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(v1.7.1.9005) ab class selectors for R-3.0 and R-3.1
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9005</span>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1719004" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9004">
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<a href="#amr-1719004" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9004</h1>
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<div id="last-updated-15-june-2021" class="section level2">
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<div id="amr-1719005" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9005">
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<a href="#amr-1719005" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9005</h1>
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<div id="last-updated-22-june-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-15-june-2021" class="anchor"></a><small>Last updated: 15 June 2021</small>
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<a href="#last-updated-22-june-2021" class="anchor"></a><small>Last updated: 22 June 2021</small>
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</h2>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed" class="anchor"></a>Changed</h3>
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<ul>
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<li>Added more antibiotic class selectors: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code>
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<li>Antibiotic class selectors (see <code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code>)
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<ul>
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<li>They now finally also work in R-3.0 and R-3.1, supporting every version of R since 2013</li>
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<li>Added more selectors: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code>
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</li>
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<li>Fix for using selectors multiple times in one call (e.g., using them in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>)</li>
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</ul>
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</li>
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<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">ggplot2::autoplot()</a></code> generic for classes <code><mic></code>, <code><disk></code>, <code><rsi></code> and <code><resistance_predict></code>
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</li>
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<li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
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<li>Added more informative error messages when any of the <code>proportion_*()</code> and <code>count_*()</code> functions fail</li>
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<li>Fix for using antibiotic selectors multiple times in one call (e.g., using in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>)</li>
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<li>When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using <code><a href="../reference/as.mo.html">as.mo()</a></code>
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</li>
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<li>Improved automatic column selector when <code>col_*</code> arguments are left blank, e.g. in <code><a href="../reference/first_isolate.html">first_isolate()</a></code>
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</li>
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<li>The right input types for <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> are now enforced</li>
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</ul>
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</div>
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</div>
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</ul>
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</li>
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<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
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<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
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<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
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</li>
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</ul>
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</div>
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<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
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</li>
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<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
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<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li>
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<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
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<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
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<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
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</ul>
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</li>
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<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
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