You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

1840 lines
136 KiB

<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Changelog • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Changelog" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-news">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9012</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1 data-toc-skip>Changelog <small></small></h1>
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309012" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9012">
<a href="#amr-1309012" class="anchor"></a>AMR 1.3.0.9012<small> Unreleased </small>
</h1>
<div id="last-updated-29-august-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-29-august-2020" class="anchor"></a><small>Last updated: 29 August 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<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="cb1"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">intrinsic_resistant</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="kw">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(<span class="kw">microorganism</span>)
<span class="co">#&gt; [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span>
</pre></div>
</li>
</ul>
</div>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Improvements for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:</p>
<ul>
<li>
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="co"># until dplyr 1.0.0</span>
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.mic</span>, <span class="kw">as.rsi</span>)
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.disk</span>, <span class="kw">as.rsi</span>)
<span class="co"># since dplyr 1.0.0</span>
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.mic</span>), <span class="kw">as.rsi</span>))
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.disk</span>), <span class="kw">as.rsi</span>))
</pre></div>
</li>
<li><p>Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.</p></li>
<li><p>Added parameter ‘add_intrinsic_resistance’ (defaults to <code>FALSE</code>), that considers intrinsic resistance according to EUCAST</p></li>
</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="cb3"><pre class="downlit">
<span class="fu"><a href="../reference/as.disk.html">as.disk</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span>))
<span class="co">#&gt; Class &lt;disk&gt;</span>
<span class="co">#&gt; [1] 24 24</span>
</pre></div>
</li>
<li><p>Speed improvement for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></p></li>
<li><p>Overall speed improvement by tweaking joining functions</p></li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li>
<li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
<li><p>Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: <code>tibble</code> printing support for classes <code>&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>
</ul>
</div>
</div>
</div>
<div id="amr-130" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small>
</h1>
<div id="new-1" class="section level3">
<h3 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h3>
<ul>
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span>())
<span class="co">#&gt; Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span>
</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><a href="../reference/filter_ab_class.html">filter_penicillins()</a></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><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></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 parameter <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
</ul>
</div>
<div id="changed-1" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
<p>As a consequence, very old microbial codes (from <code>AMR</code> v0.5.0 and lower) <strong>are not supported anymore</strong>. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> on your microorganism names or codes to transform them to current abbreviations used in this package.</p>
</li>
<li>
<p>Improvements for <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> and all <code>count_*()</code>, <code>proportion_*()</code> functions:</p>
<ul>
<li>95% speed improvement by using other base R functions for calculation</li>
<li>Using unexisting columns wil now return an error instead of dropping them silently</li>
<li>Using variables for column names (as well as selectors like <code><a href="https://tidyselect.r-lib.org/reference/all_of.html">dplyr::all_of()</a></code>) now works again</li>
</ul>
</li>
<li>
<p>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:</p>
<ul>
<li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more</li>
<li>Added progress bar</li>
<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
<li>The <code><a href="../reference/as.ab.html">as.ab()</a></code> function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.</li>
</ul>
</li>
<li><p>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</p></li>
<li><p>Fixed a bug for CLSI 2019 guidelines (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>), that also included results for animals. It now only contains interpretation guidelines for humans.</p></li>
<li><p>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</p></li>
<li>
<p>For functions <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>:</p>
<ul>
<li>Fixed a bug for using grouped versions</li>
<li>Fixed a bug where not all different antimicrobial results were added as rows</li>
<li>Fixed a bug when only calculating counts (<code><a href="../reference/count.html">count_df()</a></code>) when all antibiotics in the data set have only <code>NA</code>s</li>
</ul>
</li>
<li><p>Improved auto-determination for columns of types <code>&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><a href="../reference/filter_ab_class.html">filter_ab_class()</a></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 id="other" class="section level3">
<h3 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h3>
<ul>
<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
</ul>
</div>
</div>
<div id="amr-120" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0">
<a href="#amr-120" class="anchor"></a>AMR 1.2.0<small> 2020-05-28 </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
<ul>
<li>
<p>Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p>
<ul>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&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 id="changed-2" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-2" class="anchor"></a>Changed</h3>
<ul>
<li>Taxonomy:
<ul>
<li>Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). <strong>Note:</strong> a taxonomic update may always impact determination of first isolates (using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.</li>
<li>Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)</li>
</ul>
</li>
<li>EUCAST rules:
<ul>
<li>The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function no longer applies “other” rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzyme inhibitor = R). The default input value for <code>rules</code> is now <code><a href="https://rdrr.io/r/base/c.html">c("breakpoints", "expert")</a></code> instead of <code>"all"</code>, but this can be changed by the user. To return to the old behaviour, set <code><a href="https://rdrr.io/r/base/options.html">options(AMR.eucast_rules = "all")</a></code>.</li>
<li>Fixed a bug where checking antimicrobial results in the original data were not regarded as valid R/SI values</li>
<li>All “other” rules now apply for all drug combinations in the <code>antibiotics</code> data set these two rules:
<ol>
<li>A drug <strong>with</strong> enzyme inhibitor will be set to S if the drug <strong>without</strong> enzyme inhibitor is S</li>
<li>A drug <strong>without</strong> enzyme inhibitor will be set to R if the drug <strong>with</strong> enzyme inhibitor is R</li>
</ol>
This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/avibactam, trimethoprim/sulfamethoxazole, etc.</li>
<li>Added official drug names to verbose output of <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li>
</ul>
</li>
<li>Added function <code><a href="../reference/ab_property.html">ab_url()</a></code> to return the direct URL of an antimicrobial agent from the official WHO website</li>
<li>Improvements for algorithm in <code><a href="../reference/as.ab.html">as.ab()</a></code>, so that e.g. <code><a href="../reference/as.ab.html">as.ab("ampi sul")</a></code> and <code><a href="../reference/ab_property.html">ab_name("ampi sul")</a></code> work</li>
<li>Functions <code><a href="../reference/ab_property.html">ab_atc()</a></code> and <code><a href="../reference/ab_property.html">ab_group()</a></code> now return <code>NA</code> if no antimicrobial agent could be found</li>
<li>Small fix for some text input that could not be coerced as valid MIC values</li>
<li>Fix for interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)</li>
<li>Fix for <code><a href="../reference/mo_source.html">set_mo_source()</a></code> to make sure that column <code>mo</code> will always be the second column</li>
<li>Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam</li>
</ul>
</div>
<div id="other-1" class="section level3">
<h3 class="hasAnchor">
<a href="#other-1" class="anchor"></a>Other</h3>
<ul>
<li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code><a href="../reference/p_symbol.html">p_symbol()</a></code>
</li>
<li>Removed function <code>read.4d()</code>, that was only useful for reading data from an old test database.</li>
</ul>
</div>
</div>
<div id="amr-110" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0">
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small>
</h1>
<div id="new-2" class="section level3">
<h3 class="hasAnchor">
<a href="#new-2" class="anchor"></a>New</h3>
<ul>
<li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
</ul>
</div>
<div id="changed-3" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-3" class="anchor"></a>Changed</h3>
<ul>
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
<ul>
<li>Support for codes ending with <code>SPE</code> for species, like <code>"ESCSPE"</code> for <em>Escherichia coli</em>
</li>
<li>Support for any encoding, which means that any language-specific character with accents can be used for input</li>
<li>Support for more arbitrary IDs used in laboratory information systems</li>
<li>Small fix for preventing viruses being treated as bacteria</li>
<li>Small fix for preventing contamination and lack of growth being treated as valid microorganisms</li>
</ul>
</li>
<li>Support for all abbreviations of antibiotics and antimycotics used by the Netherlands National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu; RIVM)</li>
<li>Added more abbreviations to the <code>antibiotics</code> data set</li>
<li>Reloaded original EUCAST master tables from 2019 (2020 was already available). This seems more reliable than the data we used from WHONET.</li>
<li>Added generic CLSI rules for R/SI interpretation using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for years 2010-2019 (thanks to Anthony Underwood)</li>
</ul>
</div>
<div id="other-2" class="section level3">
<h3 class="hasAnchor">
<a href="#other-2" class="anchor"></a>Other</h3>
<ul>
<li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
<li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
</li>
</ul>
</div>
</div>
<div id="amr-101" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1">
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small>
</h1>
<div id="changed-4" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-4" class="anchor"></a>Changed</h3>
<ul>
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="kw">yourdata</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="st">"E. coli"</span>)
<span class="kw">yourdata</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="kw">.</span><span class="op">$</span><span class="kw">mybacteria</span>)
</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 parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
<li><p>Info printing in functions <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)</p></li>
</ul>
</div>
</div>
<div id="amr-100" class="section level1">
<h1 class="page-header" data-toc-text="1.0.0">
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
</h1>
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
<div id="new-3" class="section level3">
<h3 class="hasAnchor">
<a href="#new-3" class="anchor"></a>New</h3>
<ul>
<li>Support for the newest <a href="http://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/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/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
<li>Support for LOINC and SNOMED codes
<ul>
<li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</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="st">"21066-6"</span>)
<span class="co">#&gt; [1] "Ampicillin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"21066-6"</span>)
<span class="co">#&gt; [1] "J01CA01"</span>
</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="cb7"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</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="fl">115329001</span>)
<span class="co">#&gt; [1] "Staphylococcus aureus"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="fl">115329001</span>)
<span class="co">#&gt; [1] "Gram-positive"</span>
</pre></div>
</li>
</ul>
</li>
</ul>
</div>
<div id="changes" class="section level3">
<h3 class="hasAnchor">
<a href="#changes" class="anchor"></a>Changes</h3>
<ul>
<li>The <code><a href="../reference/as.mo.html">as.mo()</a></code> function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the function <code>clear_mo_history()</code> was removed.</li>
<li>Bugfix for some WHONET microorganism codes that were not interpreted correctly when using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
<ul>
<li>Support for missing spaces, e.g. in <code><a href="../reference/as.mo.html">as.mo("Methicillin-resistant S.aureus")</a></code>
</li>
<li>Better support for determination of <em>Salmonella</em> biovars</li>
<li>Speed improvements, especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K pneumoniae</em>
</li>
<li>Support for more common codes used in laboratory information systems</li>
</ul>
</li>
<li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li>
<li>Added a lifecycle state to every function, following <a href="https://www.tidyverse.org/lifecycle">the lifecycle circle of the <code>tidyverse</code></a>
</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">the combination rifampicin/isoniazid has no DDDs defined</a>, so e.g. <code><a href="../reference/ab_property.html">ab_ddd("Rimactazid")</a></code> will now return <code>NA</code>.</li>
<li>Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (<code>SMX</code>) to trimethoprim/sulfamethoxazole (<code>SXT</code>)</li>
</ul>
</li>
</ul>
</div>
<div id="other-3" class="section level3">
<h3 class="hasAnchor">
<a href="#other-3" class="anchor"></a>Other</h3>
<ul>
<li>Add a <code>CITATION</code> file</li>
<li>Full support for the upcoming R 4.0</li>
<li>Removed unnecessary <code>AMR::</code> calls</li>
</ul>
</div>
</div>
<div id="amr-090" class="section level1">
<h1 class="page-header" data-toc-text="0.9.0">
<a href="#amr-090" class="anchor"></a>AMR 0.9.0<small> 2019-11-29 </small>
</h1>
<div id="breaking-1" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking-1" class="anchor"></a>Breaking</h3>
<ul>
<li>Adopted Adeolu <em>et al.</em> (2016), <a href="https://www.ncbi.nlm.nih.gov/pubmed/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="cb8"><pre class="downlit">
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="kw">...</span>
</pre></div>
<p>then please adjust this to:</p>
<div class="sourceCode" id="cb9"><pre class="downlit">
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacterales"</span>) <span class="kw">...</span>
</pre></div>
</li>
</ul>
</li>
</ul>
</div>
<div id="new-4" class="section level3">
<h3 class="hasAnchor">
<a href="#new-4" class="anchor"></a>New</h3>
<ul>
<li>
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
<div class="sourceCode" id="cb10"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(bug = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(amoxicillin = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>),
amox_clav = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMC</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amoxicillin</span>) <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amox_clav</span>))
</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><a href="../reference/mdro.html">mdro(...., verbose = TRUE)</a></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 id="changes-1" class="section level3">
<h3 class="hasAnchor">
<a href="#changes-1" class="anchor"></a>Changes</h3>
<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">Levenshtein distance</a>:</p>
<div class="sourceCode" id="cb11"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
<span class="st">"staphylokok aureuz"</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="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>
</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 id="other-4" class="section level3">
<h3 class="hasAnchor">
<a href="#other-4" class="anchor"></a>Other</h3>
<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">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 id="amr-080" class="section level1">
<h1 class="page-header" data-toc-text="0.8.0">
<a href="#amr-080" class="anchor"></a>AMR 0.8.0<small> 2019-10-15 </small>
</h1>
<div id="breaking-2" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking-2" class="anchor"></a>Breaking</h3>
<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 parameter <code>include_unknown</code>:</p>
<div class="sourceCode" id="cb12"><pre class="downlit">
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">...</span>, include_unknown = <span class="fl">TRUE</span>)
</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="cb13"><pre class="downlit">
<span class="co"># how it works in base R:</span>
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
<span class="kw">x</span>[<span class="fl">1</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="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
<span class="kw">x</span>[<span class="fl">1</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>
</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"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">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 id="new-5" class="section level3">
<h3 class="hasAnchor">
<a href="#new-5" class="anchor"></a>New</h3>
<ul>
<li>
<p>Function <code><a href="../reference/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="cb14"><pre class="downlit">
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>)
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</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="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>, FUN = <span class="kw">mo_gramstain</span>)
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</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>
</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">format()</a></code> function:</p>
<div class="sourceCode" id="cb15"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="kw">x</span>, combine_IR = <span class="fl">FALSE</span>)
</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 parameter <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="cb16"><pre class="downlit">
<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>
</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="cb17"><pre class="downlit">
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">mo</span><span class="op">:</span><span class="kw">AMC</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span>()
</pre></div>
</li>
</ul>
</div>
<div id="changed-5" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-5" class="anchor"></a>Changed</h3>
<ul>
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
<ul>
<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 æ (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><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></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> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter 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><a href="../reference/filter_ab_class.html">filter_ab_class()</a></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><a href="../reference/AMR-deprecated.html">portion_R()</a></code> instead of <code><a href="../reference/AMR-deprecated.html">portion_IR()</a></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> parameter to remove empty values</li>
<li>Renamed function <code>p.symbol()</code> to <code><a href="../reference/p_symbol.html">p_symbol()</a></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><a href="../reference/key_antibiotics.html">key_antibiotics()</a></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 id="other-5" class="section level4">
<h4 class="hasAnchor">
<a href="#other-5" class="anchor"></a>Other</h4>
<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 id="amr-071" class="section level1">
<h1 class="page-header" data-toc-text="0.7.1">
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
</h1>
<div id="new-6" class="section level4">
<h4 class="hasAnchor">
<a href="#new-6" class="anchor"></a>New</h4>
<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><a href="../reference/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb18"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">AMX</span>, <span class="kw">CIP</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></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>
</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="cb19"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
<span class="co"># B_ESCHR_COL</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
<span class="co"># "Escherichia coli"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)
<span class="co"># "Gram-negative"</span>
</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 id="changed-6" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-6" class="anchor"></a>Changed</h4>
<ul>
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></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="https://rdrr.io/r/graphics/plot.default.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html">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 id="other-6" class="section level4">
<h4 class="hasAnchor">
<a href="#other-6" class="anchor"></a>Other</h4>
<ul>
<li>Fixed a note thrown by CRAN tests</li>
</ul>
</div>
</div>
<div id="amr-070" class="section level1">
<h1 class="page-header" data-toc-text="0.7.0">
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
</h1>
<div id="new-7" class="section level4">
<h4 class="hasAnchor">
<a href="#new-7" class="anchor"></a>New</h4>
<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">here on our website</a>.</li>
</ul>
</div>
<div id="changed-7" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-7" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<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 superceded 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/master/data-raw/translations.tsv">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 parameter <code>colours</code> to set the bar colours</li>
<li>New parameters <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><a href="../reference/AMR-deprecated.html">portion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code> this means that their new parameter <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 parameter <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="cb20"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
<span class="co"># grouped boxplots:</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu">freq</span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
</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/master/data-raw/eucast_rules.tsv">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 id="other-7" class="section level4">
<h4 class="hasAnchor">
<a href="#other-7" class="anchor"></a>Other</h4>
<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">staged install</a>
</li>
</ul>
</div>
</div>
<div id="amr-061" class="section level1">
<h1 class="page-header" data-toc-text="0.6.1">
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
</h1>
<div id="changed-8" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-8" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
</li>
<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 id="amr-060" class="section level1">
<h1 class="page-header" data-toc-text="0.6.0">
<a href="#amr-060" class="anchor"></a>AMR 0.6.0<small> 2019-03-27 </small>
</h1>
<p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p>
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
</ul>
<div id="new-8" class="section level4">
<h4 class="hasAnchor">
<a href="#new-8" class="anchor"></a>New</h4>
<ul>
<li><p><strong>BREAKING</strong>: removed deprecated functions, parameters 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/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">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 parameters 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="cb21"><pre class="downlit">
<span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()
</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="cb22"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>, scope = <span class="st">"all"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span>
</pre></div>
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb23"><pre class="downlit">
<span class="kw">ab_property</span> <span class="op">-&gt;</span> <span class="fu">atc_property</span>()
<span class="kw">ab_name</span> <span class="op">-&gt;</span> <span class="fu">atc_name</span>()
<span class="kw">ab_official</span> <span class="op">-&gt;</span> <span class="fu">atc_official</span>()
<span class="kw">ab_trivial_nl</span> <span class="op">-&gt;</span> <span class="fu">atc_trivial_nl</span>()
<span class="kw">ab_certe</span> <span class="op">-&gt;</span> <span class="fu">atc_certe</span>()
<span class="kw">ab_umcg</span> <span class="op">-&gt;</span> <span class="fu">atc_umcg</span>()
<span class="kw">ab_tradenames</span> <span class="op">-&gt;</span> <span class="fu">atc_tradenames</span>()
</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_property.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"><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 antimicrobial resistance 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="https://rdrr.io/r/graphics/plot.default.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="cb24"><pre class="downlit">
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">septic_patients</span>, col_ab = <span class="st">"amox"</span>)
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span>(<span class="kw">x</span>)
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">x</span>)
</pre></div>
</li>
<li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb25"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">...</span>)
<span class="co"># or</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)
</pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb26"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(only_firsts = <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">only_firsts</span> <span class="op">==</span> <span class="fl">TRUE</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">only_firsts</span>)
</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="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul>
</div>
<div id="changed-9" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-9" class="anchor"></a>Changed</h4>
<ul>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
<li>Updated EUCAST Clinical breakpoints to <a href="http://www.eucast.org/clinical_breakpoints/">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">J01CE01</a>)</li>
<li>New info is returned when running this function, stating exactly what has been changed or added. Use <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></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="http://ec.europa.eu/health/documents/community-register/html/atc.htm">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_property.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online_property.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="cb27"><pre class="downlit">
<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="st">"Sthafilokockus aaureuz"</span>)
<span class="co">#&gt; [1] "Staphylococcus aureus"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)
<span class="co">#&gt; [1] "Staphylococcus kloosii"</span>
</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="cb28"><pre class="downlit">
<span class="co"># equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">TRUE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">2</span>)
<span class="co"># also equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">FALSE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">0</span>)
</pre></div>
<p>Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></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>
<div class="sourceCode" id="cb29"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, language = <span class="st">"es"</span>)
<span class="co"># Warning: </span>
<span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
<span class="co">#&gt; [1] "(género desconocido)"</span>
</pre></div>
</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 (parameter <code>col_patientid</code>), when this parameter was left blank</li>
<li>Will now use a column named like “key(…)ab” or “key(…)antibiotics” for the key antibiotics (parameter <code>col_keyantibiotics()</code>), when this parameter was left blank</li>
<li>Removed parameter <code>output_logical</code>, the function will now always return a logical value</li>
<li>Renamed parameter <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> parameter)</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> parameter</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><a href="https://rdrr.io/r/base/summary.html">summary(mo)</a></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="cb30"><pre class="downlit">
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<span class="co"># OLD WAY</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(genus = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span>
<span class="fu">freq</span>(<span class="kw">genus</span>)
<span class="co"># NEW WAY</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
<span class="co"># Even supports grouping variables:</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><