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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
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<h1 data-toc-skip>Changelog <small></small></h1>
<small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.0.9010" id="amr-1809010">
<code>AMR</code> 1.8.0.9010<a class="anchor" aria-label="anchor" href="#amr-1809010"></a></h2>
<div class="section level3">
<h3 id="last-updated-march-1-8-0-9010"><small>Last updated: 15 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9010"></a></h3>
<p>All functions in this package are 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.</p>
<div class="section level4">
<h4 id="changed-1-8-0-9010">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9010"></a></h4>
<ul><li><p>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on values containing capped
values (such as <code>&gt;=</code>), sometimes leading to
<code>NA</code></p></li>
<li><p>Support for antibiotic interpretations of the MIPS laboratory
system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code>
for I (‘susceptible dose-dependent’)</p></li>
<li>
<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for
ignoring non-taxonomic text, such as:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"methicillin-resistant S. aureus (MRSA)"</span><span class="op">)</span>
<span class="co">#&gt; [1] "Staphylococcus aureus"</span></code></pre></div>
</li>
<li><p>More informative warning messages</p></li>
<li><p>Added 192 as valid MIC</p></li>
<li><p>Updated MIC printing in tibbles</p></li>
<li><p>Increased speed for loading the package</p></li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-0-9010">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9010"></a></h4>
<ul><li>Fix for unit testing on R 3.3</li>
<li>Fix for size of some image elements, as requested by CRAN</li>
</ul></div>
</div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.0" id="amr-180">
<code>AMR</code> 1.8.0<small>2022-01-07</small><a class="anchor" aria-label="anchor" href="#amr-180"></a></h2>
<div class="section level4">
<h4 id="breaking-changes-1-8-0">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-8-0"></a></h4>
<ul><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>
<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>
</li>
<li>Removed all previously implemented <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot2::ggplot()</a></code>
generics for classes <code>&lt;mic&gt;</code>,
<code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and
<code>&lt;resistance_predict&gt;</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" class="external-link">ggplot2::autoplot()</a></code> generics.</li>
<li>Renamed function <code>get_locale()</code> to
<code><a href="../reference/translate.html">get_AMR_locale()</a></code> to prevent conflicts with other
packages</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-0">New<a class="anchor" aria-label="anchor" href="#new-1-8-0"></a></h4>
<ul><li><p>Support for the CLSI 2021 guideline for interpreting MIC/disk
diffusion values, which are incorporated in the
<code>rsi_translation</code> data set. This data set now more strictly
follows the WHONET software as well.</p></li>
<li><p>Support for EUCAST Intrinsic Resistance and Unusual Phenotypes
v3.3 (October 2021). This is now the default EUCAST guideline in the
package (all older guidelines are still available) for
<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>
and <code><a href="../reference/mdro.html">mdro()</a></code>. The <code>intrinsic_resistant</code> data set
was also updated accordingly.</p></li>
<li><p>Support for all antimicrobial drug (group) names and colloquial
microorganism names in Danish, Dutch, English, French, German, Italian,
Portuguese, Russian, Spanish and Swedish</p></li>
<li>
<p>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. Its second argument can be a
tidyverse way of selecting:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">:</span><span class="va">GEN</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></code></pre></div>
</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_lpsn()</a></code> to retrieve the <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a> record ID</p></li>
<li><p>Function <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> to get units of DDDs (daily
defined doses), deprecating the use of
<code>ab_ddd(..., units = TRUE)</code> to be more consistent in data
types of function output</p></li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-0">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0"></a></h4>
<ul><li>Updated the bacterial taxonomy to 5 October 2021 (according to <a href="https://lpsn.dsmz.de" class="external-link">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" class="external-link">WHOCC website</a>, regardless of drugs being
present in more than one ATC group. This means that:
<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>
<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></li>
<li>Antibiotic selectors
<ul><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>
<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>
<li>
<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>
<div class="sourceCode" id="cb3"><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">penicillins</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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">&amp;</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="cb4"><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">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</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>Added the selector <code><a href="../reference/antibiotic_class_selectors.html">not_intrinsic_resistant()</a></code>, which
only keeps antibiotic columns that are not intrinsic resistant for all
microorganisms in a data set, based on the latest EUCAST guideline on
intrinsic resistance. For example, if a data set contains only
microorganism codes or names of <em>E. coli</em> and <em>K.
pneumoniae</em> and contains a column “vancomycin”, this column will be
removed (or rather, unselected) using this function.</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>
<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" class="external-link">dplyr::filter()</a></code> and immediately after in
<code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">dplyr::select()</a></code>)</p></li>
<li><p>Fix for using having multiple columns that are coerced to the
same antibiotic agent</p></li>
<li><p>Fixed for using <code><a href="https://rdrr.io/r/base/all.html" class="external-link">all()</a></code> or <code><a href="https://rdrr.io/r/base/any.html" class="external-link">any()</a></code> on
antibiotic selectors in an R Markdown file</p></li>
</ul></li>
<li>Added the following antimicrobial agents that are now covered by the
WHO: aztreonam/nacubactam (ANC), cefepime/nacubactam (FNC), exebacase
(EXE), ozenoxacin (OZN), zoliflodacin (ZFD), manogepix (MGX),
ibrexafungerp (IBX), and rezafungin (RZF). None of these agents have an
ATC code yet.</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 all
supported languages</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 of <code><a href="../reference/as.mo.html">as.mo()</a></code>
</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>&lt;mic&gt;</code>,
<code>&lt;disk&gt;</code> and <code>&lt;rsi&gt;</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>
<li>
<code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> can now
cope with <code>NA</code>s</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-0">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0"></a></h4>
<ul><li>This package is now being maintained by two epidemiologists and a
data scientist from two different non-profit healthcare
organisations.</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.7.1" id="amr-171">AMR 1.7.1<small>2021-06-03</small><a class="anchor" aria-label="anchor" href="#amr-171"></a></h2>
<div class="section level4">
<h4 id="breaking-change-1-7-1">Breaking change<a class="anchor" aria-label="anchor" href="#breaking-change-1-7-1"></a></h4>
<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="cb5"><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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">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" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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 class="section level4">
<h4 id="new-1-7-1">New<a class="anchor" aria-label="anchor" href="#new-1-7-1"></a></h4>
<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" class="external-link">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 class="section level4">
<h4 id="changed-1-7-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1"></a></h4>
<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" class="external-link">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>%unlike%</code> and <code>%unlike_case%</code> (as
negations of the existing <code>%like%</code> and
<code>%like_case%</code>). This greatly improves readability:</p>
<div class="sourceCode" id="cb6"><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" class="external-link">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"><a href="../reference/like.html">%unlike%</a></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>%like%</code> -&gt; <code>%unlike%</code> -&gt;
<code>%like_case%</code> -&gt; <code>%unlike_case%</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" class="external-link">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" class="external-link">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" class="external-link">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 class="section level4">
<h4 id="other-1-7-1">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1"></a></h4>
<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 class="section level2">
<h2 class="page-header" data-toc-text="1.6.0" id="amr-160">AMR 1.6.0<small>2021-03-14</small><a class="anchor" aria-label="anchor" href="#amr-160"></a></h2>
<div class="section level4">
<h4 id="new-1-6-0">New<a class="anchor" aria-label="anchor" href="#new-1-6-0"></a></h4>
<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>&lt;rsi&gt;</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="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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">#&gt; Selecting oxazolidinones: column 'LNZ' (linezolid)</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">filter_oxazolidinones</span><span class="op">(</span><span class="op">)</span>
<span class="co">#&gt; 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>&lt;mic&gt;</code> and <code>&lt;disk&gt;</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="cb8"><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" class="external-link">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">#&gt; [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" class="external-link">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">#&gt; [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" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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="cb9"><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" class="external-link">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" class="external-link">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">#&gt; [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" class="external-link">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html" class="external-link">range()</a></code>, and with
binary operators (<code>+</code>, <code>-</code>, etc.). This allows for
easy distribution analysis and fast filtering on MIC values:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">x</span> <span class="op">&lt;-</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">#&gt; Class &lt;mic&gt;</span>
<span class="co">#&gt; [1] 128 0.5 2 0.125 64 0.25 &gt;=256 8 16 4</span>
<span class="va">x</span><span class="op">[</span><span class="va">x</span> <span class="op">&gt;</span> <span class="fl">4</span><span class="op">]</span>
<span class="co">#&gt; Class &lt;mic&gt;</span>
<span class="co">#&gt; [1] 128 64 &gt;=256 8 16</span>
<span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co">#&gt; [1] 0.125 256.000</span>
<span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; [1] -3 8</span></code></pre></div>
</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-6-0">Changed<a class="anchor" aria-label="anchor" href="#changed-1-6-0"></a></h4>
<ul><li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de" class="external-link">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="external-link uri">https://lpsn.dsmz.de</a>
</li>
</ul></li>
<li>Big update for plotting classes <code>rsi</code>,
<code>&lt;mic&gt;</code>, and <code>&lt;disk&gt;</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" class="external-link">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" class="external-link">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>mdro(..., verbose = TRUE)</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" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">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" class="external-link">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>%like%</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>mo_genus("GISA")</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>&lt;rsi&gt;</code>, see <code><a href="../reference/as.rsi.html">as.rsi()</a></code>) are
empty</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-6-0">Other<a class="anchor" aria-label="anchor" href="#other-1-6-0"></a></h4>
<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 class="section level2">
<h2 class="page-header" data-toc-text="1.5.0" id="amr-150">AMR 1.5.0<small>2021-01-06</small><a class="anchor" aria-label="anchor" href="#amr-150"></a></h2>
<div class="section level4">
<h4 id="new-1-5-0">New<a class="anchor" aria-label="anchor" href="#new-1-5-0"></a></h4>
<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" class="external-link">group_by()</a></code>):</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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/" class="external-link">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 class="section level4">
<h4 id="changed-1-5-0">Changed<a class="anchor" aria-label="anchor" href="#changed-1-5-0"></a></h4>
<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" class="external-link">filter()</a></code>,
<code><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">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="cb12"><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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html" class="external-link">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="cb13"><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" class="external-link">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">&amp;</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" class="external-link">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" class="external-link"><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" class="external-link">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>&lt;disk&gt;</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>mo_genus("LA-MRSA")</code> will return
<code>"Staphylococcus"</code> and
<code>mo_is_gram_positive("LA-MRSA")</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 class="section level4">
<h4 id="other-1-5-0">Other<a class="anchor" aria-label="anchor" href="#other-1-5-0"></a></h4>
<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" class="external-link">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" class="external-link">sapply()</a></code> calls with <code><a href="https://rdrr.io/r/base/lapply.html" class="external-link">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="external-link uri">https://www.codefactor.io/repository/github/msberends/amr/</a>
</li>
<li>Added Dr. Rogier Schade as contributor</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.4.0" id="amr-140">AMR 1.4.0<small>2020-10-08</small><a class="anchor" aria-label="anchor" href="#amr-140"></a></h2>
<div class="section level4">
<h4 id="new-1-4-0">New<a class="anchor" aria-label="anchor" href="#new-1-4-0"></a></h4>
<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="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">intrinsic_resistant</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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"><a href="../reference/like.html">%like%</a></span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
<span class="co">#&gt; [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>&lt;rsi&gt;</code>,
<code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and
<code>&lt;mo&gt;</code> with the <code>skimr</code> package</p></li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-4-0">Changed<a class="anchor" aria-label="anchor" href="#changed-1-4-0"></a></h4>
<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" class="external-link">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="cb15"><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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">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>as.rsi(df, col1:col9)</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 “&gt;=” while this should have been “&lt;”</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="cb16"><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" class="external-link">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">#&gt; Class &lt;disk&gt;</span>
<span class="co">#&gt; [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>get_locale()</code> now uses at default
<code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set,
<code><a href="https://rdrr.io/r/base/locales.html" class="external-link">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>mo_genus("BORSA")</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>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>,
<code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and
<code>&lt;mo&gt;</code>. When using <code>tibble</code>s containing
antimicrobial columns (class <code>&lt;rsi&gt;</code>), “S” will print
in green, “I” will print in yellow and “R” will print in red. Microbial
IDs (class <code>&lt;mo&gt;</code>) will emphasise on the genus and
species, not on the kingdom.</p></li>
<li><p>Names of antiviral agents in data set <code>antivirals</code> now
have a starting capital letter, like it is the case in the
<code>antibiotics</code> data set</p></li>
<li><p>Updated the documentation of the <code>WHONET</code> data set to
clarify that all patient names are fictitious</p></li>
<li><p>Small <code><a href="../reference/as.ab.html">as.ab()</a></code> algorithm improvements</p></li>
<li><p>Fix for combining MIC values with raw numbers,
i.e. <code>c(as.mic(2), 2)</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" class="external-link">unique()</a></code> on classes
<code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>,
<code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and
<code>&lt;mo&gt;</code></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 class="section level4">
<h4 id="other-1-4-0">Other<a class="anchor" aria-label="anchor" href="#other-1-4-0"></a></h4>
<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 class="section level2">
<h2 class="page-header" data-toc-text="1.3.0" id="amr-130">AMR 1.3.0<small>2020-07-31</small><a class="anchor" aria-label="anchor" href="#amr-130"></a></h2>
<div class="section level4">
<h4 id="new-1-3-0">New<a class="anchor" aria-label="anchor" href="#new-1-3-0"></a></h4>
<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" class="external-link">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" class="external-link">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html" class="external-link">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">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">#&gt; 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 “&lt;” (but not “&lt;=”) will always return “S” and
values starting with “&gt;” (but not “&gt;=”) will always return “R”.
The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you
need to specifically do
<code>as.rsi(..., conserve_capped_values = TRUE)</code>.</p></li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-3-0">Changed<a class="anchor" aria-label="anchor" href="#changed-1-3-0"></a></h4>
<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" class="external-link">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>&lt;mo&gt;</code> and <code>&lt;Date&gt;</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>&lt;rsi&gt;</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>"&lt;=.25</code>)</p></li>
</ul></div>
<div class="section level4">
<h4 id="other-1-3-0">Other<a class="anchor" aria-label="anchor" href="#other-1-3-0"></a></h4>
<ul><li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR" class="external-link">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 class="section level2">
<h2 class="page-header" data-toc-text="1.2.0" id="amr-120">AMR 1.2.0<small>2020-05-28</small><a class="anchor" aria-label="anchor" href="#amr-120"></a></h2>
<div class="section level4">
<h4 id="breaking-1-2-0">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-2-0"></a></h4>
<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" class="external-link">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner" class="external-link">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>&lt;ord&gt;</code>, not
<code>&lt;rsi&gt;</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 class="section level4">
<h4 id="changed-1-2-0">Changed<a class="anchor" aria-label="anchor" href="#changed-1-2-0"></a></h4>
<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>c("breakpoints", "expert")</code> instead of <code>"all"</code>,
but this can be changed by the user. To return to the old behaviour, set
<code>options(AMR.eucast_rules = "all")</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 style="list-style-type: decimal"><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>as.ab("ampi sul")</code> and <code>ab_name("ampi sul")</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 class="section level4">
<h4 id="other-1-2-0">Other<a class="anchor" aria-label="anchor" href="#other-1-2-0"></a></h4>
<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 class="section level2">
<h2 class="page-header" data-toc-text="1.1.0" id="amr-110">AMR 1.1.0<small>2020-04-15</small><a class="anchor" aria-label="anchor" href="#amr-110"></a></h2>
<div class="section level4">
<h4 id="new-1-1-0">New<a class="anchor" aria-label="anchor" href="#new-1-1-0"></a></h4>
<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 class="section level4">
<h4 id="changed-1-1-0">Changed<a class="anchor" aria-label="anchor" href="#changed-1-1-0"></a></h4>
<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 class="section level4">
<h4 id="other-1-1-0">Other<a class="anchor" aria-label="anchor" href="#other-1-1-0"></a></h4>
<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 class="section level2">
<h2 class="page-header" data-toc-text="1.0.1" id="amr-101">AMR 1.0.1<small>2020-02-23</small><a class="anchor" aria-label="anchor" href="#amr-101"></a></h2>
<div class="section level4">
<h4 id="changed-1-0-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1-0-1"></a></h4>
<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" class="external-link">mutate_at()</a></code> of the <code>dplyr</code>
package:</p>
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">yourdata</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">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 class="section level2">
<h2 class="page-header" data-toc-text="1.0.0" id="amr-100">AMR 1.0.0<small>2020-02-17</small><a class="anchor" aria-label="anchor" href="#amr-100"></a></h2>
<p>This software is now out of beta and considered stable. Nonetheless,
this package will be developed continually.</p>
<div class="section level4">
<h4 id="new-1-0-0">New<a class="anchor" aria-label="anchor" href="#new-1-0-0"></a></h4>
<ul><li>Support for the newest <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">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="external-link 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" class="external-link">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="cb19"><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">#&gt; [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">#&gt; [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">#&gt; [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="cb20"><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">#&gt; [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">#&gt; [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">#&gt; [1] "Gram-positive"</span></code></pre></div>
</li>
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="changes-1-0-0">Changes<a class="anchor" aria-label="anchor" href="#changes-1-0-0"></a></h4>
<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>as.mo("Methicillin-resistant S.aureus")</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&amp;showdescription=no" class="external-link">the
combination rifampicin/isoniazid has no DDDs defined</a>, so
e.g. <code>ab_ddd("Rimactazid")</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 class="section level4">
<h4 id="other-1-0-0">Other<a class="anchor" aria-label="anchor" href="#other-1-0-0"></a></h4>
<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 class="section level2">
<h2 class="page-header" data-toc-text="0.9.0" id="amr-090">AMR 0.9.0<small>2019-11-29</small><a class="anchor" aria-label="anchor" href="#amr-090"></a></h2>
<div class="section level4">
<h4 id="breaking-0-9-0">Breaking<a class="anchor" aria-label="anchor" href="#breaking-0-9-0"></a></h4>
<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="cb21"><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="cb22"><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 class="section level4">
<h4 id="new-0-9-0">New<a class="anchor" aria-label="anchor" href="#new-0-9-0"></a></h4>
<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="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">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" class="external-link">is.na</a></span><span class="op">(</span><span class="va">amox_clav</span><span class="op">)</span><span class="op">)</span></code></pre></div>
</li>
<li>
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A
<em>et al.</em> “Multidrug-resistant, extensively drug-resistant and
pandrug-resistant bacteria: an international expert proposal for interim
standard definitions for acquired resistance.” Clinical Microbiology and
Infection (2012).</p>
<ul><li>This is now the new default guideline for the <code><a href="../reference/mdro.html">mdro()</a></code>
function</li>
<li>The new Verbose mode (<code>mdro(...., verbose = TRUE)</code>)
returns an informative data set where the reason for MDRO determination
is given for every isolate, and an list of the resistant antimicrobial
agents</li>
</ul></li>
<li><p>Data set <code>antivirals</code>, containing all entries from the
ATC J05 group with their DDDs for oral and parenteral treatment</p></li>
</ul></div>
<div class="section level4">
<h4 id="changes-0-9-0">Changes<a class="anchor" aria-label="anchor" href="#changes-0-9-0"></a></h4>
<ul><li>Improvements to algorithm in <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul><li><p>Now allows “ou” where “au” should have been used and vice
versa</p></li>
<li><p>More intelligent way of coping with some consonants like “l” and
“r”</p></li>
<li>
<p>Added a score (a certainty percentage) to
<code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein
distance</a>:</p>
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Stafylococcus aureus"</span>,
<span class="st">"staphylokok aureuz"</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; Warning: </span>
<span class="co">#&gt; Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co">#&gt; Class 'mo'</span>
<span class="co">#&gt; [1] B_STPHY_AURS B_STPHY_AURS</span>
<span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span>
<span class="co">#&gt; "Stafylococcus aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span>
<span class="co">#&gt; "staphylokok aureuz" -&gt; Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></code></pre></div>
</li>
</ul></li>
<li>Removed previously deprecated function <code>as.atc()</code> - this
function was replaced by <code><a href="../reference/ab_property.html">ab_atc()</a></code>
</li>
<li>Renamed all <code>portion_*</code> functions to
<code>proportion_*</code>. All <code>portion_*</code> functions are
still available as deprecated functions, and will return a warning when
used.</li>
<li>When running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> over a data set, it will now
print the guideline that will be used if it is not specified by the
user</li>
<li>Improvements for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul><li>Fix where <em>Stenotrophomonas maltophilia</em> would always become
ceftazidime R (following EUCAST v3.1)</li>
<li>Fix where <em>Leuconostoc</em> and <em>Pediococcus</em> would not
always become glycopeptides R</li>
<li>non-EUCAST rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> are now applied
first and not as last anymore. This is to improve the dependency on
certain antibiotics for the official EUCAST rules. Please see
<code><a href="../reference/eucast_rules.html">?eucast_rules</a></code>.</li>
</ul></li>
<li>Fix for interpreting MIC values with <code><a href="../reference/as.rsi.html">as.rsi()</a></code> where the
input is <code>NA</code>
</li>
<li>Added “imi” and “imp” as allowed abbreviation for Imipenem
(IPM)</li>
<li>Fix for automatically determining columns with antibiotic results in
<code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li>
<li>Added ATC codes for ceftaroline, ceftobiprole and faropenem and
fixed two typos in the <code>antibiotics</code> data set</li>
<li>More robust way of determining valid MIC values</li>
<li>Small changed to the <code>example_isolates</code> data set to
better reflect reality</li>
<li>Added more microorganisms codes from laboratory systems
(esp. species of <em>Pseudescherichia</em> and
<em>Rodentibacter</em>)</li>
<li>Added Gram-stain to <code><a href="../reference/mo_property.html">mo_info()</a></code>
</li>
</ul></div>
<div class="section level4">
<h4 id="other-0-9-0">Other<a class="anchor" aria-label="anchor" href="#other-0-9-0"></a></h4>
<ul><li>Rewrote the complete documentation to markdown format, to be able to
use the very latest version of the great <a href="https://roxygen2.r-lib.org/index.html" class="external-link">Roxygen2</a>, released in
November 2019. This tremously improved the documentation quality, since
the rewrite forced us to go over all texts again and make changes where
needed.</li>
<li>Change dependency on <code>clean</code> to <code>cleaner</code>, as
this package was renamed accordingly upon CRAN request</li>
<li>Added Dr. Sofia Ny as contributor</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.8.0" id="amr-080">AMR 0.8.0<small>2019-10-15</small><a class="anchor" aria-label="anchor" href="#amr-080"></a></h2>
<div class="section level4">
<h4 id="breaking-0-8-0">Breaking<a class="anchor" aria-label="anchor" href="#breaking-0-8-0"></a></h4>
<ul><li>
<p>Determination of first isolates now <strong>excludes</strong> all
‘unknown’ microorganisms at default, i.e. microbial code
<code>"UNKNOWN"</code>. They can be included with the new argument
<code>include_unknown</code>:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">...</span>, include_unknown <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>For WHONET users, this means that all records/isolates with organism
code <code>"con"</code> (<em>contamination</em>) will be excluded at
default, since <code>as.mo("con") = "UNKNOWN"</code>. The function
always shows a note with the number of ‘unknown’ microorganisms that
were included or excluded.</p>
</li>
<li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code>
will now be preserved in any subsetting or assignment. For the sake of
data integrity, this means that invalid assignments will now result in
<code>NA</code>:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># how it works in base R:</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="st">"A"</span><span class="op">)</span>
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="st">"B"</span>
<span class="co">#&gt; Warning message:</span>
<span class="co">#&gt; invalid factor level, NA generated</span>
<span class="co"># how it now works similarly for classes 'mo' and 'ab':</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="st">"testvalue"</span>
<span class="co">#&gt; Warning message:</span>
<span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
<p>This is important, because a value like <code>"testvalue"</code>
could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the
class would suggest a valid microbial code.</p>
</li>
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since
creating frequency tables actually does not fit the scope of this
package. The <code>freq()</code> function still works, since it is
re-exported from the <code>clean</code> package (which will be installed
automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Renamed data set <code>septic_patients</code> to
<code>example_isolates</code></p></li>
</ul></div>
<div class="section level4">
<h4 id="new-0-8-0">New<a class="anchor" aria-label="anchor" href="#new-0-8-0"></a></h4>
<ul><li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a
<code>data.frame</code> with the results of all bug-drug combinations in
a data set. The column containing microorganism codes is guessed
automatically and its input is transformed with
<code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span>
<span class="co">#&gt; mo ab S I R total</span>
<span class="co">#&gt; 1 A. baumannii AMC 0 0 3 3</span>
<span class="co">#&gt; 2 A. baumannii AMK 0 0 0 0</span>
<span class="co">#&gt; 3 A. baumannii AMP 0 0 3 3</span>
<span class="co">#&gt; 4 A. baumannii AMX 0 0 3 3</span>
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
<span class="co"># change the transformation with the FUN argument to anything you like:</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span>, FUN <span class="op">=</span> <span class="va">mo_gramstain</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span>
<span class="co">#&gt; mo ab S I R total</span>
<span class="co">#&gt; 1 Gram-negative AMC 469 89 174 732</span>
<span class="co">#&gt; 2 Gram-negative AMK 251 0 2 253</span>
<span class="co">#&gt; 3 Gram-negative AMP 227 0 405 632</span>
<span class="co">#&gt; 4 Gram-negative AMX 227 0 405 632</span>
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></code></pre></div>
<p>You can format this to a printable format, ready for reporting or
exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code>
function:</p>
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, combine_IR <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
</li>
<li>
<p>Additional way to calculate co-resistance, i.e. when using
multiple antimicrobials as input for <code>portion_*</code> functions or
<code>count_*</code> functions. This can be used to determine the
empiric susceptibility of a combination therapy. A new argument
<code>only_all_tested</code> (<strong>which defaults to
<code>FALSE</code></strong>) replaces the old
<code>also_single_tested</code> and can be used to select one of the two
methods to count isolates and calculate portions. The difference can be
seen in this example table (which is also on the <code>portion</code>
and <code>count</code> help pages), where the %SI is being
determined:</p>
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># --------------------------------------------------------------------</span>
<span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span>
<span class="co"># ----------------------- -----------------------</span>
<span class="co"># Drug A Drug B include as include as include as include as</span>
<span class="co"># numerator denominator numerator denominator</span>
<span class="co"># -------- -------- ---------- ----------- ---------- -----------</span>
<span class="co"># S or I S or I X X X X</span>
<span class="co"># R S or I X X X X</span>
<span class="co"># &lt;NA&gt; S or I X X - -</span>
<span class="co"># S or I R X X X X</span>
<span class="co"># R R - X - X</span>
<span class="co"># &lt;NA&gt; R - - - -</span>
<span class="co"># S or I &lt;NA&gt; X X - -</span>
<span class="co"># R &lt;NA&gt; - - - -</span>
<span class="co"># &lt;NA&gt; &lt;NA&gt; - - - -</span>
<span class="co"># --------------------------------------------------------------------</span></code></pre></div>
<p>Since this is a major change, usage of the old
<code>also_single_tested</code> will throw an informative error that it
has been replaced by <code>only_all_tested</code>.</p>
</li>
<li>
<p><code>tibble</code> printing support for classes
<code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code>
<code>mo</code>. When using <code>tibble</code>s containing
antimicrobial columns, values <code>S</code> will print in green, values
<code>I</code> will print in yellow and values <code>R</code> will print
in red. Microbial IDs (class <code>mo</code>) will emphasise on the
genus and species, not on the kingdom.</p>
<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span><span class="op">:</span><span class="va">AMC</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html" class="external-link">as_tibble</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</li>
</ul></div>
<div class="section level4">
<h4 id="changed-0-8-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-8-0"></a></h4>
<ul><li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some
led to additions to the <code>microorganisms</code> data set). Many
thanks to all contributors that helped improving the algorithms.
<ul><li>Self-learning algorithm - the function now gains experience from
previously determined microorganism IDs and learns from it (yielding
80-95% speed improvement for any guess after the first try)</li>
<li>Big improvement for misspelled input</li>
<li>These new trivial names known to the field are now understood:
meningococcus, gonococcus, pneumococcus</li>
<li>Updated to the latest taxonomic data (updated to August 2019, from
the International Journal of Systematic and Evolutionary
Microbiology</li>
<li>Added support for Viridans Group Streptococci (VGS) and Milleri
Group Streptococci (MGS)</li>
<li>Added support for <em>Blastocystis</em>
</li>
<li>Added support for 5,000 new fungi</li>
<li>Added support for unknown yeasts and fungi</li>
<li>Changed most microorganism IDs to improve readability. For example,
the old code <code>B_ENTRC_FAE</code> could have been both <em>E.
faecalis</em> and <em>E. faecium</em>. Its new code is
<code>B_ENTRC_FCLS</code> and <em>E. faecium</em> has become
<code>B_ENTRC_FACM</code>. Also, the Latin character ae is now preserved
at the start of each genus and species abbreviation. For example, the
old code for <em>Aerococcus urinae</em> was <code>B_ARCCC_NAE</code>.
This is now <code>B_AERCC_URIN</code>. <strong>IMPORTANT:</strong> Old
microorganism IDs are still supported, but support will be dropped in a
future version. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> on your old codes to transform
them to the new format. Using 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>) on
old codes, will throw a warning.</li>
</ul></li>
<li>More intelligent guessing for <code><a href="../reference/as.ab.html">as.ab()</a></code>, including
bidirectional language support</li>
<li>Added support for the German national guideline (3MRGN/4MRGN) in the
<code><a href="../reference/mdro.html">mdro()</a></code> function, to determine multi-drug resistant
organisms</li>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul><li>Fixed a bug for <em>Yersinia pseudotuberculosis</em>
</li>
<li>Added more informative errors and warnings</li>
<li>Printed info now distinguishes between added and changes values</li>
<li>Using Verbose mode
(i.e. <code>eucast_rules(..., verbose = TRUE)</code>) returns more
informative and readable output</li>
<li>Using factors as input now adds missing factors levels when the
function changes antibiotic results</li>
</ul></li>
<li>Improved the internal auto-guessing function for determining
antimicrobials in your data set
(<code>AMR:::get_column_abx()</code>)</li>
<li>Removed class <code>atc</code> - using <code>as.atc()</code> is now
deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a
character, not the <code>atc</code> class anymore</li>
<li>Removed deprecated functions <code>abname()</code>,
<code>ab_official()</code>, <code>atc_name()</code>,
<code>atc_official()</code>, <code>atc_property()</code>,
<code>atc_tradenames()</code>, <code>atc_trivial_nl()</code>
</li>
<li>Fix and speed improvement for <code><a href="../reference/mo_property.html">mo_shortname()</a></code>
</li>
<li>Fix for using <code>mo_*</code> functions where the coercion
uncertainties and failures would not be available through
<code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><a href="../reference/as.mo.html">mo_failures()</a></code>
anymore</li>
<li>Deprecated the <code>country</code> argument of <code><a href="../reference/mdro.html">mdro()</a></code>
in favour of the already existing <code>guideline</code> argument to
support multiple guidelines within one country</li>
<li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead
of Rifampin</li>
<li>The <code>antibiotics</code> data set is now sorted by name and all
cephalosporins now have their generation between brackets</li>
<li>Speed improvement for <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30
times faster for antibiotic abbreviations</li>
<li>Improved <code>filter_ab_class()</code> to be more reliable and to
support 5th generation cephalosporins</li>
<li>Function <code><a href="../reference/availability.html">availability()</a></code> now uses
<code>portion_R()</code> instead of <code>portion_IR()</code>, to comply
with EUCAST insights</li>
<li>Functions <code><a href="../reference/age.html">age()</a></code> and <code><a href="../reference/age_groups.html">age_groups()</a></code> now have
a <code>na.rm</code> argument to remove empty values</li>
<li>Renamed function <code>p.symbol()</code> to <code>p_symbol()</code>
(the former is now deprecated and will be removed in a future
version)</li>
<li>Using negative values for <code>x</code> in
<code><a href="../reference/age_groups.html">age_groups()</a></code> will now introduce <code>NA</code>s and not
return an error anymore</li>
<li>Fix for determining the system’s language</li>
<li>Fix for <code>key_antibiotics()</code> on foreign systems</li>
<li>Added 80 new LIS codes for microorganisms</li>
<li>Relabeled the factor levels of <code><a href="../reference/mdro.html">mdr_tb()</a></code>
</li>
<li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
</ul><div class="section level5">
<h5 id="other-0-8-0">Other<a class="anchor" aria-label="anchor" href="#other-0-8-0"></a></h5>
<ul><li>Added Prof. Dr. Casper Albers as doctoral advisor and added
Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis
Souverein and Annick Lenglet as contributors</li>
<li>Cleaned the coding style of every single syntax line in this package
with the help of the <code>lintr</code> package</li>
</ul></div>
</div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.7.1" id="amr-071">AMR 0.7.1<small>2019-06-23</small><a class="anchor" aria-label="anchor" href="#amr-071"></a></h2>
<div class="section level5">
<h5 id="new-0-7-1">New<a class="anchor" aria-label="anchor" href="#new-0-7-1"></a></h5>
<ul><li>
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a
<code>data.frame</code> to a data set containing only the microbial
interpretation (S, I, R), the antibiotic, the percentage of S/I/R and
the number of available isolates. This is a convenient combination of
the existing functions <code><a href="../reference/count.html">count_df()</a></code> and
<code>portion_df()</code> to immediately show resistance percentages and
number of available isolates:</p>
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># antibiotic interpretation value isolates</span>
<span class="co"># 1 Amoxicillin SI 0.4442636 546</span>
<span class="co"># 2 Amoxicillin R 0.5557364 683</span>
<span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span>
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></code></pre></div>
</li>
<li>
<p>Support for all scientifically published pathotypes of <em>E.
coli</em> to date (that we could find). Supported are:</p>
<ul><li>AIEC (Adherent-Invasive <em>E. coli</em>)</li>
<li>ATEC (Atypical Entero-pathogenic <em>E. coli</em>)</li>
<li>DAEC (Diffusely Adhering <em>E. coli</em>)</li>
<li>EAEC (Entero-Aggresive <em>E. coli</em>)</li>
<li>EHEC (Entero-Haemorrhagic <em>E. coli</em>)</li>
<li>EIEC (Entero-Invasive <em>E. coli</em>)</li>
<li>EPEC (Entero-Pathogenic <em>E. coli</em>)</li>
<li>ETEC (Entero-Toxigenic <em>E. coli</em>)</li>
<li>NMEC (Neonatal Meningitis-causing <em>E. coli</em>)</li>
<li>STEC (Shiga-toxin producing <em>E. coli</em>)</li>
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
</ul><p>All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
<span class="co"># B_ESCHR_COL</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
<span class="co"># "Escherichia coli"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span>
<span class="co"># "Gram-negative"</span></code></pre></div>
</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to
<code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with
the full taxonomy, authors, and the URL to the online database of a
microorganism</p></li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously
accepted taxonomic names of a microorganism</p></li>
</ul></div>
<div class="section level5">
<h5 id="changed-0-7-1">Changed<a class="anchor" aria-label="anchor" href="#changed-0-7-1"></a></h5>
<ul><li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and
<code>portion_df()</code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li>
<li>Fixed bug in determining taxonomic kingdoms</li>
<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and
<code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled
input</li>
<li>Function <code><a href="../reference/as.ab.html">as.ab()</a></code> now allows spaces for coercing
antibiotics names</li>
<li>Added <code>ggplot2</code> methods for automatically determining the
scale type of classes <code>mo</code> and <code>ab</code>
</li>
<li>Added names of object in the header in frequency tables, even when
using pipes</li>
<li>Prevented <code>"bacteria"</code> from getting coerced by
<code><a href="../reference/as.ab.html">as.ab()</a></code> because Bacterial is a brand name of trimethoprim
(TMP)</li>
<li>Fixed a bug where setting an antibiotic would not work for
<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>
</li>
<li>Fixed a EUCAST rule for Staphylococci, where amikacin resistance
would not be inferred from tobramycin</li>
<li>Removed <code>latest_annual_release</code> from the
<code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
<li>Removed antibiotic code <code>PVM1</code> from the
<code>antibiotics</code> data set as this was a duplicate of
<code>PME</code>
</li>
<li>Fixed bug where not all old taxonomic names would be printed, when
using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of
Protozoa, which is missing from the Catalogue of Life</li>
<li>Small improvements to <code><a href="../reference/plot.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>
for MIC and RSI classes</li>
<li>Allow Catalogue of Life IDs to be coerced by
<code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
</ul></div>
<div class="section level5">
<h5 id="other-0-7-1">Other<a class="anchor" aria-label="anchor" href="#other-0-7-1"></a></h5>
<ul><li>Fixed a note thrown by CRAN tests</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.7.0" id="amr-070">AMR 0.7.0<small>2019-06-03</small><a class="anchor" aria-label="anchor" href="#amr-070"></a></h2>
<div class="section level5">
<h5 id="new-0-7-0">New<a class="anchor" aria-label="anchor" href="#new-0-7-0"></a></h5>
<ul><li>Support for translation of disk diffusion and MIC values to RSI
values (i.e. antimicrobial interpretations). Supported guidelines are
EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion
value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete
date set containing columns with MIC or disk diffusion values.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of
<code><a href="../reference/mo_property.html">mo_fullname()</a></code>
</li>
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR)
for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read
this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html" class="external-link">here on our
website</a>.</li>
</ul></div>
<div class="section level5">
<h5 id="changed-0-7-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-7-0"></a></h5>
<ul><li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing
species would lead to incorrect FALSEs. This bug was not present in AMR
v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from
WHONET software would not be recognised</li>
<li>Completely reworked the <code>antibiotics</code> data set:
<ul><li>All entries now have 3 different identifiers:
<ul><li>Column <code>ab</code> contains a human readable EARS-Net code, used
by ECDC and WHO/WHONET - this is the primary identifier used in this
package</li>
<li>Column <code>atc</code> contains the ATC code, used by
WHO/WHOCC</li>
<li>Column <code>cid</code> contains the CID code (Compound ID), used by
PubChem</li>
</ul></li>
<li>Based on the Compound ID, almost 5,000 official brand names have
been added from many different countries</li>
<li>All references to antibiotics in our package now use EARS-Net codes,
like <code>AMX</code> for amoxicillin</li>
<li>Functions <code>atc_certe</code>, <code>ab_umcg</code> and
<code>atc_trivial_nl</code> have been removed</li>
<li>All <code>atc_*</code> functions are superseded by <code>ab_*</code>
functions</li>
<li>All output will be translated by using an included translation file
which <a href="https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv" class="external-link">can
be viewed here</a>
</li>
</ul></li>
<li>Improvements to plotting AMR results with <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>:
<ul><li>New argument <code>colours</code> to set the bar colours</li>
<li>New arguments <code>title</code>, <code>subtitle</code>,
<code>caption</code>, <code>x.title</code> and <code>y.title</code> to
set titles and axis descriptions</li>
</ul></li>
<li>Improved intelligence of looking up antibiotic columns in a data set
using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li>
<li>Added ~5,000 more old taxonomic names to the
<code>microorganisms.old</code> data set, which leads to better results
finding when using the <code><a href="../reference/as.mo.html">as.mo()</a></code> function</li>
<li>This package now honours the new EUCAST insight (2019) that S and I
are but classified as susceptible, where I is defined as ‘increased
exposure’ and not ‘intermediate’ anymore. For functions like
<code>portion_df()</code> and <code><a href="../reference/count.html">count_df()</a></code> this means that
their new argument <code>combine_SI</code> is TRUE at default. Our
plotting function <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> also reflects this change
since it uses <code><a href="../reference/count.html">count_df()</a></code> internally.</li>
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument
<code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>,
<code>guess_atc()</code>, <code>EUCAST_rules()</code>,
<code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
</li>
<li>Frequency tables (<code>freq()</code>):
<ul><li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li>
<li><p>when all values are unique it now shows a message instead of a
warning</p></li>
<li>
<p>support for boxplots:</p>
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># grouped boxplots:</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</li>
</ul></li>
<li>Removed all hardcoded EUCAST rules and replaced them with a new
reference file which <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">can
be viewed here</a>
</li>
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let
groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code>freq()</code> for when all values are
<code>NA</code>
</li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li>
<li>Function <code><a href="../reference/as.mo.html">as.mo()</a></code> now gently interprets any number of
whitespace characters (like tabs) as one space</li>
<li>Function <code><a href="../reference/as.mo.html">as.mo()</a></code> now returns <code>UNKNOWN</code> for
<code>"con"</code> (WHONET ID of ‘contamination’) and returns
<code>NA</code> for <code>"xxx"</code>(WHONET ID of ‘no growth’)</li>
<li>Small algorithm fix for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Removed viruses from data set <code>microorganisms.codes</code> and
cleaned it up</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be
determined correctly</li>
</ul></div>
<div class="section level5">
<h5 id="other-0-7-0">Other<a class="anchor" aria-label="anchor" href="#other-0-7-0"></a></h5>
<ul><li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html" class="external-link">staged
install</a>
</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.6.1" id="amr-061">AMR 0.6.1<small>2019-03-29</small><a class="anchor" aria-label="anchor" href="#amr-061"></a></h2>
<div class="section level5">
<h5 id="changed-0-6-1">Changed<a class="anchor" aria-label="anchor" href="#changed-0-6-1"></a></h5>
<ul><li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with
<code>verbose = TRUE</code>
</li>
<li>Coercion of microbial IDs are now written to the package namespace
instead of the user’s home folder, to comply with the CRAN policy</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.6.0" id="amr-060">AMR 0.6.0<small>2019-03-27</small><a class="anchor" aria-label="anchor" href="#amr-060"></a></h2>
<p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/" class="external-link">https://msberends.gitlab.io/AMR</a>
(built with the great <a href="https://pkgdown.r-lib.org/" class="external-link"><code>pkgdown</code></a>)</p>
<ul><li>Contains the complete manual of this package and all of its
functions with an explanation of their arguments</li>
<li>Contains a comprehensive tutorial about how to conduct AMR data
analysis, import data from WHONET or SPSS and many more.</li>
</ul><div class="section level5">
<h5 id="new-0-6-0">New<a class="anchor" aria-label="anchor" href="#new-0-6-0"></a></h5>
<ul><li><p><strong>BREAKING</strong>: removed deprecated functions,
arguments and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to
identify an MO code.</p></li>
<li>
<p>Catalogue of Life as a new taxonomic source for data about
microorganisms, which also contains all ITIS data we used previously.
The <code>microorganisms</code> data set now contains:</p>
<ul><li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria
and Protozoa</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of
Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and
Schizosaccharomycetales (covering at least like all species of
<em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>,
<em>Saccharomyces</em> and <em>Trichophyton</em>)</p></li>
<li><p>All ~2,000 (sub)species from ~100 other relevant genera, from the
kingdoms of Animalia and Plantae (like <em>Strongyloides</em> and
<em>Taenia</em>)</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species
that have been taxonomically renamed</p></li>
<li>
<p>The responsible author(s) and year of scientific publication</p>
<p>This data is updated annually - check the included version with the
new function <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</li>
<li><p>Due to this change, some <code>mo</code> codes changed
(e.g. <em>Streptococcus</em> changed from <code>B_STRPTC</code> to
<code>B_STRPT</code>). A translation table is used internally to support
older microorganism IDs, so users will not notice this
difference.</p></li>
<li><p>New function <code><a href="../reference/mo_property.html">mo_rank()</a></code> for the taxonomic rank
(genus, species, infraspecies, etc.)</p></li>
<li><p>New function <code><a href="../reference/mo_property.html">mo_url()</a></code> to get the direct URL of a
species from the Catalogue of Life</p></li>
</ul></li>
<li>
<p>Support for data from <a href="https://whonet.org/" class="external-link">WHONET</a>
and <a href="https://www.ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net" class="external-link">EARS-Net</a>
(European Antimicrobial Resistance Surveillance Network):</p>
<ul><li>Exported files from WHONET can be read and used in this package. For
functions like <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and
<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, all arguments will be filled in
automatically.</li>
<li>This package now knows all antibiotic abbrevations by EARS-Net
(which are also being used by WHONET) - the <code>antibiotics</code>
data set now contains a column <code>ears_net</code>.</li>
<li>The function <code><a href="../reference/as.mo.html">as.mo()</a></code> now knows all WHONET species
abbreviations too, because almost 2,000 microbial abbreviations were
added to the <code>microorganisms.codes</code> data set.</li>
</ul></li>
<li>
<p>New filters for antimicrobial classes. Use these functions to
filter isolates on results in one of more antibiotics from a specific
class:</p>
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu">filter_aminoglycosides</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_carbapenems</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_cephalosporins</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_1st_cephalosporins</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_2nd_cephalosporins</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_3rd_cephalosporins</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_4th_cephalosporins</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_fluoroquinolones</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_glycopeptides</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_macrolides</span><span class="op">(</span><span class="op">)</span>
<span class="fu">filter_tetracyclines</span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>The <code>antibiotics</code> data set will be searched, after which
the input data will be checked for column names with a value in any
abbreviations, codes or official names found in the
<code>antibiotics</code> data set. For example:</p>
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">filter_glycopeptides</span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">filter_glycopeptides</span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span>, scope <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span>
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></code></pre></div>
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by
<code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">ab_property</span> <span class="op">-&gt;</span> <span class="fu">atc_property</span><span class="op">(</span><span class="op">)</span>
<span class="va">ab_name</span> <span class="op">-&gt;</span> <span class="fu">atc_name</span><span class="op">(</span><span class="op">)</span>
<span class="va">ab_official</span> <span class="op">-&gt;</span> <span class="fu">atc_official</span><span class="op">(</span><span class="op">)</span>
<span class="va">ab_trivial_nl</span> <span class="op">-&gt;</span> <span class="fu">atc_trivial_nl</span><span class="op">(</span><span class="op">)</span>
<span class="va">ab_certe</span> <span class="op">-&gt;</span> <span class="fu">atc_certe</span><span class="op">(</span><span class="op">)</span>
<span class="va">ab_umcg</span> <span class="op">-&gt;</span> <span class="fu">atc_umcg</span><span class="op">(</span><span class="op">)</span>
<span class="va">ab_tradenames</span> <span class="op">-&gt;</span> <span class="fu">atc_tradenames</span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>These functions use <code>as.atc()</code> internally. The old
<code>atc_property</code> has been renamed
<code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons:
firstly, not all ATC codes are of antibiotics (ab) but can also be of
antivirals or antifungals. Secondly, the input must have class
<code>atc</code> or must be coerable to this class. Properties of these
classes should start with the same class name, analogous to
<code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</p>
</li>
<li><p>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and
<code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as
input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code>
functions</p></li>
<li><p>Support for the upcoming <a href="https://dplyr.tidyverse.org" class="external-link"><code>dplyr</code></a> version
0.8.0</p></li>
<li><p>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic
column in a table</p></li>
<li><p>New function <code><a href="../reference/as.mo.html">mo_failures()</a></code> to review values that
could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>.
This latter function will now only show a maximum of 10 uncoerced values
and will refer to <code><a href="../reference/as.mo.html">mo_failures()</a></code>.</p></li>
<li><p>New function <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> to review values
that could be coerced to a valid MO code using <code><a href="../reference/as.mo.html">as.mo()</a></code>, but
with uncertainty.</p></li>
<li><p>New function <code><a href="../reference/as.mo.html">mo_renamed()</a></code> to get a list of all
returned values from <code><a href="../reference/as.mo.html">as.mo()</a></code> that have had taxonomic
renaming</p></li>
<li><p>New function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age
in years</p></li>
<li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom
or predefined groups (like children or elderly). This allows for easier
demographic AMR data analysis per age group.</p></li>
<li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the
base R <code><a href="../reference/plot.html">plot()</a></code> function can now be used for resistance
prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span><span class="va">septic_patients</span>, col_ab <span class="op">=</span> <span class="st">"amox"</span><span class="op">)</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
</li>
<li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and
<code>filter_first_weighted_isolate()</code> to shorten and fasten
filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>
<span class="co"># or</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">only_firsts</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">only_firsts</span><span class="op">)</span></code></pre></div>
</li>
<li><p>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of
available (non-empty) results in a <code>data.frame</code></p></li>
<li><p>New vignettes about how to conduct AMR analysis, predict
antimicrobial resistance, use the <em>G</em>-test and more. These are
also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="external-link uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul></div>
<div class="section level5">
<h5 id="changed-0-6-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-6-0"></a></h5>
<ul><li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul><li>Updated EUCAST Clinical breakpoints to <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">version 9.0 of 1
January 2019</a>, the data set <code>septic_patients</code> now reflects
these changes</li>
<li>Fixed a critical bug where some rules that depend on previous
applied rules would not be applied adequately</li>
<li>Emphasised in manual that penicillin is meant as benzylpenicillin
(ATC <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01" class="external-link">J01CE01</a>)</li>
<li>New info is returned when running this function, stating exactly
what has been changed or added. Use
<code>eucast_rules(..., verbose = TRUE)</code> to get a data set with
all changed per bug and drug combination.</li>
</ul></li>
<li>Removed data sets <code>microorganisms.oldDT</code>,
<code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code>
and <code>microorganismsDT</code> since they were no longer needed and
only contained info already available in the <code>microorganisms</code>
data set</li>
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from
the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
Community Register</a> of the European Commission</li>
<li>Removed columns <code>atc_group1_nl</code> and
<code>atc_group2_nl</code> from the <code>antibiotics</code> data
set</li>
<li>Functions <code>atc_ddd()</code> and <code>atc_groups()</code> have
been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and
<code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and
will be removed in a future version.</li>
<li>Function <code>guess_mo()</code> is now deprecated in favour of
<code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Function <code>guess_atc()</code> is now deprecated in favour of
<code>as.atc()</code> and will be removed in future versions</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul><li>
<p>Now handles incorrect spelling, like <code>i</code> instead of
<code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># mo_fullname() uses as.mo() internally</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"Sthafilokockus aaureuz"</span><span class="op">)</span>
<span class="co">#&gt; [1] "Staphylococcus aureus"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. klossi"</span><span class="op">)</span>
<span class="co">#&gt; [1] "Staphylococcus kloosii"</span></code></pre></div>
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0
to 3, where the default <code>allow_uncertain = TRUE</code> is equal to
uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these
levels.</p>
<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># also equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div>
<p>Using <code>as.mo(..., allow_uncertain = 3)</code> could lead to very
unreliable results.</p>
</li>
<li><p>Implemented the latest publication of Becker <em>et al.</em>
(2019), for categorising coagulase-negative
<em>Staphylococci</em></p></li>
<li><p>All microbial IDs that found are now saved to a local file
<code>~/.Rhistory_mo</code>. Use the new function
<code>clean_mo_history()</code> to delete this file, which resets the
algorithms.</p></li>
<li><p>Incoercible results will now be considered ‘unknown’, MO code
<code>UNKNOWN</code>. On foreign systems, properties of these will be
translated to all languages already previously supported: German, Dutch,
French, Italian, Spanish and Portuguese.</p></li>
<li><p>Fix for vector containing only empty values</p></li>
<li><p>Finds better results when input is in other languages</p></li>
<li><p>Better handling for subspecies</p></li>
<li><p>Better handling for <em>Salmonellae</em>, especially the ‘city
like’ serovars like <em>Salmonella London</em></p></li>
<li><p>Understanding of highly virulent <em>E. coli</em> strains like
EIEC, EPEC and STEC</p></li>
<li><p>There will be looked for uncertain results at default - these
results will be returned with an informative warning</p></li>
<li><p>Manual (help page) now contains more info about the
algorithms</p></li>
<li><p>Progress bar will be shown when it takes more than 3 seconds to
get results</p></li>
<li><p>Support for formatted console text</p></li>
<li><p>Console will return the percentage of uncoercable input</p></li>
</ul></li>
<li>Function <code><a href="../reference/first_isolate.html">first_isolate()</a></code>:
<ul><li>Fixed a bug where distances between dates would not be calculated
right - in the <code>septic_patients</code> data set this yielded a
difference of 0.15% more isolates</li>
<li>Will now use a column named like “patid” for the patient ID
(argument <code>col_patientid</code>), when this argument was left
blank</li>
<li>Will now use a column named like “key(…)ab” or “key(…)antibiotics”
for the key antibiotics (argument <code>col_keyantibiotics()</code>),
when this argument was left blank</li>
<li>Removed argument <code>output_logical</code>, the function will now
always return a logical value</li>
<li>Renamed argument <code>filter_specimen</code> to
<code>specimen_group</code>, although using <code>filter_specimen</code>
will still work</li>
</ul></li>
<li>A note to the manual pages of the <code>portion</code> functions,
that low counts can influence the outcome and that the
<code>portion</code> functions may camouflage this, since they only
return the portion (albeit being dependent on the <code>minimum</code>
argument)</li>
<li>Merged data sets <code>microorganisms.certe</code> and
<code>microorganisms.umcg</code> into
<code>microorganisms.codes</code>
</li>
<li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom
too</li>
<li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> using the
new <code>threshold</code> argument</li>
<li>New colours for <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code>
</li>
<li>Summaries of class <code>mo</code> will now return the top 3 and the
unique count, e.g. using <code>summary(mo)</code>
</li>
<li>Small text updates to summaries of class <code>rsi</code> and
<code>mic</code>
</li>
<li>Function <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:
<ul><li>Now gives a warning when inputting MIC values</li>
<li>Now accepts high and low resistance: <code>"HIGH S"</code> will
return <code>S</code>
</li>
</ul></li>
<li>Frequency tables (<code>freq()</code> function):
<ul><li>
<p>Support for tidyverse quasiquotation! Now you can create
frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<span class="co"># OLD WAY</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
<span class="co"># NEW WAY</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
<span class="co"># Even supports grouping variables:</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
</li>
<li><p>Header info is now available as a list, with the
<code>header</code> function</p></li>
<li><p>The argument <code>header</code> is now set to <code>TRUE</code>
at default, even for markdown</p></li>
<li><p>Added header info for class <code>mo</code> to show unique count
of families, genera and species</p></li>
<li><p>Now honours the <code>decimal.mark</code> setting, which just
like <code>format</code> defaults to
<code>getOption("OutDec")</code></p></li>
<li><p>The new <code>big.mark</code> argument will at default be
<code>","</code> when <code>decimal.mark = "."</code> and
<code>"."</code> otherwise</p></li>
<li><p>Fix for header text where all observations are
<code>NA</code></p></li>
<li><p>New argument <code>droplevels</code> to exclude empty factor
levels when input is a factor</p></li>
<li><p>Factor levels will be in header when present in input data
(maximum of 5)</p></li>
<li><p>Fix for using <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code> on frequency tables</p></li>
</ul></li>
<li>Function <code><a href="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the
<code>limits</code> argument</li>
<li>Automatic argument filling for <code><a href="../reference/mdro.html">mdro()</a></code>,
<code>key_antibiotics()</code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li>
<li>Updated examples for resistance prediction
(<code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> function)</li>
<li>Fix for <code><a href="../reference/as.mic.html">as.mic()</a></code> to support more values ending in
(several) zeroes</li>
<li>if using different lengths of pattern and x in <code>%like%</code>,
it will now return the call</li>
</ul></div>
<div class="section level5">
<h5 id="other-0-6-0">Other<a class="anchor" aria-label="anchor" href="#other-0-6-0"></a></h5>
<ul><li>Updated licence text to emphasise GPL 2.0 and that this is an R
package.</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.5.0" id="amr-050">AMR 0.5.0<small>2018-11-30</small><a class="anchor" aria-label="anchor" href="#amr-050"></a></h2>
<div class="section level5">
<h5 id="new-0-5-0">New<a class="anchor" aria-label="anchor" href="#new-0-5-0"></a></h5>
<ul><li>Repository moved to GitLab</li>
<li>Function <code>count_all</code> to get all available isolates (that
like all <code>portion_*</code> and <code>count_*</code> functions also
supports <code>summarise</code> and <code>group_by</code>), the old
<code>n_rsi</code> is now an alias of <code>count_all</code>
</li>
<li>Function <code>get_locale</code> to determine language for
language-dependent output for some <code>mo_*</code> functions. This is
now the default value for their <code>language</code> argument, by which
the system language will be used at default.</li>
<li>Data sets <code>microorganismsDT</code>,
<code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code>
and <code>microorganisms.oldDT</code> to improve the speed of
<code>as.mo</code>. They are for reference only, since they are
primarily for internal use of <code>as.mo</code>.</li>
<li>Function <code>read.4D</code> to read from the 4D database of the
MMB department of the UMCG</li>
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get
specific values about the scientific reference of a taxonomic entry</li>
</ul></div>
<div class="section level5">
<h5 id="changed-0-5-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-5-0"></a></h5>
<ul><li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code>
and <code>EUCAST_exceptional_phenotypes</code> were renamed to
<code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and
<code>eucast_exceptional_phenotypes</code></p></li>
<li><p><code>EUCAST_rules</code> was renamed to
<code>eucast_rules</code>, the old function still exists as a deprecated
function</p></li>
<li>
<p>Big changes to the <code>eucast_rules</code> function:</p>
<ul><li>Now also applies rules from the EUCAST ‘Breakpoint tables for
bacteria’, version 8.1, 2018, <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link uri">https://www.eucast.org/clinical_breakpoints/</a> (see Source
of the function)</li>
<li>New argument <code>rules</code> to specify which rules should be
applied (expert rules, breakpoints, others or all)</li>
<li>New argument <code>verbose</code> which can be set to
<code>TRUE</code> to get very specific messages about which columns and
rows were affected</li>
<li>Better error handling when rules cannot be applied (i.e. new values
could not be inserted)</li>
<li>The number of affected values will now only be measured once per
row/column combination</li>
<li>Data set <code>septic_patients</code> now reflects these
changes</li>
<li>Added argument <code>pipe</code> for piperacillin (J01CA12), also to
the <code>mdro</code> function</li>
<li>Small fixes to EUCAST clinical breakpoint rules</li>
</ul></li>
<li><p>Added column <code>kingdom</code> to the microorganisms data set,
and function <code>mo_kingdom</code> to look up values</p></li>
<li><p>Tremendous speed improvement for <code>as.mo</code> (and
subsequently all <code>mo_*</code> functions), as empty values wil be
ignored <em>a priori</em></p></li>
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will
return NA</p></li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers)
now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. species"</span><span class="op">)</span> <span class="co"># B_ESCHR</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"E. spp."</span><span class="op">)</span> <span class="co"># "Escherichia species"</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. spp"</span><span class="op">)</span> <span class="co"># B_STPHY</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. species"</span><span class="op">)</span> <span class="co"># "Staphylococcus species"</span></code></pre></div>
</li>
<li><p>Added argument <code>combine_IR</code> (TRUE/FALSE) to functions
<code>portion_df</code> and <code>count_df</code>, to indicate that all
values of I and R must be merged into one, so the output only consists
of S vs. IR (susceptible vs. non-susceptible)</p></li>
<li><p>Fix for <code>portion_*(..., as_percent = TRUE)</code> when
minimal number of isolates would not be met</p></li>
<li><p>Added argument <code>also_single_tested</code> for
<code>portion_*</code> and <code>count_*</code> functions to also
include cases where not all antibiotics were tested but at least one of
the tested antibiotics includes the target antimicribial interpretation,
see <code><a href="../reference/proportion.html">?portion</a></code></p></li>
<li><p>Using <code>portion_*</code> functions now throws a warning when
total available isolate is below argument <code>minimum</code></p></li>
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>,
<code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not
set package name as attribute anymore</p></li>
<li>
<p>Frequency tables - <code>freq()</code>:</p>
<ul><li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
</li>
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html" class="external-link">hms::is.hms</a></code></p></li>
<li><p>Now prints in markdown at default in non-interactive
sessions</p></li>
<li><p>No longer adds the factor level column and sorts factors on count
again</p></li>
<li><p>Support for class <code>difftime</code></p></li>
<li><p>New argument <code>na</code>, to choose which character to print
for empty values</p></li>
<li><p>New argument <code>header</code> to turn the header info off
(default when <code>markdown = TRUE</code>)</p></li>
<li><p>New argument <code>title</code> to manually setbthe title of the
frequency table</p></li>
</ul></li>
<li><p><code>first_isolate</code> now tries to find columns to use as
input when arguments are left blank</p></li>
<li><p>Improvements for MDRO algorithm (function
<code>mdro</code>)</p></li>
<li><p>Data set <code>septic_patients</code> is now a
<code>data.frame</code>, not a tibble anymore</p></li>
<li><p>Removed diacritics from all authors (columns
<code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>)
to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would
become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for
<code>top_freq()</code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have
<code>breaks</code> argument</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
<ul><li>
<code>"CRS"</code> -&gt; <em>Stenotrophomonas maltophilia</em>
</li>
<li>
<code>"CRSM"</code> -&gt; <em>Stenotrophomonas maltophilia</em>
</li>
<li>
<code>"MSSA"</code> -&gt; <em>Staphylococcus aureus</em>
</li>
<li>
<code>"MSSE"</code> -&gt; <em>Staphylococcus epidermidis</em>
</li>
</ul></li>
<li><p>Fix for <code>join</code> functions</p></li>
<li><p>Speed improvement for <code>is.rsi.eligible</code>, now 15-20
times faster</p></li>
<li><p>In <code>g.test</code>, when <code>sum(x)</code> is below 1000 or
any of the expected values is below 5, Fisher’s Exact Test will be
suggested</p></li>
<li><p><code>ab_name</code> will try to fall back on <code>as.atc</code>
when no results are found</p></li>
<li><p>Removed the addin to view data sets</p></li>
<li><p>Percentages will now will rounded more logically (e.g. in
<code>freq</code> function)</p></li>
</ul></div>
<div class="section level5">
<h5 id="other-0-5-0">Other<a class="anchor" aria-label="anchor" href="#other-0-5-0"></a></h5>
<ul><li>New dependency on package <code>crayon</code>, to support formatted
text in the console</li>
<li>Dependency <code>tidyr</code> is now mandatory (went to
<code>Import</code> field) since <code>portion_df</code> and
<code>count_df</code> rely on it</li>
<li>Updated vignettes to comply with README</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.4.0" id="amr-040">AMR 0.4.0<small>2018-10-01</small><a class="anchor" aria-label="anchor" href="#amr-040"></a></h2>
<div class="section level5">
<h5 id="new-0-4-0">New<a class="anchor" aria-label="anchor" href="#new-0-4-0"></a></h5>
<ul><li><p>The data set <code>microorganisms</code> now contains <strong>all
microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi
and Protozoa), the Integrated Taxonomy Information System, available via
<a href="https://itis.gov" class="external-link uri">https://itis.gov</a>. The data
set now contains more than 18,000 microorganisms with all known
bacteria, fungi and protozoa according ITIS with genus, species,
subspecies, family, order, class, phylum and subkingdom. The new data
set <code>microorganisms.old</code> contains all previously known
taxonomic names from those kingdoms.</p></li>
<li>
<p>New functions based on the existing function
<code>mo_property</code>:</p>
<ul><li>Taxonomic names: <code>mo_phylum</code>, <code>mo_class</code>,
<code>mo_order</code>, <code>mo_family</code>, <code>mo_genus</code>,
<code>mo_species</code>, <code>mo_subspecies</code>
</li>
<li>Semantic names: <code>mo_fullname</code>,
<code>mo_shortname</code>
</li>
<li>Microbial properties: <code>mo_type</code>,
<code>mo_gramstain</code>
</li>
<li>Author and year: <code>mo_ref</code>
</li>
</ul><p>They also come with support for German, Dutch, French, Italian,
Spanish and Portuguese:</p>
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="co"># [1] "Gram negative"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># German</span>
<span class="co"># [1] "Gramnegativ"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># Spanish</span>
<span class="co"># [1] "Gram negativo"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. group A"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span> <span class="co"># Portuguese</span>
<span class="co"># [1] "Streptococcus grupo A"</span></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the
current taxonomic name:</p>
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Esc blattae"</span><span class="op">)</span>
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
<span class="co"># [1] "Gram negative"</span></code></pre></div>
</li>
<li>
<p>Functions <code>count_R</code>, <code>count_IR</code>,
<code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to
selectively count resistant or susceptible isolates</p>
<ul><li>Extra function <code>count_df</code> (which works like
<code>portion_df</code>) to get all counts of S, I and R of a data set
with antibiotic columns, with support for grouped variables</li>
</ul></li>
<li><p>Function <code>is.rsi.eligible</code> to check for columns that
have valid antimicrobial results, but do not have the <code>rsi</code>
class yet. Transform the columns of your raw data with:
<code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as
replacements for <code>as.bactid</code> and <code>is.bactid</code>
(since the <code>microoganisms</code> data set not only contains
bacteria). These last two functions are deprecated and will be removed
in a future release. The <code>as.mo</code> function determines
microbial IDs using intelligent rules:</p>
<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="co"># [1] B_ESCHR_COL</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>
<span class="co"># [1] B_STPHY_AUR</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S group A"</span><span class="op">)</span>
<span class="co"># [1] B_STRPTC_GRA</span></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007
it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="fl">25000</span><span class="op">)</span>
<span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
<span class="co"># Unit: seconds</span>
<span class="co"># min median max neval</span>
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span></code></pre></div>
</li>
<li><p>Added argument <code>reference_df</code> for <code>as.mo</code>,
so users can supply their own microbial IDs, name or codes as a
reference table</p></li>
<li>
<p>Renamed all previous references to <code>bactid</code> to
<code>mo</code>, like:</p>
<ul><li>Column names inputs of <code>EUCAST_rules</code>,
<code>first_isolate</code> and <code>key_antibiotics</code>
</li>
<li>Column names of datasets <code>microorganisms</code> and
<code>septic_patients</code>
</li>
<li>All old syntaxes will still work with this version, but will throw
warnings</li>
</ul></li>
<li><p>Function <code>labels_rsi_count</code> to print datalabels on a
RSI <code>ggplot2</code> model</p></li>
<li><p>Functions <code>as.atc</code> and <code>is.atc</code> to
transform/look up antibiotic ATC codes as defined by the WHO. The
existing function <code>guess_atc</code> is now an alias of
<code>as.atc</code>.</p></li>
<li><p>Function <code>ab_property</code> and its aliases:
<code>ab_name</code>, <code>ab_tradenames</code>, <code>ab_certe</code>,
<code>ab_umcg</code> and <code>ab_trivial_nl</code></p></li>
<li><p>Introduction to AMR as a vignette</p></li>
<li><p>Removed clipboard functions as it violated the CRAN
policy</p></li>
<li><p>Renamed <code>septic_patients$sex</code> to
<code>septic_patients$gender</code></p></li>
</ul></div>
<div class="section level5">
<h5 id="changed-0-4-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-4-0"></a></h5>
<ul><li><p>Added three antimicrobial agents to the <code>antibiotics</code>
data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole
(D01AC05)</p></li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set,
it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu">ab_official</span><span class="op">(</span><span class="st">"Bactroban"</span><span class="op">)</span>
<span class="co"># [1] "Mupirocin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span><span class="op">)</span><span class="op">)</span>
<span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span><span class="op">)</span><span class="op">)</span>
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></code></pre></div>
</li>
<li><p>For <code>first_isolate</code>, rows will be ignored when there’s
no species available</p></li>
<li><p>Function <code>ratio</code> is now deprecated and will be removed
in a future release, as it is not really the scope of this
package</p></li>
<li><p>Fix for <code>as.mic</code> for values ending in zeroes after a
real number</p></li>
<li><p>Small fix where <em>B. fragilis</em> would not be found in the
<code>microorganisms.umcg</code> data set</p></li>
<li><p>Added <code>prevalence</code> column to the
<code>microorganisms</code> data set</p></li>
<li><p>Added arguments <code>minimum</code> and <code>as_percent</code>
to <code>portion_df</code></p></li>
<li>
<p>Support for quasiquotation in the functions series
<code>count_*</code> and <code>portions_*</code>, and
<code>n_rsi</code>. This allows to check for more than 2 vectors or
columns.</p>
<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># which is the same as:</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span><span class="op">)</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span>, <span class="va">gent</span><span class="op">)</span>
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span>, <span class="va">gent</span>, <span class="va">pita</span><span class="op">)</span></code></pre></div>
</li>
<li><p>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they
can cope with <code>count_df</code>. The new <code>fun</code> argument
has value <code>portion_df</code> at default, but can be set to
<code>count_df</code>.</p></li>
<li><p>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code>
package was not loaded</p></li>
<li><p>Added datalabels function <code>labels_rsi_count</code> to
<code>ggplot_rsi</code></p></li>
<li><p>Added possibility to set any argument to <code>geom_rsi</code>
(and <code>ggplot_rsi</code>) so you can set your own
preferences</p></li>
<li><p>Fix for joins, where predefined suffices would not be
honoured</p></li>
<li><p>Added argument <code>quote</code> to the <code>freq</code>
function</p></li>
<li><p>Added generic function <code>diff</code> for frequency
tables</p></li>
<li><p>Added longest en shortest character length in the frequency table
(<code>freq</code>) header of class <code>character</code></p></li>
<li>
<p>Support for types (classes) list and matrix for
<code>freq</code></p>
<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
</li>
</ul></div>
<div class="section level5">
<h5 id="other-0-4-0">Other<a class="anchor" aria-label="anchor" href="#other-0-4-0"></a></h5>
<ul><li>More unit tests to ensure better integrity of functions</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.3.0" id="amr-030">AMR 0.3.0<small>2018-08-14</small><a class="anchor" aria-label="anchor" href="#amr-030"></a></h2>
<div class="section level5">
<h5 id="new-0-3-0">New<a class="anchor" aria-label="anchor" href="#new-0-3-0"></a></h5>
<ul><li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour
of new functions <code>portion_R</code>, <code>portion_IR</code>,
<code>portion_I</code>, <code>portion_SI</code> and
<code>portion_S</code> to selectively calculate resistance or
susceptibility. These functions are 20 to 30 times faster than the old
<code>rsi</code> function. The old function still works, but is
deprecated.
<ul><li>New function <code>portion_df</code> to get all portions of S, I and
R of a data set with antibiotic columns, with support for grouped
variables</li>
</ul></li>
<li>
<strong>BREAKING</strong>: the methodology for determining first
weighted isolates was changed. The antibiotics that are compared between
isolates (call <em>key antibiotics</em>) to include more first isolates
(afterwards called first <em>weighted</em> isolates) are now as follows:
<ul><li>Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime,
piperacillin/tazobactam, ciprofloxacin,
trimethoprim/sulfamethoxazole</li>
<li>Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin,
oxacillin, rifampicin</li>
<li>Gram-negative: gentamicin, tobramycin, colistin, cefotaxime,
ceftazidime, meropenem</li>
</ul></li>
<li>Support for <code>ggplot2</code>
<ul><li>New functions <code>geom_rsi</code>, <code>facet_rsi</code>,
<code>scale_y_percent</code>, <code>scale_rsi_colours</code> and
<code>theme_rsi</code>
</li>
<li>New wrapper function <code>ggplot_rsi</code> to apply all above
functions on a data set:
<ul><li>
<code>septic_patients %&gt;% select(tobr, gent) %&gt;% ggplot_rsi</code>
will show portions of S, I and R immediately in a pretty plot</li>
<li>Support for grouped variables, see <code><a href="../reference/ggplot_rsi.html">?ggplot_rsi</a></code>
</li>
</ul></li>
</ul></li>
<li>Determining bacterial ID:
<ul><li>New functions <code>as.bactid</code> and <code>is.bactid</code> to
transform/ look up microbial ID’s.</li>
<li>The existing function <code>guess_bactid</code> is now an alias of
<code>as.bactid</code>
</li>
<li>New Becker classification for <em>Staphylococcus</em> to categorise
them into Coagulase Negative <em>Staphylococci</em> (CoNS) and Coagulase
Positve <em>Staphylococci</em> (CoPS)</li>
<li>New Lancefield classification for <em>Streptococcus</em> to
categorise them into Lancefield groups</li>
</ul></li>
<li>For convience, new descriptive statistical functions
<code>kurtosis</code> and <code>skewness</code> that are lacking in base
R - they are generic functions and have support for vectors, data.frames
and matrices</li>
<li>Function <code>g.test</code> to perform the X<sup>2</sup>
distributed <a href="https://en.wikipedia.org/wiki/G-test" class="external-link"><em>G</em>-test</a>, which
use is the same as <code>chisq.test</code>
</li>
<li>
<del>Function <code>ratio</code> to transform a vector of values to
a preset ratio</del>
<ul><li><del>For example:
<code>ratio(c(10, 500, 10), ratio = "1:2:1")</code> would return
<code>130, 260, 130</code></del></li>
</ul></li>
<li>Support for Addins menu in RStudio to quickly insert
<code>%in%</code> or <code>%like%</code> (and give them keyboard
shortcuts), or to view the datasets that come with this package</li>
<li>Function <code>p.symbol</code> to transform p values to their
related symbols:
<code>0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code>
</li>
<li>Functions <code>clipboard_import</code> and
<code>clipboard_export</code> as helper functions to quickly copy and
paste from/to software like Excel and SPSS. These functions use the
<code>clipr</code> package, but are a little altered to also support
headless Linux servers (so you can use it in RStudio Server)</li>
<li>New for frequency tables (function <code>freq</code>):
<ul><li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as
input</li>
<li>Support for <code>table</code> to use as input:
<code>freq(table(x, y))</code>
</li>
<li>Support for existing functions <code>hist</code> and
<code>plot</code> to use a frequency table as input:
<code>hist(freq(df$age))</code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>,
<code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is
the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below
<em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton
(MAD) and Interquartile Range (IQR)</li>
<li>Possibility to globally set the default for the amount of items to
print, with <code>options(max.print.freq = n)</code> where <em>n</em> is
your preset value</li>
</ul></li>
</ul></div>
<div class="section level5">
<h5 id="changed-0-3-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-3-0"></a></h5>
<ul><li>Improvements for forecasting with <code>resistance_predict</code>
and added more examples</li>
<li>More antibiotics added as arguments for EUCAST rules</li>
<li>Updated version of the <code>septic_patients</code> data set to
better reflect the reality</li>
<li>Pretty printing for tibbles removed as it is not really the scope of
this package</li>
<li>Printing of <code>mic</code> and <code>rsi</code> classes now
returns all values - use <code>freq</code> to check distributions</li>
<li>Improved speed of key antibiotics comparison for determining first
isolates</li>
<li>Column names for the <code>key_antibiotics</code> function are now
generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for
Gram-negative specific ABs</li>
<li>Speed improvement for the <code>abname</code> function</li>
<li>
<code>%like%</code> now supports multiple patterns</li>
<li>Frequency tables are now actual <code>data.frame</code>s with
altered console printing to make it look like a frequency table. Because
of this, the argument <code>toConsole</code> is not longer needed.</li>
<li>Fix for <code>freq</code> where the class of an item would be
lost</li>
<li>Small translational improvements to the <code>septic_patients</code>
dataset and the column <code>bactid</code> now has the new class
<code>"bactid"</code>
</li>
<li>Small improvements to the <code>microorganisms</code> dataset
(especially for <em>Salmonella</em>) and the column <code>bactid</code>
now has the new class <code>"bactid"</code>
</li>
<li>Combined MIC/RSI values will now be coerced by the <code>rsi</code>
and <code>mic</code> functions:
<ul><li>
<code>as.rsi("&lt;=0.002; S")</code> will return <code>S</code>
</li>
<li>
<code>as.mic("&lt;=0.002; S")</code> will return
<code>&lt;=0.002</code>
</li>
</ul></li>
<li>Now possible to coerce MIC values with a space between operator and
value, i.e. <code>as.mic("&lt;= 0.002")</code> now works</li>
<li>Classes <code>rsi</code> and <code>mic</code> do not add the
attribute <code>package.version</code> anymore</li>
<li>Added <code>"groups"</code> option for
<code>atc_property(..., property)</code>. It will return a vector of the
ATC hierarchy as defined by the <a href="https://www.whocc.no/atc/structure_and_principles/" class="external-link">WHO</a>. The
new function <code>atc_groups</code> is a convenient wrapper around
this.</li>
<li>Build-in host check for <code>atc_property</code> as it requires the
host set by <code>url</code> to be responsive</li>
<li>Improved <code>first_isolate</code> algorithm to exclude isolates
where bacteria ID or genus is unavailable</li>
<li>Fix for warning <em>hybrid evaluation forced for row_number</em> (<a href="https://github.com/tidyverse/dplyr/commit/924b62" class="external-link"><code>924b62</code></a>)
from the <code>dplyr</code> package v0.7.5 and above</li>
<li>Support for empty values and for 1 or 2 columns as input for
<code>guess_bactid</code> (now called <code>as.bactid</code>)
<ul><li>So
<code>yourdata %&gt;% select(genus, species) %&gt;% as.bactid()</code>
now also works</li>
</ul></li>
<li>Other small fixes</li>
</ul></div>
<div class="section level5">
<h5 id="other-0-3-0">Other<a class="anchor" aria-label="anchor" href="#other-0-3-0"></a></h5>
<ul><li>Added integration tests (check if everything works as expected) for
all releases of R 3.1 and higher
<ul><li>Linux and macOS: <a href="https://travis-ci.org/msberends/AMR" class="external-link uri">https://travis-ci.org/msberends/AMR</a>
</li>
<li>Windows: <a href="https://ci.appveyor.com/project/msberends/amr" class="external-link uri">https://ci.appveyor.com/project/msberends/amr</a>
</li>
</ul></li>
<li>Added thesis advisors to DESCRIPTION file</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.2.0" id="amr-020">AMR 0.2.0<small>2018-05-03</small><a class="anchor" aria-label="anchor" href="#amr-020"></a></h2>
<div class="section level5">
<h5 id="new-0-2-0">New<a class="anchor" aria-label="anchor" href="#new-0-2-0"></a></h5>
<ul><li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later
is needed (needed packages may have other dependencies)</li>
<li>Function <code>n_rsi</code> to count cases where antibiotic test
results were available, to be used in conjunction with
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">dplyr::summarise</a></code>, see ?rsi</li>
<li>Function <code>guess_bactid</code> to <strong>determine the
ID</strong> of a microorganism based on genus/species or known
abbreviations like MRSA</li>
<li>Function <code>guess_atc</code> to <strong>determine the
ATC</strong> of an antibiotic based on name, trade name, or known
abbreviations</li>
<li>Function <code>freq</code> to create <strong>frequency
tables</strong>, with additional info in a header</li>
<li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant
Organisms (MDRO)</strong> with support for country-specific guidelines.
<ul><li>
<a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">Exceptional
resistances defined by EUCAST</a> are also supported instead of
countries alone</li>
<li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for
Dutch and German guidelines, respectively</li>
</ul></li>
<li>New algorithm to determine weighted isolates, can now be
<code>"points"</code> or <code>"keyantibiotics"</code>, see
<code><a href="../reference/first_isolate.html">?first_isolate</a></code>
</li>
<li>New print format for <code>tibble</code>s and
<code>data.table</code>s</li>
</ul></div>
<div class="section level5">
<h5 id="changed-0-2-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-2-0"></a></h5>
<ul><li>Fixed <code>rsi</code> class for vectors that contain only invalid
antimicrobial interpretations</li>
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
</li>
<li>Renamed dataset <code>bactlist</code> to
<code>microorganisms</code>
</li>
<li>Added common abbreviations and trade names to the
<code>antibiotics</code> dataset</li>
<li>Added more microorganisms to the <code>microorganisms</code>
dataset</li>
<li>Added analysis examples on help page of dataset
<code>septic_patients</code>
</li>
<li>Added support for character vector in <code>join</code>
functions</li>
<li>Added warnings when a join results in more rows after than before
the join</li>
<li>Altered <code>%like%</code> to make it case insensitive</li>
<li>For arguments of functions <code>first_isolate</code> and
<code>EUCAST_rules</code> column names are now case-insensitive</li>
<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the
package name and version as attributes</li>
</ul></div>
<div class="section level5">
<h5 id="other-0-2-0">Other<a class="anchor" aria-label="anchor" href="#other-0-2-0"></a></h5>
<ul><li>Expanded <code>README.md</code> with more examples</li>
<li>Added <a href="https://orcid.org" class="external-link">ORCID</a> of authors to
DESCRIPTION file</li>
<li>Added unit testing with the <code>testthat</code> package</li>
<li>Added build tests for Linux and macOS using Travis CI (<a href="https://travis-ci.org/msberends/AMR" class="external-link uri">https://travis-ci.org/msberends/AMR</a>)</li>
<li>Added line coverage checking using CodeCov (<a href="https://codecov.io/gh/msberends/AMR/tree/main/R" class="external-link uri">https://codecov.io/gh/msberends/AMR/tree/main/R</a>)</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.1.1" id="amr-011">AMR 0.1.1<small>2018-03-14</small><a class="anchor" aria-label="anchor" href="#amr-011"></a></h2>
<ul><li>
<code>EUCAST_rules</code> applies for amoxicillin even if ampicillin
is missing</li>
<li>Edited column names to comply with GLIMS, the laboratory information
system</li>
<li>Added more valid MIC values</li>
<li>Renamed ‘Daily Defined Dose’ to ‘Defined Daily Dose’</li>
<li>Added barplots for <code>rsi</code> and <code>mic</code>
classes</li>
</ul></div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.1.0" id="amr-010">AMR 0.1.0<small>2018-02-22</small><a class="anchor" aria-label="anchor" href="#amr-010"></a></h2>
<ul><li>First submission to CRAN.</li>
</ul></div>
</div>
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