</h1>
|
||
<div id="breaking-change" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#breaking-change" class="anchor"></a>Breaking change</h3>
|
||
<ul>
|
||
<li>
|
||
<p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code>filter_carbapenems()</code>, <code>filter_aminoglycosides()</code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
|
||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="co"># select columns with results for carbapenems</span>
|
||
<span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span> <span class="co"># base R</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span>
|
||
|
||
<span class="co"># filter rows for resistance in any carbapenem</span>
|
||
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span> <span class="co"># base R</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">if_any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>, <span class="op">~</span><span class="va">.x</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr (formal)</span>
|
||
|
||
<span class="co"># filter rows for resistance in all carbapenems</span>
|
||
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span> <span class="co"># base R</span>
|
||
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span>, <span class="op">]</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></code></pre></div>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="new-1" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-1" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
|
||
<li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
|
||
</li>
|
||
<li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>
|
||
<li>Support for all four methods to determine first isolates as summarised by Hindler <em>et al.</em> (doi: <a href="https://doi.org/10.1086/511864">10.1086/511864</a>): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
|
||
<ul>
|
||
<li>The <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function gained the argument <code>method</code> that has to be “phenotype-based”, “episode-based”, “patient-based”, or “isolate-based”. The old behaviour is equal to “episode-based”. The new default is “phenotype-based” if antimicrobial test results are available, and “episode-based” otherwise. This new default will yield slightly more isolates for selection (which is a good thing).</li>
|
||
<li>Since fungal isolates can also be selected, the functions <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> are now deprecated in favour of the <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><a href="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code> functions. Also, the new <code><a href="../reference/key_antimicrobials.html">all_antimicrobials()</a></code> function works like the old <code>key_antibiotics()</code> function, but includes any column with antimicrobial test results. Using <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new <code>antifungal</code> argument to set antifungal agents (antimycotics).</li>
|
||
<li>Using <code>type == "points"</code> in the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the new <code><a href="../reference/key_antimicrobials.html">all_antimicrobials()</a></code>
|
||
</li>
|
||
<li>The <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function can now take a vector of values for <code>col_keyantibiotics</code> and can have an episode length of <code>Inf</code>
|
||
</li>
|
||
<li>Since the phenotype-based method is the new default, <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> renders the <code>filter_first_weighted_isolate()</code> function redundant. For this reason, <code>filter_first_weighted_isolate()</code> is now deprecated.</li>
|
||
<li>The documentation of the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> functions has been completely rewritten.</li>
|
||
</ul>
|
||
</li>
|
||
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code>filter_betalactams()</code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
|
||
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="changed-1" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<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>
|
||
<li>Custom MDRO guidelines (<code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code>):
|
||
<ul>
|
||
<li>Custom MDRO guidelines can now be combined with other custom MDRO guidelines using <code><a href="https://rdrr.io/r/base/c.html">c()</a></code>
|
||
</li>
|
||
<li>Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule</li>
|
||
</ul>
|
||
</li>
|
||
<li>Fix for <code><a href="../reference/age_groups.html">age_groups()</a></code> for persons aged zero</li>
|
||
<li>The <code>example_isolates</code> data set now contains some (fictitious) zero-year old patients</li>
|
||
<li>Fix for minor translation errors</li>
|
||
<li>Printing of microbial codes in a <code>data.frame</code> or <code>tibble</code> now gives a warning if the data contains old microbial codes (from a previous AMR package version)</li>
|
||
<li>Extended the <code><a href="../reference/like.html">like()</a></code> functions:
|
||
<ul>
|
||
<li><p>Now checks if <code>pattern</code> is a <em>valid</em> regular expression</p></li>
|
||
<li>
|
||
<p>Added <code><a href="../reference/like.html">%unlike%</a></code> and <code><a href="../reference/like.html">%unlike_case%</a></code> (as negations of the existing <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>). This greatly improves readability:</p>
|
||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html">grepl</a></span><span class="op">(</span><span class="st">"EUCAST"</span>, <span class="va">guideline</span><span class="op">)</span><span class="op">)</span> <span class="va">...</span>
|
||
<span class="co"># same:</span>
|
||
<span class="kw">if</span> <span class="op">(</span><span class="va">guideline</span> <span class="op">%unlike%</span> <span class="st">"EUCAST"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
|
||
</li>
|
||
<li><p>Altered the RStudio addin, so it now iterates over <code><a href="../reference/like.html">%like%</a></code> -> <code><a href="../reference/like.html">%unlike%</a></code> -> <code><a href="../reference/like.html">%like_case%</a></code> -> <code><a href="../reference/like.html">%unlike_case%</a></code> if you keep pressing your keyboard shortcut</p></li>
|
||
</ul>
|
||
</li>
|
||
<li>Fixed an installation error on R-3.0</li>
|
||
<li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li>
|
||
<li>Fixed a bug where <code>col_mo</code> in some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be a column name of the <code>microorganisms</code> data set as it would throw an error</li>
|
||
<li>Fix for transforming numeric values to RSI (<code><a href="../reference/as.rsi.html">as.rsi()</a></code>) when the <code>vctrs</code> package is loaded (i.e., when using tidyverse)</li>
|
||
<li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> on an RSI class</li>
|
||
<li>Added 25 common system codes for bacteria to the <code>microorganisms.codes</code> data set</li>
|
||
<li>Added 16 common system codes for antimicrobial agents to the <code>antibiotics</code> data set</li>
|
||
<li>Fix for using <code><a href="https://docs.ropensci.org/skimr/reference/skim.html">skimr::skim()</a></code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
|
||
<li>Updated <code><a href="https://docs.ropensci.org/skimr/reference/skim.html">skimr::skim()</a></code> usage for MIC values to also include 25th and 75th percentiles</li>
|
||
<li>Fix for plotting missing MIC/disk diffusion values</li>
|
||
<li>Updated join functions to always use <code>dplyr</code> join functions if the <code>dplyr</code> package is installed - now also preserving grouped variables</li>
|
||
<li>Antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>) now maintain the column order from the original data</li>
|
||
<li>Fix for selecting columns using <code><a href="../reference/antibiotic_class_selectors.html">fluoroquinolones()</a></code>
|
||
</li>
|
||
<li>
|
||
<code><a href="../reference/age.html">age()</a></code> now vectorises over both <code>x</code> and <code>reference</code>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-1" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-1" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package</li>
|
||
<li>All unit tests are now processed by the <code>tinytest</code> package, instead of the <code>testthat</code> package. The <code>testthat</code> package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the <code>tinytest</code> package is very lightweight and dependency-free.</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-160" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.6.0">
|
||
<a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> 2021-03-14 </small>
|
||
</h1>
|
||
<div id="new-2" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-2" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li>
|
||
<p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p>
|
||
<ul>
|
||
<li>Added function <code><a href="../reference/eucast_rules.html">eucast_dosage()</a></code> to get a <code>data.frame</code> with advised dosages of a certain bug-drug combination, which is based on the new <code>dosage</code> data set</li>
|
||
<li>Added data set <code>dosage</code> to fuel the new <code><a href="../reference/eucast_rules.html">eucast_dosage()</a></code> function and to make this data available in a structured way</li>
|
||
<li>Existing data set <code>example_isolates</code> now reflects the latest EUCAST rules</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>Added argument <code>only_rsi_columns</code> for some functions, which defaults to <code>FALSE</code>, to indicate if the functions must only be applied to columns that are of class <code><rsi></code> (i.e., transformed with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:</p>
|
||
<ul>
|
||
<li>All antibiotic selector functions (<code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code> and its wrappers, such as <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code>)</li>
|
||
<li>All antibiotic filter functions (<code>filter_ab_class()</code> and its wrappers, such as <code>filter_aminoglycosides()</code>, <code>filter_carbapenems()</code>, <code>filter_penicillins()</code>)</li>
|
||
<li><code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></li>
|
||
<li>
|
||
<code><a href="../reference/mdro.html">mdro()</a></code> (including wrappers such as <code><a href="../reference/mdro.html">brmo()</a></code>, <code><a href="../reference/mdro.html">mrgn()</a></code> and <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>)</li>
|
||
<li><code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code></li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>Functions <code><a href="../reference/antibiotic_class_selectors.html">oxazolidinones()</a></code> (an antibiotic selector function) and <code>filter_oxazolidinones()</code> (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid</p>
|
||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||
<span class="va">x</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="va">hospital_id</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">oxazolidinones</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="co">#> Selecting oxazolidinones: column 'LNZ' (linezolid)</span>
|
||
|
||
<span class="va">x</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu">filter_oxazolidinones</span><span class="op">(</span><span class="op">)</span>
|
||
<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
|
||
</li>
|
||
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
|
||
<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
|
||
<li>
|
||
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
|
||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><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">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="co">#> [1] "Fungi" "Fungi"</span>
|
||
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_is_yeast</a></span><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">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="co">#> [1] FALSE TRUE</span>
|
||
|
||
<span class="co"># usage for filtering data:</span>
|
||
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_yeast</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span> <span class="co"># base R</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_yeast</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
|
||
<p>The <code><a href="../reference/mo_property.html">mo_type()</a></code> function has also been updated to reflect this change:</p>
|
||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_type</a></span><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">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="co"># [1] "Fungi" "Yeasts"</span>
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_type</a></span><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">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># also supported: de, nl, fr, it, pt</span>
|
||
<span class="co">#> [1] "Hongos" "Levaduras"</span></code></pre></div>
|
||
</li>
|
||
<li><p>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</p></li>
|
||
<li>
|
||
<p>MIC values (see <code><a href="../reference/as.mic.html">as.mic()</a></code>) can now be used in any mathematical processing, such as usage inside functions <code><a href="https://rdrr.io/r/base/Extremes.html">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html">range()</a></code>, and with binary operators (<code><a href="https://rdrr.io/r/base/Arithmetic.html">+</a></code>, <code><a href="https://rdrr.io/r/base/Arithmetic.html">-</a></code>, etc.). This allows for easy distribution analysis and fast filtering on MIC values:</p>
|
||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>
|
||
<span class="va">x</span>
|
||
<span class="co">#> Class <mic></span>
|
||
<span class="co">#> [1] 128 0.5 2 0.125 64 0.25 >=256 8 16 4</span>
|
||
<span class="va">x</span><span class="op">[</span><span class="va">x</span> <span class="op">></span> <span class="fl">4</span><span class="op">]</span>
|
||
<span class="co">#> Class <mic></span>
|
||
<span class="co">#> [1] 128 64 >=256 8 16</span>
|
||
<span class="fu"><a href="https://rdrr.io/r/base/range.html">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||
<span class="co">#> [1] 0.125 256.000</span>
|
||
<span class="fu"><a href="https://rdrr.io/r/base/range.html">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html">log2</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="co">#> [1] -3 8</span></code></pre></div>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="changed-2" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<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>
|
||
<li>Added 3,372 new species and 1,523 existing species became synomyms</li>
|
||
<li>The URL of a bacterial species (<code><a href="../reference/mo_property.html">mo_url()</a></code>) will now lead to <a href="https://lpsn.dsmz.de" class="uri">https://lpsn.dsmz.de</a>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>Big update for plotting classes <code>rsi</code>, <code><mic></code>, and <code><disk></code>:
|
||
<ul>
|
||
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
|
||
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
|
||
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
|
||
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
|
||
</ul>
|
||
</li>
|
||
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
|
||
<li>
|
||
<code><a href="../reference/as.rsi.html">is.rsi()</a></code> and <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now return a vector of <code>TRUE</code>/<code>FALSE</code> when the input is a data set, by iterating over all columns</li>
|
||
<li>Using functions without setting a data set (e.g., <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>) now work with <code>dplyr</code>s <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> again</li>
|
||
<li>
|
||
<code><a href="../reference/first_isolate.html">first_isolate()</a></code> can be used with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> (also when using a dot <code>.</code> as input for the data) and now returns the names of the groups</li>
|
||
<li>Updated the data set <code>microorganisms.codes</code> (which contains popular LIS and WHONET codes for microorganisms) for some species of <em>Mycobacterium</em> that previously incorrectly returned <em>M. africanum</em>
|
||
</li>
|
||
<li>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</li>
|
||
<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only <em>P. aeruginosa</em>)</li>
|
||
<li>
|
||
<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
|
||
<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
|
||
<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
|
||
<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
|
||
</li>
|
||
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
|
||
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
|
||
<li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package (e.g., <code><a href="../reference/as.mo.html">as.mo()</a></code> is now up to 4 times faster)</li>
|
||
<li>
|
||
<em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</li>
|
||
<li>
|
||
<code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_mic()</a></code> now have an expanded range in their randomisation</li>
|
||
<li>Support for GISA (glycopeptide-intermediate <em>S. aureus</em>), so e.g. <code><a href="../reference/mo_property.html">mo_genus("GISA")</a></code> will return <code>"Staphylococcus"</code>
|
||
</li>
|
||
<li>Added translations of German and Spanish for more than 200 antimicrobial drugs</li>
|
||
<li>Speed improvement for <code><a href="../reference/as.ab.html">as.ab()</a></code> when the input is an official name or ATC code</li>
|
||
<li>Added argument <code>include_untested_rsi</code> to the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> functions (defaults to <code>TRUE</code> to keep existing behaviour), to be able to exclude rows where all R/SI values (class <code><rsi></code>, see <code><a href="../reference/as.rsi.html">as.rsi()</a></code>) are empty</li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-2" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-2" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>Big documentation updates</li>
|
||
<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-150" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.5.0">
|
||
<a href="#amr-150" class="anchor"></a>AMR 1.5.0<small> 2021-01-06 </small>
|
||
</h1>
|
||
<div id="new-3" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-3" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li>
|
||
<p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
|
||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">patient_id</span>, <span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/get_episode.html">is_new_episode</a></span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||
</li>
|
||
<li><p>Functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p></li>
|
||
<li><p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
|
||
<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-3" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<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>
|
||
<p>Interpretation of antimicrobial resistance - <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:</p>
|
||
<ul>
|
||
<li>Reference data used for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now be set by the user, using the <code>reference_data</code> argument. This allows for using own interpretation guidelines. The user-set data must have the same structure as <code>rsi_translation</code>.</li>
|
||
<li>Better determination of disk zones and MIC values when running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</li>
|
||
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame in older R versions</li>
|
||
<li>
|
||
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame will not print a message anymore if the values are already clean R/SI values</li>
|
||
<li>If using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this</li>
|
||
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a <code>data.frame</code> that only contains one column for antibiotic interpretations</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>. This means that then the data argument does not need to be set anymore. This is the case for the new functions:</p>
|
||
<ul>
|
||
<li><code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code></li>
|
||
<li><code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code></li>
|
||
<li><code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code></li>
|
||
</ul>
|
||
<p>… and for the existing functions:</p>
|
||
<ul>
|
||
<li>
|
||
<code><a href="../reference/first_isolate.html">first_isolate()</a></code>,</li>
|
||
<li>
|
||
<code>key_antibiotics()</code>,</li>
|
||
<li>
|
||
<code><a href="../reference/mdro.html">mdro()</a></code>,</li>
|
||
<li>
|
||
<code><a href="../reference/mdro.html">brmo()</a></code>,</li>
|
||
<li>
|
||
<code><a href="../reference/mdro.html">mrgn()</a></code>,</li>
|
||
<li>
|
||
<code><a href="../reference/mdro.html">mdr_tb()</a></code>,</li>
|
||
<li>
|
||
<code><a href="../reference/mdro.html">mdr_cmi2012()</a></code>,</li>
|
||
<li><code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code></li>
|
||
</ul>
|
||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="co"># to select first isolates that are Gram-negative </span>
|
||
<span class="co"># and view results of cephalosporins and aminoglycosides:</span>
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||
</li>
|
||
<li>
|
||
<p>For antibiotic selection functions (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) to select columns based on a certain antibiotic group, the dependency on the <code>tidyselect</code> package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):</p>
|
||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="co"># above example in base R:</span>
|
||
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&</span> <span class="fu"><a href="../reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><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">"mo"</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
|
||
</li>
|
||
<li><p>For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined.</p></li>
|
||
<li><p>Fix for <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, that previously would not remember the file location of the original file</p></li>
|
||
<li><p>Deprecated function <code>p_symbol()</code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</p></li>
|
||
<li><p>Updated coagulase-negative staphylococci determination with Becker <em>et al.</em> 2020 (PMID 32056452), meaning that the species <em>S. argensis</em>, <em>S. caeli</em>, <em>S. debuckii</em>, <em>S. edaphicus</em> and <em>S. pseudoxylosus</em> are now all considered CoNS</p></li>
|
||
<li><p>Fix for using argument <code>reference_df</code> in <code><a href="../reference/as.mo.html">as.mo()</a></code> and <code>mo_*()</code> functions that contain old microbial codes (from previous package versions)</p></li>
|
||
<li><p>Fixed a bug where <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> would not return the results based on the MO matching score</p></li>
|
||
<li><p>Fixed a bug where <code><a href="../reference/as.mo.html">as.mo()</a></code> would not return results for known laboratory codes for microorganisms</p></li>
|
||
<li><p>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would sometimes fail</p></li>
|
||
<li><p>Better tibble printing for MIC values</p></li>
|
||
<li><p>Fix for plotting MIC values with <code><a href="../reference/plot.html">plot()</a></code></p></li>
|
||
<li><p>Added <code><a href="../reference/plot.html">plot()</a></code> generic to class <code><disk></code></p></li>
|
||
<li><p>LA-MRSA and CA-MRSA are now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("LA-MRSA")</a></code> will return <code>"Staphylococcus"</code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive("LA-MRSA")</a></code> will return <code>TRUE</code>.</p></li>
|
||
<li><p>Fix for printing class <mo> in tibbles when all values are <code>NA</code></mo></p></li>
|
||
<li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> when the input contains <code>NA</code></p></li>
|
||
<li><p>If <code><a href="../reference/as.mo.html">as.mo()</a></code> takes more than 30 seconds, some suggestions will be done to improve speed</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-3" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-3" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>All messages and warnings thrown by this package now break sentences on whole words</li>
|
||
<li>More extensive unit tests</li>
|
||
<li>Internal calls to <code><a href="https://rdrr.io/r/base/options.html">options()</a></code> were all removed in favour of a new internal environment <code>pkg_env</code>
|
||
</li>
|
||
<li>Improved internal type setting (among other things: replaced all <code><a href="https://rdrr.io/r/base/lapply.html">sapply()</a></code> calls with <code><a href="https://rdrr.io/r/base/lapply.html">vapply()</a></code>)</li>
|
||
<li>Added CodeFactor as a continuous code review to this package: <a href="https://www.codefactor.io/repository/github/msberends/amr/" class="uri">https://www.codefactor.io/repository/github/msberends/amr/</a>
|
||
</li>
|
||
<li>Added Dr. Rogier Schade as contributor</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-140" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.4.0">
|
||
<a href="#amr-140" class="anchor"></a>AMR 1.4.0<small> 2020-10-08 </small>
|
||
</h1>
|
||
<div id="new-4" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-4" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics and the <code><a href="../reference/mdro.html">mdro()</a></code> function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the arguments <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2. The <code><a href="../reference/mdro.html">mdro()</a></code> function now accepts <code>guideline == "EUCAST3.1"</code> and <code>guideline == "EUCAST3.2"</code>.</p></li>
|
||
<li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
|
||
<li>
|
||
<p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
|
||
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
|
||
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||
<span class="va">intrinsic_resistant</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
|
||
<span class="co">#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span></code></pre></div>
|
||
</li>
|
||
<li><p>Support for veterinary ATC codes</p></li>
|
||
<li><p>Support for skimming classes <code><rsi></code>, <code><mic></code>, <code><disk></code> and <code><mo></code> with the <code>skimr</code> package</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="changed-4" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<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>
|
||
<p>Improvements for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:</p>
|
||
<ul>
|
||
<li>
|
||
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
|
||
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="co"># until dplyr 1.0.0</span>
|
||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||
|
||
<span class="co"># since dplyr 1.0.0</span>
|
||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||
</li>
|
||
<li><p>Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g. <code><a href="../reference/as.rsi.html">as.rsi(df, col1:col9)</a></code></p></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 argument ‘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 “>=” while this should have been “<”</p></li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>Added intelligent data cleaning to <code><a href="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
|
||
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="fu"><a href="../reference/as.disk.html">as.disk</a></span><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">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="co">#> Class <disk></span>
|
||
<span class="co">#> [1] 24 24</span></code></pre></div>
|
||
</li>
|
||
<li>
|
||
<p>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</p>
|
||
<ul>
|
||
<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 argument <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>
|
||
</li>
|
||
<li><p><code><a href="../reference/translate.html">get_locale()</a></code> now uses at default <code><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html">Sys.getlocale()</a></code>. This can be overwritten by setting the option <code>AMR_locale</code>.</p></li>
|
||
<li><p>Big speed improvement for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></p></li>
|
||
<li><p>Overall speed improvement by tweaking joining functions</p></li>
|
||
<li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li>
|
||
<li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
|
||
<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><rsi></code>, <code><mic></code>, <code><disk></code>, <code><ab></code> and <code><mo></code>. When using <code>tibble</code>s containing antimicrobial columns (class <code><rsi></code>), “S” will print in green, “I” will print in yellow and “R” will print in red. Microbial IDs (class <code><mo></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 arguments <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>Changes in the <code>antibiotics</code> data set:</p>
|
||
<ul>
|
||
<li>Updated oral and parental DDDs from the WHOCC</li>
|
||
<li>Added abbreviation “piptazo” to ‘Piperacillin/tazobactam’ (TZP)</li>
|
||
<li>‘Penicillin G’ (for intravenous use) is now named ‘Benzylpenicillin’ (code <code>PEN</code>)</li>
|
||
<li>‘Penicillin V’ (for oral use, code <code>PNV</code>) was removed, since its actual entry ‘Phenoxymethylpenicillin’ (code <code>PHN</code>) already existed</li>
|
||
<li>The group name (<code>antibiotics$group</code>) of ‘Linezolid’ (<code>LNZ</code>), ‘Cycloserine’ (<code>CYC</code>), ‘Tedizolid’ (<code>TZD</code>) and ‘Thiacetazone’ (<code>THA</code>) is now “Oxazolidinones” instead of “Other antibacterials”</li>
|
||
</ul>
|
||
</li>
|
||
<li><p>Added support for using <code><a href="https://rdrr.io/r/base/unique.html">unique()</a></code> on classes <code><rsi></code>, <code><mic></code>, <code><disk></code>, <code><ab></code> and <code><mo></code></p></li>
|
||
<li><p>Added argument <code>excess</code> to the <code><a href="../reference/kurtosis.html">kurtosis()</a></code> function (defaults to <code>FALSE</code>), to return the <em>excess kurtosis</em>, defined as the kurtosis minus three.</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-4" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-4" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>Removed functions <code>portion_R()</code>, <code>portion_S()</code> and <code>portion_I()</code> that were deprecated since version 0.9.0 (November 2019) and were replaced with <code><a href="../reference/proportion.html">proportion_R()</a></code>, <code><a href="../reference/proportion.html">proportion_S()</a></code> and <code><a href="../reference/proportion.html">proportion_I()</a></code>
|
||
</li>
|
||
<li>Removed unnecessary references to the <code>base</code> package</li>
|
||
<li>Added packages that could be useful for some functions to the <code>Suggests</code> field of the <code>DESCRIPTION</code> file</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-130" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.3.0">
|
||
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small>
|
||
</h1>
|
||
<div id="new-5" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-5" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
|
||
<li>
|
||
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
|
||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||
|
||
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||
<span class="co">#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span></code></pre></div>
|
||
</li>
|
||
<li><p>Added <code><a href="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><a href="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
|
||
<li><p>Added function <code>filter_penicillins()</code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</p></li>
|
||
<li><p>Added official antimicrobial names to all <code>filter_ab_class()</code> functions, such as <code>filter_aminoglycosides()</code></p></li>
|
||
<li><p>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</p></li>
|
||
<li><p>Added Monuril as trade name for fosfomycin</p></li>
|
||
<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 “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) 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-5" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<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>
|
||
<p>As a consequence, very old microbial codes (from <code>AMR</code> v0.5.0 and lower) <strong>are not supported anymore</strong>. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> on your microorganism names or codes to transform them to current abbreviations used in this package.</p>
|
||
</li>
|
||
<li>
|
||
<p>Improvements for <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> and all <code>count_*()</code>, <code>proportion_*()</code> functions:</p>
|
||
<ul>
|
||
<li>95% speed improvement by using other base R functions for calculation</li>
|
||
<li>Using unexisting columns wil now return an error instead of dropping them silently</li>
|
||
<li>Using variables for column names (as well as selectors like <code><a href="https://tidyselect.r-lib.org/reference/all_of.html">dplyr::all_of()</a></code>) now works again</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:</p>
|
||
<ul>
|
||
<li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more</li>
|
||
<li>Added progress bar</li>
|
||
<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
|
||
<li>The <code><a href="../reference/as.ab.html">as.ab()</a></code> function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.</li>
|
||
</ul>
|
||
</li>
|
||
<li><p>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</p></li>
|
||
<li><p>Fixed a bug for CLSI 2019 guidelines (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>), that also included results for animals. It now only contains interpretation guidelines for humans.</p></li>
|
||
<li><p>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</p></li>
|
||
<li>
|
||
<p>For functions <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>:</p>
|
||
<ul>
|
||
<li>Fixed a bug for using grouped versions</li>
|
||
<li>Fixed a bug where not all different antimicrobial results were added as rows</li>
|
||
<li>Fixed a bug when only calculating counts (<code><a href="../reference/count.html">count_df()</a></code>) when all antibiotics in the data set have only <code>NA</code>s</li>
|
||
</ul>
|
||
</li>
|
||
<li><p>Improved auto-determination for columns of types <code><mo></code> and <code><Date></code></p></li>
|
||
<li><p>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</p></li>
|
||
<li><p>Changed the summary for class <code><rsi></code>, to highlight the %SI vs. %R</p></li>
|
||
<li><p>Improved error handling, giving more useful info when functions return an error</p></li>
|
||
<li><p>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</p></li>
|
||
<li><p>Speed improvement for <code><a href="../reference/mdro.html">mdro()</a></code> and <code>filter_ab_class()</code></p></li>
|
||
<li><p>New option <code>arrows_textangled</code> for <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> to indicate whether the text at the end of the arrows should be angled (defaults to <code>TRUE</code>, as it was in previous versions)</p></li>
|
||
<li><p>Added parenteral DDD to benzylpenicillin</p></li>
|
||
<li><p>Fixed a bug where <code><a href="../reference/as.mic.html">as.mic()</a></code> could not handle dots without a leading zero (like <code>"<=.25</code>)</p></li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-5" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-5" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-120" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.2.0">
|
||
<a href="#amr-120" class="anchor"></a>AMR 1.2.0<small> 2020-05-28 </small>
|
||
</h1>
|
||
<div id="breaking" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#breaking" class="anchor"></a>Breaking</h3>
|
||
<ul>
|
||
<li>
|
||
<p>Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
|
||
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
|
||
<p>Negative effects of this change are:</p>
|
||
<ul>
|
||
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
|
||
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
|
||
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
|
||
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="changed-6" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#changed-6" class="anchor"></a>Changed</h3>
|
||
<ul>
|
||
<li>Taxonomy:
|
||
<ul>
|
||
<li>Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). <strong>Note:</strong> a taxonomic update may always impact determination of first isolates (using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.</li>
|
||
<li>Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)</li>
|
||
</ul>
|
||
</li>
|
||
<li>EUCAST rules:
|
||
<ul>
|
||
<li>The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function no longer applies “other” rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzyme inhibitor = R). The default input value for <code>rules</code> is now <code><a href="https://rdrr.io/r/base/c.html">c("breakpoints", "expert")</a></code> instead of <code>"all"</code>, but this can be changed by the user. To return to the old behaviour, set <code><a href="https://rdrr.io/r/base/options.html">options(AMR.eucast_rules = "all")</a></code>.</li>
|
||
<li>Fixed a bug where checking antimicrobial results in the original data were not regarded as valid R/SI values</li>
|
||
<li>All “other” rules now apply for all drug combinations in the <code>antibiotics</code> data set these two rules:
|
||
<ol>
|
||
<li>A drug <strong>with</strong> enzyme inhibitor will be set to S if the drug <strong>without</strong> enzyme inhibitor is S</li>
|
||
<li>A drug <strong>without</strong> enzyme inhibitor will be set to R if the drug <strong>with</strong> enzyme inhibitor is R</li>
|
||
</ol>
|
||
This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/avibactam, trimethoprim/sulfamethoxazole, etc.</li>
|
||
<li>Added official drug names to verbose output of <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>Added function <code><a href="../reference/ab_property.html">ab_url()</a></code> to return the direct URL of an antimicrobial agent from the official WHO website</li>
|
||
<li>Improvements for algorithm in <code><a href="../reference/as.ab.html">as.ab()</a></code>, so that e.g. <code><a href="../reference/as.ab.html">as.ab("ampi sul")</a></code> and <code><a href="../reference/ab_property.html">ab_name("ampi sul")</a></code> work</li>
|
||
<li>Functions <code><a href="../reference/ab_property.html">ab_atc()</a></code> and <code><a href="../reference/ab_property.html">ab_group()</a></code> now return <code>NA</code> if no antimicrobial agent could be found</li>
|
||
<li>Small fix for some text input that could not be coerced as valid MIC values</li>
|
||
<li>Fix for interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)</li>
|
||
<li>Fix for <code><a href="../reference/mo_source.html">set_mo_source()</a></code> to make sure that column <code>mo</code> will always be the second column</li>
|
||
<li>Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam</li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-6" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-6" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code>p_symbol()</code>
|
||
</li>
|
||
<li>Removed function <code>read.4d()</code>, that was only useful for reading data from an old test database.</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-110" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.1.0">
|
||
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small>
|
||
</h1>
|
||
<div id="new-6" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-6" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
|
||
<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-7" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<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>
|
||
<li>Support for codes ending with <code>SPE</code> for species, like <code>"ESCSPE"</code> for <em>Escherichia coli</em>
|
||
</li>
|
||
<li>Support for any encoding, which means that any language-specific character with accents can be used for input</li>
|
||
<li>Support for more arbitrary IDs used in laboratory information systems</li>
|
||
<li>Small fix for preventing viruses being treated as bacteria</li>
|
||
<li>Small fix for preventing contamination and lack of growth being treated as valid microorganisms</li>
|
||
</ul>
|
||
</li>
|
||
<li>Support for all abbreviations of antibiotics and antimycotics used by the Netherlands National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu; RIVM)</li>
|
||
<li>Added more abbreviations to the <code>antibiotics</code> data set</li>
|
||
<li>Reloaded original EUCAST master tables from 2019 (2020 was already available). This seems more reliable than the data we used from WHONET.</li>
|
||
<li>Added generic CLSI rules for R/SI interpretation using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for years 2010-2019 (thanks to Anthony Underwood)</li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-7" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-7" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
|
||
<li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-101" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.0.1">
|
||
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small>
|
||
</h1>
|
||
<div id="changed-8" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<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>
|
||
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
|
||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
|
||
|
||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">mybacteria</span><span class="op">)</span></code></pre></div>
|
||
</li>
|
||
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
|
||
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as argument to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
|
||
<li><p>Info printing in functions <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)</p></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-100" class="section level1">
|
||
<h1 class="page-header" data-toc-text="1.0.0">
|
||
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
|
||
</h1>
|
||
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
|
||
<div id="new-7" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-7" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li>Support for the newest <a href="https://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
|
||
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://github.com/msberends/AMR/blob/main/data-raw/read_EUCAST.R">can be found here</a>.</li>
|
||
<li>Support for LOINC and SNOMED codes
|
||
<ul>
|
||
<li>
|
||
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
|
||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span>
|
||
<span class="co">#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
|
||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span>
|
||
<span class="co">#> [1] "Ampicillin"</span>
|
||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span>
|
||
<span class="co">#> [1] "J01CA01"</span></code></pre></div>
|
||
</li>
|
||
<li>
|
||
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
|
||
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
|
||
<span class="co">#> [1] 115329001 3092008 113961008</span>
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span>
|
||
<span class="co">#> [1] "Staphylococcus aureus"</span>
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span>
|
||
<span class="co">#> [1] "Gram-positive"</span></code></pre></div>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="changes" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#changes" class="anchor"></a>Changes</h3>
|
||
<ul>
|
||
<li>The <code><a href="../reference/as.mo.html">as.mo()</a></code> function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the function <code>clear_mo_history()</code> was removed.</li>
|
||
<li>Bugfix for some WHONET microorganism codes that were not interpreted correctly when using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
|
||
</li>
|
||
<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>
|
||
<li>Support for missing spaces, e.g. in <code><a href="../reference/as.mo.html">as.mo("Methicillin-resistant S.aureus")</a></code>
|
||
</li>
|
||
<li>Better support for determination of <em>Salmonella</em> biovars</li>
|
||
<li>Speed improvements, especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K pneumoniae</em>
|
||
</li>
|
||
<li>Support for more common codes used in laboratory information systems</li>
|
||
</ul>
|
||
</li>
|
||
<li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li>
|
||
<li>Added a lifecycle state to every function, following the lifecycle circle of the <code>tidyverse</code>
|
||
</li>
|
||
<li>For in <code><a href="../reference/as.ab.html">as.ab()</a></code>: support for drugs starting with “co-” like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)</li>
|
||
<li>Changes to the <code>antibiotics</code> data set (thanks to Peter Dutey):
|
||
<ul>
|
||
<li>Added more synonyms to colistin, imipenem and piperacillin/tazobactam</li>
|
||
<li>Moved synonyms Rifinah and Rimactazid from rifampicin (<code>RIF</code>) to rifampicin/isoniazid (<code>RFI</code>). Please note that <a href="https://www.whocc.no/atc_ddd_index/?code=J04AM02&showdescription=no">the combination rifampicin/isoniazid has no DDDs defined</a>, so e.g. <code><a href="../reference/ab_property.html">ab_ddd("Rimactazid")</a></code> will now return <code>NA</code>.</li>
|
||
<li>Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (<code>SMX</code>) to trimethoprim/sulfamethoxazole (<code>SXT</code>)</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="other-8" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#other-8" class="anchor"></a>Other</h3>
|
||
<ul>
|
||
<li>Add a <code>CITATION</code> file</li>
|
||
<li>Full support for the upcoming R 4.0</li>
|
||
<li>Removed unnecessary <code>AMR::</code> calls</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div id="amr-090" class="section level1">
|
||
<h1 class="page-header" data-toc-text="0.9.0">
|
||
<a href="#amr-090" class="anchor"></a>AMR 0.9.0<small> 2019-11-29 </small>
|
||
</h1>
|
||
<div id="breaking-1" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#breaking-1" class="anchor"></a>Breaking</h3>
|
||
<ul>
|
||
<li>Adopted Adeolu <em>et al.</em> (2016), <a href="https:/pubmed.ncbi.nlm.nih.gov/27620848/">PMID 27620848</a> for the <code>microorganisms</code> data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like <em>Morganellaceae</em> and <em>Yersiniaceae</em>). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with <code><a href="../reference/mdro.html">mdro()</a></code> will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
|
||
<ul>
|
||
<li>
|
||
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
|
||
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
|
||
<p>then please adjust this to:</p>
|
||
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacterales"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div id="new-8" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#new-8" class="anchor"></a>New</h3>
|
||
<ul>
|
||
<li>
|
||
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
|
||
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R">
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span>bug <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>,
|
||
amox_clav <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">)</span> <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amox_clav</span><span class="op">)</span><span class="op">)</span>&l |