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(v1.2.0.9001) filter_ab_class() update

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dr. M.S. (Matthijs) Berends
2020-06-03 11:48:00 +02:00
parent 02d07b9fb3
commit 5dc4c96b7d
18 changed files with 159 additions and 77 deletions
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docs/404.html
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@ -81,7 +81,7 @@
</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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>

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docs/LICENSE-text.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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>

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docs/articles/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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>

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docs/authors.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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>

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docs/index.html
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@ -43,7 +43,7 @@
</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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>

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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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>
@ -229,20 +229,24 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209000" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9000">
<a href="#amr-1209000" class="anchor"></a>AMR 1.2.0.9000<small> Unreleased </small>
<div id="amr-1209001" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9001">
<a href="#amr-1209001" class="anchor"></a>AMR 1.2.0.9001<small> Unreleased </small>
</h1>
<div id="last-updated-02-jun-2020" class="section level2">
<div id="last-updated-03-jun-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-02-jun-2020" class="anchor"></a><small>Last updated: 02-Jun-2020</small>
<a href="#last-updated-03-jun-2020" class="anchor"></a><small>Last updated: 03-Jun-2020</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<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>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>
</ul>
</div>
</div>
@ -274,7 +278,7 @@
<ul>
<li>Taxonomy:
<ul>
<li>Updated the taxonomy of microorganisms tot May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). <strong>Note:</strong> a taxonomic update may always impact determination of first isolates (using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.</li>
<li>Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). <strong>Note:</strong> a taxonomic update may always impact determination of first isolates (using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.</li>
<li>Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)</li>
</ul>
</li>

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docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-06-02T14:04Z
last_built: 2020-06-03T09:44Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

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<script src="../extra.js"></script>
<meta property="og:title" content="Filter isolates on result in antimicrobial class — filter_ab_class" />
<meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>
@ -232,7 +232,7 @@
</div>
<div class="ref-description">
<p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.</p>
<p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.</p>
</div>
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='no'>x</span>, <span class='no'>ab_class</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
@ -259,6 +259,8 @@
<span class='fu'>filter_macrolides</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_penicillins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_tetracyclines</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -288,7 +290,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>group</code> column in <a href='antibiotics.html'>antibiotics</a> data set will be searched for <code>ab_class</code> (case-insensitive). If no results are found, the <code>atc_group1</code> and <code>atc_group2</code> columns will be searched. Next, <code>x</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
<p>The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched for the input given in <code>ab_class</code> (case-insensitive). Next, <code>x</code> will be checked for column names with a value in any abbreviation, code or official name found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -302,6 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># filter on isolates that have any result for any aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>()
<span class='co'># this is essentially the same as (but without determination of column names):</span>
@ -311,7 +314,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># filter on isolates that show resistance to ANY aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
<span class='co'># filter on isolates that show resistance to ALL aminoglycosides</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)

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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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>
@ -421,7 +421,7 @@
</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter isolates on result in antimicrobial class</p></td>
</tr><tr>