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dr. M.S. (Matthijs) Berends
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12
docs/reference/AMR-deprecated.html
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<meta property="og:title" content="Deprecated functions — AMR-deprecated" />
<meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Deprecated functions</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<div class="hidden name"><code>AMR-deprecated.Rd</code></div>
</div>
@ -258,7 +258,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

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docs/reference/AMR.html
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<meta property="og:title" content="The <code>AMR</code> Package — AMR" />
<meta property="og:description" content="Welcome to the AMR package." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<div class="hidden name"><code>AMR.Rd</code></div>
</div>
@ -263,7 +263,7 @@
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
@ -278,7 +278,7 @@ Post Office Box 30001 <br />
9700 RB Groningen <br />
The Netherlands</p>
<p>If you have found a bug, please file a new issue at: <br />
<a href='https://gitlab.com/msberends/AMR/issues'>https://gitlab.com/msberends/AMR/issues</a></p>
<a href='https://github.com/msberends/AMR/issues'>https://github.com/msberends/AMR/issues</a></p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

12
docs/reference/WHOCC.html
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<meta property="og:title" content="WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
<meta property="og:description" content="All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
<div class="hidden name"><code>WHOCC.Rd</code></div>
</div>
@ -250,7 +250,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)

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docs/reference/WHONET.html
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<meta property="og:title" content="Data set with 500 isolates - WHONET example — WHONET" />
<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our example_isolates data set." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 500 isolates - WHONET example</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>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>WHONET.Rd</code></div>
</div>
@ -273,7 +273,7 @@
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

14
docs/reference/ab_from_text.html
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<meta property="og:title" content="Retrieve antimicrobial drug names and doses from clinical text — ab_from_text" />
<meta property="og:description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs, doses and forms of administration found in the texts." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Retrieve antimicrobial drug names and doses from clinical text</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
<div class="hidden name"><code>ab_from_text.Rd</code></div>
</div>
@ -299,12 +299,12 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='co'># mind the bad spelling of amoxicillin in this line, </span>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Property of an antibiotic — ab_property" />
<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of an antibiotic</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<div class="hidden name"><code>ab_property.Rd</code></div>
</div>
@ -330,7 +330,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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><a href='antibiotics.html'>antibiotics</a></p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Age in years of individuals — age" />
<meta property="og:description" content="Calculates age in years based on a reference date, which is the sytem date at default." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Age in years of individuals</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age.Rd</code></div>
</div>
@ -272,7 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Split ages into age groups — age_groups" />
<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Split ages into age groups</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age_groups.Rd</code></div>
</div>
@ -281,7 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>

20
docs/reference/antibiotics.html
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@ -50,7 +50,7 @@
<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" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<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>
<small class="dont-index">Source: <a href='https://github.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>
@ -291,13 +291,13 @@
<p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
</ul>
<p>Files in R format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda'>https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://github.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antivirals.rda'>https://github.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
</ul>
@ -314,7 +314,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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><a href='microorganisms.html'>microorganisms</a></p></div>

14
docs/reference/as.ab.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Transform to antibiotic ID — as.ab" />
<meta property="og:description" content="Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to antibiotic ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
<div class="hidden name"><code>as.ab.Rd</code></div>
</div>
@ -282,7 +282,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
@ -296,7 +296,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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'>

12
docs/reference/as.disk.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Class 'disk' — as.disk" />
<meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'disk'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<div class="hidden name"><code>as.disk.Rd</code></div>
</div>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='as.rsi.html'>as.rsi()</a></code></p></div>

12
docs/reference/as.mic.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Class 'mic' — as.mic" />
<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'mic'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
<div class="hidden name"><code>as.mic.Rd</code></div>
</div>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='as.rsi.html'>as.rsi()</a></code></p></div>

12
docs/reference/as.mo.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Transform to microorganism ID — as.mo" />
<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (like &quot;S. aureus&quot;), an abbreviation known in the field (like &quot;MRSA&quot;), or just a genus. Please see Examples." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to microorganism ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
@ -378,7 +378,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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><a href='microorganisms.html'>microorganisms</a> for the <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that is being used to determine ID's.</p>

14
docs/reference/as.rsi.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'rsi'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<div class="hidden name"><code>as.rsi.Rd</code></div>
</div>
@ -308,7 +308,7 @@
<p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
<p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p>
<p>The repository of this package <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -336,7 +336,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='as.mic.html'>as.mic()</a></code></p></div>

12
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@ -51,7 +51,7 @@
<meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
This function requires an internet connection." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ This function requires an internet connection." />
</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">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ This function requires an internet connection." />
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ This function requires an internet connection." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get ATC properties from WHOCC website</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<div class="hidden name"><code>atc_online.Rd</code></div>
</div>
@ -312,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='kw'>if</span> (<span class='fl'>FALSE</span>) {

12
docs/reference/availability.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Check availability of columns — availability" />
<meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Check availability of columns</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
<div class="hidden name"><code>availability.Rd</code></div>
</div>
@ -267,7 +267,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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'>availability</span>(<span class='no'>example_isolates</span>)

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Determine bug-drug combinations — bug_drug_combinations" />
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine bug-drug combinations</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
</div>
@ -333,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='co'># \donttest{</span>

14
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@ -50,7 +50,7 @@
<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
<meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life.Rd</code></div>
</div>
@ -258,12 +258,12 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Version info of included Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
</div>
@ -255,7 +255,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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><a href='microorganisms.html'>microorganisms</a></p></div>

12
docs/reference/count.html
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@ -51,7 +51,7 @@
<meta property="og:title" content="Count available isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, please see Examples.
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ 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">1.2.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<div class="col-md-9 contents">
<div class="page-header">
<h1>Count available isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
<div class="hidden name"><code>count.Rd</code></div>
</div>
@ -360,7 +360,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</p></div>

16
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@ -51,7 +51,7 @@
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ 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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<div class="col-md-9 contents">
<div class="page-header">
<h1>Apply EUCAST rules</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
<div class="hidden name"><code>eucast_rules.Rd</code></div>
</div>
@ -307,7 +307,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
</ul>
<p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</p>
<p>The file containing all EUCAST rules is located here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -398,12 +398,12 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='co'># \donttest{</span>

14
docs/reference/example_isolates.html
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@ -50,7 +50,7 @@
<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.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,12 +227,12 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 2,000 example isolates</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>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates.Rd</code></div>
</div>
<div class="ref-description">
<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>
<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.github.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
</div>
<pre class="usage"><span class='no'>example_isolates</span></pre>
@ -257,7 +257,7 @@
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

12
docs/reference/example_isolates_unclean.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
<meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with unclean data</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>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
</div>
@ -252,7 +252,7 @@
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

10
docs/reference/filter_ab_class.html
View File

@ -50,7 +50,7 @@
<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, 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" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Filter isolates on result in antimicrobial class</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
<div class="hidden name"><code>filter_ab_class.Rd</code></div>
</div>

12
docs/reference/first_isolate.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Determine first (weighted) isolates — first_isolate" />
<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine first (weighted) isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
<div class="hidden name"><code>first_isolate.Rd</code></div>
</div>
@ -393,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='key_antibiotics.html'>key_antibiotics()</a></code></p></div>

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="<em>G</em>-test for Count Data — g.test" />
<meta property="og:description" content="g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable (1). A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence)." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1><em>G</em>-test for Count Data</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
<div class="hidden name"><code>g.test.Rd</code></div>
</div>
@ -334,7 +334,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

12
docs/reference/ggplot_pca.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="PCA biplot with <code>ggplot2</code> — ggplot_pca" />
<meta property="og:description" content="Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>PCA biplot with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
<div class="hidden name"><code>ggplot_pca.Rd</code></div>
</div>
@ -376,7 +376,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

24
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View File

@ -49,8 +49,8 @@
<script src="../extra.js"></script>
<meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot2 functions." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on ggplot2 functions." />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,12 +227,12 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>AMR plots with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div>
<div class="ref-description">
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
</div>
<pre class="usage"><span class='fu'>ggplot_rsi</span>(
@ -393,10 +393,10 @@
<p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi()</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>ggplot2::facet_wrap()</a></code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code>ggplot2::scale_continuous()</code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>ggplot2::scale_brewer()</code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>ggplot2::scale_y_continuous()</a></code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code><a href='https://ggplot2.tidyverse.org/reference/scale_manual.html'>ggplot2::scale_fill_manual()</a></code>.</p>
<p><code>theme_rsi()</code> is a [ggplot2 theme][<code><a href='https://ggplot2.tidyverse.org/reference/theme.html'>ggplot2::theme()</a></code> with minimal distraction.</p>
<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code></p>
<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code>.</p>
<p><code>ggplot_rsi()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
@ -404,12 +404,12 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {

14
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@ -50,7 +50,7 @@
<meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Guess antibiotic column</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
<div class="hidden name"><code>guess_ab_col.Rd</code></div>
</div>
@ -265,12 +265,12 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"S"</span>,

10
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View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Function reference" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -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">1.2.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -199,8 +199,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -484,7 +484,7 @@
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with 67,108 microorganisms</p></td>
<td><p>Data set with 67,150 microorganisms</p></td>
</tr><tr>
<td>

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Join <a href='microorganisms.html'>microorganisms</a> to a data set — join" />
<meta property="og:description" content="Join the data set microorganisms easily to an existing table or character vector." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Join <a href='microorganisms.html'>microorganisms</a> to a data set</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
<div class="hidden name"><code>join.Rd</code></div>
</div>
@ -283,7 +283,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Key antibiotics for first <em>weighted</em> isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/key_antibiotics.R'><code>R/key_antibiotics.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/key_antibiotics.R'><code>R/key_antibiotics.R</code></a></small>
<div class="hidden name"><code>key_antibiotics.Rd</code></div>
</div>
@ -379,7 +379,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='first_isolate.html'>first_isolate()</a></code></p></div>

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Kurtosis of the sample — kurtosis" />
<meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Kurtosis of the sample</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
<div class="hidden name"><code>kurtosis.Rd</code></div>
</div>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='skewness.html'>skewness()</a></code></p></div>

12
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@ -52,7 +52,7 @@
<meta property="og:description" content="Functions in this AMR package are categorised using the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle.
This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -202,8 +202,8 @@ This page contains a section for every lifecycle (with text borrowed from the af
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -229,7 +229,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
<div class="col-md-9 contents">
<div class="page-header">
<h1>Lifecycles of functions in the <code>AMR</code> package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
<div class="hidden name"><code>lifecycle.Rd</code></div>
</div>
@ -252,7 +252,7 @@ The lifecycle of this function is <strong>experimental</strong>. An experimental
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Pattern Matching — like" />
<meta property="og:description" content="Convenient wrapper around grep() to match a pattern: x %like% pattern. It always returns a logical vector and is always case-insensitive (use x %like_case% pattern for case-sensitive matching). Also, pattern can be as long as x to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
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@ -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">1.2.0.9026</span>
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@ -200,8 +200,8 @@
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@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Pattern Matching</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
<div class="hidden name"><code>like.Rd</code></div>
</div>
@ -285,7 +285,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='https://rdrr.io/r/base/grep.html'>base::grep()</a></code></p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
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<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine multidrug-resistant organisms (MDRO)</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mdro.R'><code>R/mdro.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mdro.R'><code>R/mdro.R</code></a></small>
<div class="hidden name"><code>mdro.Rd</code></div>
</div>
@ -326,14 +326,14 @@ The German national guideline - Mueller et al. (2015) Antimicrobial Resistance a
The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href='https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'>link</a>)</p></li>
</ul>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://gitlab.com/msberends/AMR/issues/new'>https://gitlab.com/msberends/AMR/issues/new</a>.</p>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://github.com/msberends/AMR/issues/new'>https://github.com/msberends/AMR/issues/new</a>.</p>
<p><strong>Note:</strong> Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu <em>et al.</em> in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this <code>mdro()</code> function makes sure that results from before 2016 and after 2016 are identical.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -437,7 +437,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='kw'>if</span> (<span class='fl'>FALSE</span>) {

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@ -50,7 +50,7 @@
<meta property="og:title" content="Translation table with 5,582 common microorganism codes — microorganisms.codes" />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
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<a href="https://gitlab.com/msberends/AMR">
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@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Translation table with 5,582 common microorganism codes</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>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
</div>
@ -256,7 +256,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='as.mo.html'>as.mo()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>

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@ -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 67,108 microorganisms — microorganisms • AMR (for R)</title>
<title>Data set with 67,150 microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,9 +48,9 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with 67,108 microorganisms — microorganisms" />
<meta property="og:title" content="Data set with 67,150 microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
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<a href="https://gitlab.com/msberends/AMR">
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Source Code
</a>
@ -226,8 +226,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 67,108 microorganisms</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>
<h1>Data set with 67,150 microorganisms</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
@ -240,7 +240,7 @@
<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 67,108 observations and 16 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,150 observations and 16 variables:</p><ul>
<li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
<li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>
@ -266,17 +266,17 @@
<li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
<li><p>7,369 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
<li><p>7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
</ul>
<h3>Direct download</h3>
<p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
</ul>
<p>The file in R format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://github.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
</ul>
@ -297,7 +297,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a></p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Data set with previously accepted taxonomic names — microorganisms.old" />
<meta property="og:description" content="A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by as.mo()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
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<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with previously accepted taxonomic names</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>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.old.Rd</code></div>
</div>
@ -262,7 +262,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='as.mo.html'>as.mo()</a></code> <code><a href='mo_property.html'>mo_property()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Property of a microorganism — mo_property" />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
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<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of a microorganism</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<div class="hidden name"><code>mo_property.Rd</code></div>
</div>
@ -361,7 +361,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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><a href='microorganisms.html'>microorganisms</a></p></div>

12
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@ -51,7 +51,7 @@
<meta property="og:title" content="User-defined reference data set for microorganisms — mo_source" />
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ 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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<div class="col-md-9 contents">
<div class="page-header">
<h1>User-defined reference data set for microorganisms</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>
@ -316,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

12
docs/reference/p_symbol.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Symbol of a p-value — p_symbol" />
<meta property="og:description" content="Return the symbol related to the p-value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above p = 1 will return NA." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Symbol of a p-value</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/p_symbol.R'><code>R/p_symbol.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/p_symbol.R'><code>R/p_symbol.R</code></a></small>
<div class="hidden name"><code>p_symbol.Rd</code></div>
</div>
@ -263,7 +263,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

12
docs/reference/pca.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Principal Component Analysis (for AMR) — pca" />
<meta property="og:description" content="Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Principal Component Analysis (for AMR)</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
<div class="hidden name"><code>pca.Rd</code></div>
</div>
@ -309,7 +309,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

14
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@ -51,7 +51,7 @@
<meta property="og:title" content="Calculate microbial resistance — proportion" />
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, please see Examples.
resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ 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">1.2.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<div class="col-md-9 contents">
<div class="page-header">
<h1>Calculate microbial resistance</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
<div class="hidden name"><code>proportion.Rd</code></div>
</div>
@ -379,10 +379,10 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='count.html'>AMR::count()</a></code> to count resistant and susceptible isolates.</p></div>
<div class='dont-index'><p><code><a href='count.html'>count()</a></code> to count resistant and susceptible isolates.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>

14
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@ -50,7 +50,7 @@
<meta property="og:title" content="Predict antimicrobial resistance — resistance_predict" />
<meta property="og:description" content="Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Predict antimicrobial resistance</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
<div class="hidden name"><code>resistance_predict.Rd</code></div>
</div>
@ -362,7 +362,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -381,7 +381,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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>The <code><a href='proportion.html'>proportion()</a></code> functions to calculate resistance</p>

14
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@ -50,7 +50,7 @@
<meta property="og:title" content="Data set for R/SI interpretation — rsi_translation" />
<meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set for R/SI interpretation</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>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>rsi_translation.Rd</code></div>
</div>
@ -255,12 +255,12 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

12
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View File

@ -51,7 +51,7 @@
<meta property="og:title" content="Skewness of the sample — skewness" />
<meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ 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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<div class="col-md-9 contents">
<div class="page-header">
<h1>Skewness of the sample</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/skewness.R'><code>R/skewness.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/skewness.R'><code>R/skewness.R</code></a></small>
<div class="hidden name"><code>skewness.Rd</code></div>
</div>
@ -271,7 +271,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='kurtosis.html'>kurtosis()</a></code></p></div>

18
docs/reference/translate.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Translate strings from AMR package — translate" />
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_name(), mo_gramstain(), mo_type() and ab_name()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.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">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Translate strings from AMR package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/translate.R'><code>R/translate.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/translate.R'><code>R/translate.R</code></a></small>
<div class="hidden name"><code>translate.Rd</code></div>
</div>
@ -240,9 +240,9 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
<p>Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Not all these languages currently have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
<p>Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property()</a></code> functions (<code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.).</p>
<p>The system language will be used at default, if that language is supported. The system language can be overwritten with <code><a href='https://rdrr.io/r/base/Sys.setenv.html'>Sys.setenv(AMR_locale = yourlanguage)</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -256,7 +256,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 comprehensive 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>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.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='co'># The 'language' parameter of below functions</span>