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(v1.2.0.9004) rsi_df() fix for groups

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dr. M.S. (Matthijs) Berends
2020-06-09 16:18:03 +02:00
parent 40221e5244
commit 8b692ecfcf
17 changed files with 68 additions and 32 deletions
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docs/404.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>

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docs/LICENSE-text.html
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</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">1.2.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>

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docs/articles/index.html
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</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">1.2.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>

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docs/authors.html
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</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">1.2.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>

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docs/index.html
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</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">1.2.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>

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docs/news/index.html
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</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">1.2.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209003" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9003">
<a href="#amr-1209003" class="anchor"></a>AMR 1.2.0.9003<small> Unreleased </small>
<div id="amr-1209004" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9004">
<a href="#amr-1209004" class="anchor"></a>AMR 1.2.0.9004<small> Unreleased </small>
</h1>
<div id="last-updated-05-jun-2020" class="section level2">
<div id="last-updated-09-jun-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-05-jun-2020" class="anchor"></a><small>Last updated: 05-Jun-2020</small>
<a href="#last-updated-09-jun-2020" class="anchor"></a><small>Last updated: 09-Jun-2020</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
@ -244,9 +244,12 @@
<li>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</li>
<li>All <code>*_join_microorganisms()</code> functions now return the original data class (e.g. tibbles and data.tables)</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>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>
</li>
<li>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>)</li>
<li>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>
</li>
<li>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</li>
</ul>
</div>
</div>

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docs/pkgdown.yml
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WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-06-05T11:55Z
last_built: 2020-06-09T14:15Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

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docs/reference/antibiotics.html
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>
<title>Data sets with 558 antimicrobials — antibiotics • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data sets with 557 antimicrobials — antibiotics" />
<meta property="og:title" content="Data sets with 558 antimicrobials — antibiotics" />
<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
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</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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>
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<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data sets with 557 antimicrobials</h1>
<h1>Data sets with 558 antimicrobials</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>antibiotics.Rd</code></div>
</div>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 455 observations and 14 variables:</h3>
<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>

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</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">1.2.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span>
</div>
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<td>
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
</td>
<td><p>Data sets with 557 antimicrobials</p></td>
<td><p>Data sets with 558 antimicrobials</p></td>
</tr><tr>
<td>