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(v1.5.0.9028) Updated taxonomy until March 2021
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@ -81,7 +81,7 @@
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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">1.5.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9028</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-1509027" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9027">
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<a href="#amr-1509027" class="anchor"></a>AMR 1.5.0.9027<small> Unreleased </small>
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<div id="amr-1509028" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9028">
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<a href="#amr-1509028" class="anchor"></a>AMR 1.5.0.9028<small> Unreleased </small>
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</h1>
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<div id="last-updated-26-february-2021" class="section level2">
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<div id="last-updated-4-march-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-26-february-2021" class="anchor"></a><small>Last updated: 26 February 2021</small>
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<a href="#last-updated-4-march-2021" class="anchor"></a><small>Last updated: 4 March 2021</small>
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<h3 class="hasAnchor">
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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>Microbial taxonomy updated to 3 March 2021 (according to the <a href="https://lpsn.dsmz.de">LSPN</a>)
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<ul>
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<li>Added 3,372 new names and 1,523 existing names became synomyms</li>
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<li>The URL of a bacterial species (<code><a href="../reference/mo_property.html">mo_url()</a></code>) will now lead to <a href="https://lpsn.dsmz.de" class="uri">https://lpsn.dsmz.de</a>
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</li>
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</ul>
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</li>
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<li>Big update for plotting classes <code>rsi</code>, <code><mic></code>, and <code><disk></code>:
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<ul>
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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><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>
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<code><a href="../reference/as.rsi.html">is.rsi()</a></code> and <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now return a vector of <code>TRUE</code>/<code>FALSE</code> when the input is a data set, by iterating over all columns</li>
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<li>Using functions without setting a data set (e.g., <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>) now work with <code>dplyr</code>s <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> again</li>
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@ -322,8 +337,6 @@
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<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
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<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
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<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
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<li>Updated <code><a href="../reference/plot.html">plot()</a></code> functions for classes <code><mic></code>, <code><disk></code> and <code><rsi></code> - the former two now support colouring if you supply the microorganism and antimicrobial agent</li>
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<li>Updated colours to colour-blind friendly version for values R, S and I in tibble printing and for all plot methods (<code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> and using <code><a href="../reference/plot.html">plot()</a></code> on classes <code><mic></code>, <code><disk></code> and <code><rsi></code>)</li>
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<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
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</li>
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<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
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<code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_mic()</a></code> now have an expanded range in their randomisation</li>
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<li>Support for GISA (glycopeptide-intermediate <em>S. aureus</em>), so e.g. <code><a href="../reference/mo_property.html">mo_genus("GISA")</a></code> will return <code>"Staphylococcus"</code>
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</li>
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<li>Added translations of German and Spanish for more than 200 antimicrobial drugs</li>
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</ul>
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</div>
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<div id="other" class="section level3">
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