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(v1.2.0.9037) survey on website

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dr. M.S. (Matthijs) Berends
2020-07-28 18:39:57 +02:00
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34
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -176,7 +176,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -190,7 +190,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -206,10 +206,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -229,13 +229,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209036" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9036">
<a href="#amr-1209036" class="anchor"></a>AMR 1.2.0.9036<small> Unreleased </small>
<div id="amr-1209037" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9037">
<a href="#amr-1209037" class="anchor"></a>AMR 1.2.0.9037<small> Unreleased </small>
</h1>
<div id="last-updated-22-july-2020" class="section level2">
<div id="last-updated-28-july-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-22-july-2020" class="anchor"></a><small>Last updated: 22 July 2020</small>
<a href="#last-updated-28-july-2020" class="anchor"></a><small>Last updated: 28 July 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
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<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 selections</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 Tidyverse selections, 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>
<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="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
@ -285,13 +285,21 @@
</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>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>Fixed a bug for using grouped versions of <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>, and fixed a bug where not all different antimicrobial results were added as rows</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>
</ul>
</div>
<div id="other" class="section level3">