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(v1.7.1.9020) autoplot generics
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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">1.7.1.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
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</span>
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</div>
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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-1719019" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9019">
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<a href="#amr-1719019" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9019</h1>
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<div id="amr-1719020" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9020">
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<a href="#amr-1719020" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9020</h1>
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<div id="last-updated-12-july-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-12-july-2021" class="anchor"></a><small>Last updated: 12 July 2021</small>
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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>Previously implemented <code>ggplot2::gggplot()</code> generics for classes <code><mic></code>, <code><disk></code>, <code><rsi></code> and <code><resistance_predict></code> did not follow the <code>ggplot2</code> logic, and were replaced with <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">autoplot()</a></code> generics.</li>
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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 also work in R-3.0 and R-3.1, supporting every version of R since 2013</li>
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</ul>
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</li>
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<li>Fix for duplicate ATC codes in the <code>antibiotics</code> data set</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>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>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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<li>
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<code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now correct for textual input (such as “Susceptible”, “Resistant”) in Dutch, English, French, German, Italian, Portuguese and Spanish</li>
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<li>When warnings are throws because of too few isolates in any <code>count_*()</code>, <code>proportion_*()</code> function (or <code>resistant()</code> or <code>susceptible()</code>), the <code>dplyr</code> group will be shown, if available</li>
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<li>Taxonomic names now print in italic in tibbles, if created with <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/mo_property.html">mo_fullname()</a></code>, <code><a href="../reference/mo_property.html">mo_shortname()</a></code>, <code><a href="../reference/mo_property.html">mo_genus()</a></code> or <code><a href="../reference/mo_property.html">mo_family()</a></code>
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</li>
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<li>When warnings are thrown because of too few isolates in any <code>count_*()</code>, <code>proportion_*()</code> function (or <code>resistant()</code> or <code>susceptible()</code>), the <code>dplyr</code> group will be shown, if available</li>
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<li>
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<code><a href="../reference/ab_property.html">ab_name()</a></code> gained argument <code>snake_case</code>, which is useful for column renaming</li>
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<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is bug ggplot2<a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
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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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