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(v0.8.0.9033) antivirals data set, cleanup
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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">0.8.0.9029</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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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">0.8.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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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">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
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This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
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This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
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<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
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<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
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<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
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</button>
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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">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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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">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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</button>
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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">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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</button>
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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">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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@ -85,7 +85,7 @@
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</button>
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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">0.8.0.9027</span>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
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@ -253,7 +253,7 @@
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<dt><code>abbr</code></dt><dd><p>List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></dd>
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<dt><code>synonyms</code></dt><dd><p>Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></dd>
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<dt><code>oral_ddd</code></dt><dd><p>Defined Daily Dose (DDD), oral treatment</p></dd>
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<dt><code>oral_units</code></dt><dd><p>Units of <code>ddd_units</code></p></dd>
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<dt><code>oral_units</code></dt><dd><p>Units of <code>oral_ddd</code></p></dd>
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<dt><code>iv_ddd</code></dt><dd><p>Defined Daily Dose (DDD), parenteral treatment</p></dd>
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<dt><code>iv_units</code></dt><dd><p>Units of <code>iv_ddd</code></p></dd>
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@ -272,7 +272,7 @@
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<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
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This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
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This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
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<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
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<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
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@ -283,7 +283,7 @@ This package contains <strong>all ~450 antimicrobial drugs</strong> and their An
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<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<div class='dont-index'><p><code>antivirals</code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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docs/reference/antivirals.html
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|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data set with ~100 antivirals</h1>
|
||||
|
||||
<div class="hidden name"><code>antivirals.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>A data set containing all antivirals, according to the ATC code group 'J05' (Antivirals for systemic use).</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='no'>antivirals</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 102 observations and 7 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></dd>
|
||||
<dt><code>name</code></dt><dd><p>Official name as used by WHONET/EARS-Net or the WHO</p></dd>
|
||||
<dt><code>atc_group</code></dt><dd><p>Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></dd>
|
||||
<dt><code>oral_ddd</code></dt><dd><p>Defined Daily Dose (DDD), oral treatment</p></dd>
|
||||
<dt><code>oral_units</code></dt><dd><p>Units of <code>oral_ddd</code></p></dd>
|
||||
<dt><code>iv_ddd</code></dt><dd><p>Defined Daily Dose (DDD), parenteral treatment</p></dd>
|
||||
<dt><code>iv_units</code></dt><dd><p>Units of <code>iv_ddd</code></p></dd>
|
||||
|
||||
</dl>
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='antibiotics.html'>antibiotics</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
<li><a href="#source">Source</a></li>
|
||||
<li><a href="#whocc">WHOCC</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
</ul>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
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|
||||
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
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indexName: 'amr',
|
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inputSelector: 'input#search-input.form-control',
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transformData: function(hits) {
|
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return hits.map(function (hit) {
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hit.url = updateHitURL(hit);
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||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -273,7 +273,7 @@
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9029</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</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">0.8.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</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">0.8.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -394,7 +394,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='no'>a</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
|
||||
<span class='st'>"Enterococcus faecalis"</span>,
|
||||
<span class='st'>"Escherichia coli"</span>,
|
||||
<span class='st'>"Klebsiella pneumoniae"</span>,
|
||||
@ -429,7 +430,6 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
|
||||
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
|
||||
<span class='co'># with 18 rows, containing all details about the transformations:</span>
|
||||
<span class='no'>c</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Data set with 2,000 blood culture isolates — example_isolates • AMR (for R)</title>
|
||||
<title>Data set with 2,000 example isolates — example_isolates • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
@ -50,8 +50,8 @@
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Data set with 2,000 blood culture isolates — example_isolates" />
|
||||
<meta property="og:description" content="An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This data.frame can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
|
||||
<meta property="og:title" content="Data set with 2,000 example isolates — example_isolates" />
|
||||
<meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -228,13 +228,13 @@
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data set with 2,000 blood culture isolates</h1>
|
||||
<h1>Data set with 2,000 example isolates</h1>
|
||||
|
||||
<div class="hidden name"><code>example_isolates.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This <code>data.frame</code> can be used to practice AMR analysis. For examples, please read <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
|
||||
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='no'>example_isolates</span></pre>
|
||||
@ -250,7 +250,7 @@
|
||||
<dt><code>ward_outpatient</code></dt><dd><p>logical to determine if ward is an outpatient clinic</p></dd>
|
||||
<dt><code>age</code></dt><dd><p>age of the patient</p></dd>
|
||||
<dt><code>gender</code></dt><dd><p>gender of the patient</p></dd>
|
||||
<dt><code>patient_id</code></dt><dd><p>ID of the patient, first 10 characters of an SHA hash containing irretrievable information</p></dd>
|
||||
<dt><code>patient_id</code></dt><dd><p>ID of the patient</p></dd>
|
||||
<dt><code>mo</code></dt><dd><p>ID of microorganism created with <code><a href='as.mo.html'>as.mo</a></code>, see also <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
|
||||
<dt><code>PEN:RIF</code></dt><dd><p>40 different antibiotics with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>); these column names occur in <code><a href='antibiotics.html'>antibiotics</a></code> data set and can be translated with <code><a href='ab_property.html'>ab_name</a></code></p></dd>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9029</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9029</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9032</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9033</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -239,38 +239,6 @@
|
||||
</colgroup>
|
||||
|
||||
<tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
|
||||
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="AMR.html">AMR</a></code> </p>
|
||||
</td>
|
||||
<td><p>The <code>AMR</code> Package</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
|
||||
</td>
|
||||
<td><p>The Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Version info of included Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
|
||||
</td>
|
||||
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
|
||||
@ -309,80 +277,50 @@
|
||||
<td><p>Class 'rsi'</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Use predefined reference data set</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
|
||||
</td>
|
||||
<td><p>EUCAST rules</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set for RSI interpretation</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Guess antibiotic column</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Use predefined reference data set</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="read.4D.html">read.4D()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Read data from 4D database</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set for RSI interpretation</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2>
|
||||
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
|
||||
<h2 id="section-enhancing-your-data" class="hasAnchor"><a href="#section-enhancing-your-data" class="anchor"></a>Enhancing your data</h2>
|
||||
<p class="section-desc"><p>Functions to add new data to your existing data, such as the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Determine first (weighted) isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of a microorganism</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of an antibiotic</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="age.html">age()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Age in years of individuals</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
|
||||
</td>
|
||||
@ -390,9 +328,21 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="p_symbol.html">p_symbol()</a></code> </p>
|
||||
<p><code><a href="age.html">age()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Symbol of a p value</p></td>
|
||||
<td><p>Age in years of individuals</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Determine first (weighted) isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@ -402,9 +352,27 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||||
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||||
<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of a microorganism</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="p_symbol.html">p_symbol()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Symbol of a p value</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@ -433,12 +401,6 @@
|
||||
<td><p>Count isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Calculate microbial resistance</p></td>
|
||||
</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>
|
||||
</td>
|
||||
@ -463,6 +425,12 @@
|
||||
<td><p>Kurtosis of the sample</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Calculate microbial resistance</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
|
||||
</td>
|
||||
@ -478,7 +446,7 @@
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-included-data-sets" class="hasAnchor"><a href="#section-included-data-sets" class="anchor"></a>Included data sets</h2>
|
||||
<p class="section-desc"><p>References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.</p></p>
|
||||
<p class="section-desc"><p>Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
@ -490,21 +458,15 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||||
<p><code><a href="antivirals.html">antivirals</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with ~70,000 microorganisms</p></td>
|
||||
<td><p>Data set with ~100 antivirals</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="example_isolates.html">example_isolates</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with 2,000 blood culture isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHONET.html">WHONET</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with 500 isolates - WHONET example</p></td>
|
||||
<td><p>Data set with 2,000 example isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@ -517,6 +479,50 @@
|
||||
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with previously accepted taxonomic names</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with ~70,000 microorganisms</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHONET.html">WHONET</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with 500 isolates - WHONET example</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
|
||||
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="AMR.html">AMR</a></code> </p>
|
||||
</td>
|
||||
<td><p>The <code>AMR</code> Package</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
|
||||
</td>
|
||||
<td><p>The Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Version info of included Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
|
||||
</td>
|
||||
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@ -551,12 +557,18 @@
|
||||
<p><code><a href="extended-functions.html">scale_type.mo()</a></code> <code><a href="extended-functions.html">scale_type.ab()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Extended functions</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="reexports.html">reexports</a></code> </p>
|
||||
</td>
|
||||
<td><p>Objects exported from other packages</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-functions" class="hasAnchor"><a href="#section-functions" class="anchor"></a>functions</h2>
|
||||
<p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
|
||||
<p class="section-desc"><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
@ -573,11 +585,11 @@
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#section-background-information">Background information</a></li>
|
||||
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
|
||||
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
|
||||
<li><a href="#section-enhancing-your-data">Enhancing your data</a></li>
|
||||
<li><a href="#section-analysing-your-data">Analysing your data</a></li>
|
||||
<li><a href="#section-included-data-sets">Included data sets</a></li>
|
||||
<li><a href="#section-background-information">Background information</a></li>
|
||||
<li><a href="#section-other-functions">Other functions</a></li>
|
||||
<li><a href="#section-extended-functions">Extended functions</a></li>
|
||||
<li><a href="#section-functions">functions</a></li>
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -419,22 +419,17 @@
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>mdro</span>() <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>()
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>.</span>),
|
||||
<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>),
|
||||
<span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))
|
||||
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>rename</a></span>(<span class='kw'>PIP</span> <span class='kw'>=</span> <span class='no'>TZP</span>) <span class='kw'>%>%</span> <span class='co'># no piperacillin, so take piperacillin/tazobactam</span>
|
||||
<span class='fu'>mrgn</span>() <span class='kw'>%>%</span> <span class='co'># check German guideline</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>() <span class='co'># check frequencies</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</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">0.8.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -90,7 +90,7 @@ below to see their documentation.
|
||||
</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">0.8.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -242,16 +242,16 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 11,559 observations and 9 variables:</p><dl class='dl-horizontal'>
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 13,975 observations and 9 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>guideline</code></dt><dd><p>Name of the guideline</p></dd>
|
||||
<dt><code>method</code></dt><dd><p>Either "MIC" or "DISK"</p></dd>
|
||||
<dt><code>site</code></dt><dd><p>Body site, e.g. "Oral" or "Respiratory"</p></dd>
|
||||
<dt><code>mo</code></dt><dd><p>Microbial ID, see <code><a href='as.mo.html'>as.mo</a></code></p></dd>
|
||||
<dt><code>ab</code></dt><dd><p>Antibiotic ID, see <code><a href='as.ab.html'>as.ab</a></code></p></dd>
|
||||
<dt><code>ref_tbl</code></dt><dd><p>Info about where the guideline rule can be found</p></dd>
|
||||
<dt><code>S_mic</code></dt><dd><p>Lowest MIC value that leads to "S"</p></dd>
|
||||
<dt><code>R_mic</code></dt><dd><p>Highest MIC value that leads to "R"</p></dd>
|
||||
<dt><code>dose_disk</code></dt><dd><p>Dose of the used disk diffusion method</p></dd>
|
||||
<dt><code>S_disk</code></dt><dd><p>Lowest number of millimeters that leads to "S"</p></dd>
|
||||
<dt><code>R_disk</code></dt><dd><p>Highest number of millimeters that leads to "R"</p></dd>
|
||||
<dt><code>disk_dose</code></dt><dd><p>Dose of the used disk diffusion method</p></dd>
|
||||
<dt><code>breakpoint_S</code></dt><dd><p>Lowest MIC value or highest number of millimeters that leads to "S"</p></dd>
|
||||
<dt><code>breakpoint_R</code></dt><dd><p>Highest MIC value or lowest number of millimeters that leads to "R"</p></dd>
|
||||
|
||||
</dl>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -85,7 +85,7 @@
|
||||
</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">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user