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(v1.7.1.9022) rely on vctrs for ab selectors

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dr. M.S. (Matthijs) Berends
2021-07-23 21:42:11 +02:00
parent 0ec81cc12e
commit 4e1efd902c
130 changed files with 3785 additions and 2960 deletions
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52
docs/reference/AMR-deprecated.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>
<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -415,7 +423,7 @@
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -444,11 +452,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
</div>
</footer>
@@ -457,6 +465,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
</body>
</html>

48
docs/reference/AMR.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -306,11 +314,11 @@ The Netherlands
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
</div>
</footer>
@@ -319,6 +327,8 @@ The Netherlands
</body>
</html>

52
docs/reference/WHOCC.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -260,11 +268,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01DH02"</span><span class='op'>)</span>
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span><span class='op'>(</span><span class='st'>"flucloxacillin"</span><span class='op'>)</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -276,11 +284,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
</div>
</footer>
@@ -289,6 +297,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</body>
</html>

50
docs/reference/WHONET.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
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Data sets for download / own use
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Conduct principal component analysis for AMR
</a>
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<a href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
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Manual
</a>
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<a href="../authors.html">
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<span class="fa fa-users"></span>
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</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>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 antibiotic results are from our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
</div>
<pre class="usage"><span class='va'>WHONET</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>WHONET</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -298,11 +306,11 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -311,6 +319,8 @@
</body>
</html>

72
docs/reference/ab_from_text.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
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Home
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How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
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Data sets for download / own use
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<a href="../articles/PCA.html">
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Conduct principal component analysis for AMR
</a>
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<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
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<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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<a href="../articles/EUCAST.html">
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
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@@ -242,7 +250,7 @@
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href='https://rdrr.io/r/base/list.html'>list</a> with all antimicrobial drugs, doses and forms of administration found in the texts.</p>
</div>
<pre class="usage"><span class='fu'>ab_from_text</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ab_from_text</span><span class='op'>(</span>
<span class='va'>text</span>,
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span><span class='op'>)</span>,
collapse <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -250,7 +258,7 @@
thorough_search <span class='op'>=</span> <span class='cn'>NULL</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -290,14 +298,26 @@
<p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the <code><a href='as.ab.html'>as.ab()</a></code> function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>type</code></h3>
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the <code><a href='as.ab.html'>as.ab()</a></code> function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.</p><h3 class='hasAnchor' id='argument-'><a class='anchor' aria-hidden='true' href='#argument-'></a>Argument <code>type</code></h3>
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> values that are higher than 100 and do not resemble years. The output will be <a href='https://rdrr.io/r/base/numeric.html'>numeric</a>. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p><h3 class='hasAnchor' id='list-type-'><a class='anchor' aria-hidden='true' href='#list-type-'></a>Argument <code>type</code></h3>
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> values that are higher than 100 and do not resemble years. The output will be <a href='https://rdrr.io/r/base/numeric.html'>numeric</a>. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>collapse</code></h3>
<h3 class='hasAnchor' id='argument-'><a class='anchor' aria-hidden='true' href='#argument-'></a>Argument <code>collapse</code></h3>
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text))</code></p>
<p>The returned AB codes can be transformed to official names, groups, etc. with all <code><a href='ab_property.html'>ab_*</a></code> functions such as <code><a href='ab_property.html'>ab_name()</a></code> and <code><a href='ab_property.html'>ab_group()</a></code>, or by using the <code>translate_ab</code> argument.</p>
<p>With using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/character.html'>character</a>:<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text, collapse = "|"))</code></p><h3 class='hasAnchor' id='list-collapse-'><a class='anchor' aria-hidden='true' href='#list-collapse-'></a>Argument <code>collapse</code></h3>
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
@@ -320,7 +340,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># mind the bad spelling of amoxicillin in this line, </span>
<span class='co'># straight from a true health care record:</span>
<span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span><span class='op'>)</span>
@@ -353,7 +373,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -365,11 +385,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -378,6 +398,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

24
docs/reference/ab_property.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Use these functions to return a specific property of an antibiotic from the <a href='antibiotics.html'>antibiotics</a> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, snake_case <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, snake_case <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -266,7 +274,7 @@
<span class='fu'>ab_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"name"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>ab_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"name"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -352,7 +360,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># all properties:</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># all properties:</span>
<span class='fu'>ab_name</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "Amoxicillin"</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># J01CA04 (ATC code from the WHO)</span>
<span class='fu'>ab_cid</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># 33613 (Compound ID from PubChem)</span>
@@ -389,7 +397,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"cephtriaxone"</span><span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"cephthriaxone"</span><span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"seephthriaaksone"</span><span class='op'>)</span>
</pre>
</code></pre></div>
</div>
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@@ -401,11 +409,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -414,6 +422,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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54
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View File

@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -185,14 +193,14 @@
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@@ -242,7 +250,7 @@
<p>Calculates age in years based on a reference date, which is the sytem date at default.</p>
</div>
<pre class="usage"><span class='fu'>age</span><span class='op'>(</span><span class='va'>x</span>, reference <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>, exact <span class='op'>=</span> <span class='cn'>FALSE</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>age</span><span class='op'>(</span><span class='va'>x</span>, reference <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>, exact <span class='op'>=</span> <span class='cn'>FALSE</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -293,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># 10 random birth dates</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># 10 random birth dates</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>birth_date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span><span class='op'>(</span><span class='fl'>10</span><span class='op'>)</span> <span class='op'>*</span> <span class='fl'>25000</span><span class='op'>)</span>
<span class='co'># add ages</span>
<span class='va'>df</span><span class='op'>$</span><span class='va'>age</span> <span class='op'>&lt;-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span><span class='op'>)</span>
@@ -301,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='va'>df</span><span class='op'>$</span><span class='va'>age_exact</span> <span class='op'>&lt;-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span>, exact <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>df</span>
</pre>
</code></pre></div>
</div>
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@@ -313,11 +321,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -326,6 +334,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

54
docs/reference/age_groups.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Get properties of an antibiotic
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@@ -242,7 +250,7 @@
<p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis.</p>
</div>
<pre class="usage"><span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>x</span>, split_at <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span><span class='op'>)</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>x</span>, split_at <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span><span class='op'>)</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -294,7 +302,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>ages</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>ages</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span><span class='op'>)</span>
<span class='co'># split into 0-49 and 50+</span>
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='fl'>50</span><span class='op'>)</span>
@@ -325,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span>, minimum <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
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@@ -337,11 +345,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -350,6 +358,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
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26
docs/reference/antibiotic_class_selectors.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<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">1.7.1.9019</span>
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</span>
</div>
@@ -242,7 +250,7 @@
<p>These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -286,7 +294,7 @@
<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<span class='fu'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -308,7 +316,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selection helpers</a> such as <code><a href='https://tidyselect.r-lib.org/reference/everything.html'>everything()</a></code>, but also work in base <span style="R">R</span> and not only in <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, see <em>Examples</em>.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the <code>ab_class()</code> function to filter/select on a manually defined antibiotic class.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the <code>ab_class()</code> function to filter/select on a manually defined antibiotic class.</p>
<h2 class="hasAnchor" id="full-list-of-supported-agents"><a class="anchor" href="#full-list-of-supported-agents"></a>Full list of supported agents</h2>
@@ -357,7 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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'># `example_isolates` is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># base R ------------------------------------------------------------------</span>
@@ -436,7 +444,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.x</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -448,11 +456,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -461,6 +469,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

182
docs/reference/antibiotics.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
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<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
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<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
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Apply EUCAST rules
</a>
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<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
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Get properties of a microorganism
</a>
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
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Manual
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@@ -215,7 +223,7 @@
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<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,15 +250,87 @@
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href='as.ab.html'>as.ab()</a></code> or one of the <code><a href='ab_property.html'>ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes.</p>
</div>
<pre class="usage"><span class='va'>antibiotics</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>antibiotics</span>
<span class='va'>antivirals</span></pre>
<span class='va'>antivirals</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='list-antibiotics-'><a class='anchor' aria-hidden='true' href='#list-antibiotics-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
@@ -270,7 +350,59 @@
</ul>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='list-antivirals-'><a class='anchor' aria-hidden='true' href='#list-antivirals-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
@@ -294,7 +426,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='direct-download'><a class='anchor' aria-hidden='true' href='#direct-download'></a>Direct download</h3>
<p>These data sets are available as 'flat files' for use even without <span style="R">R</span> - you can find the files here:</p><ul>
@@ -342,11 +474,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -355,6 +487,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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56
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
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<header>
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@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
</a>
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<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
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Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,9 +250,9 @@
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
</div>
<pre class="usage"><span class='fu'>as.ab</span><span class='op'>(</span><span class='va'>x</span>, flag_multiple_results <span class='op'>=</span> <span class='cn'>TRUE</span>, info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.ab</span><span class='op'>(</span><span class='va'>x</span>, flag_multiple_results <span class='op'>=</span> <span class='cn'>TRUE</span>, info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is.ab</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<span class='fu'>is.ab</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -325,7 +333,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"J01FA01"</span><span class='op'>)</span>
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"J 01 FA 01"</span><span class='op'>)</span>
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"Erythromycin"</span><span class='op'>)</span>
@@ -356,7 +364,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -368,11 +376,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -381,6 +389,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</body>
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56
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Conduct principal component analysis for AMR
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
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Get properties of an antibiotic
</a>
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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Survey
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@@ -242,9 +250,9 @@
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<pre class="usage"><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -282,7 +290,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='co'># transform existing disk zones to the `disk` class</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
AMP <span class='op'>=</span> <span class='fl'>20</span>,
@@ -301,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -313,11 +321,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -326,6 +334,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -66,9 +68,15 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -242,7 +250,7 @@
<p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>as.mo</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.mo</span><span class='op'>(</span>
<span class='va'>x</span>,
Becker <span class='op'>=</span> <span class='cn'>FALSE</span>,
Lancefield <span class='op'>=</span> <span class='cn'>FALSE</span>,
@@ -260,7 +268,7 @@
<span class='fu'>mo_uncertainties</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></pre>
<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -311,10 +319,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>General Info</h3>
<h3 class='hasAnchor' id='general-info'><a class='anchor' aria-hidden='true' href='#general-info'></a>General Info</h3>
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre> Code Full name
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre><code> Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
@@ -326,7 +334,7 @@
| \----&gt; genus, a 5-7 letter acronym
\----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>
</code></pre>
<p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
@@ -339,7 +347,7 @@
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Coping with Uncertain Results</h3>
<h3 class='hasAnchor' id='coping-with-uncertain-results'><a class='anchor' aria-hidden='true' href='#coping-with-uncertain-results'></a>Coping with Uncertain Results</h3>
<p>In addition, the <code>as.mo()</code> function can differentiate four levels of uncertainty to guess valid results:</p><ul>
@@ -363,7 +371,7 @@
</ul>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Microbial Prevalence of Pathogens in Humans</h3>
<h3 class='hasAnchor' id='microbial-prevalence-of-pathogens-in-humans'><a class='anchor' aria-hidden='true' href='#microbial-prevalence-of-pathogens-in-humans'></a>Microbial Prevalence of Pathogens in Humans</h3>
<p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href='microorganisms.html'>microorganisms</a> and <a href='microorganisms.old.html'>microorganisms.old</a> data sets. The grouping into human pathogenic prevalence is explained in the section <em>Matching Score for Microorganisms</em> below.</p>
@@ -429,7 +437,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>The <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_genus()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>) to get properties based on the returned code.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='co'># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"sau"</span><span class='op'>)</span> <span class='co'># WHONET code</span>
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"stau"</span><span class='op'>)</span>
@@ -466,7 +474,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># returns "Gram negative"</span>
<span class='fu'><a href='mo_property.html'>mo_is_intrinsic_resistant</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"vanco"</span><span class='op'>)</span> <span class='co'># returns TRUE</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -478,11 +486,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -491,6 +499,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<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">1.7.1.9020</span>
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</span>
</div>
@@ -242,7 +250,7 @@
<p>Interpret minimum inhibitory concentration (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 <code>rsi</code>, which is an ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <code>S &lt; I &lt; R</code>.</p>
</div>
<pre class="usage"><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
@@ -283,7 +291,7 @@
conserve_capped_values <span class='op'>=</span> <span class='cn'>FALSE</span>,
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>,
reference_data <span class='op'>=</span> <span class='fu'>AMR</span><span class='fu'>::</span><span class='va'><a href='rsi_translation.html'>rsi_translation</a></span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -340,43 +348,43 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How it Works</h3>
<h3 class='hasAnchor' id='how-it-works'><a class='anchor' aria-hidden='true' href='#how-it-works'></a>How it Works</h3>
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre class='sourceCode r'><code><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
</code></pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre class='sourceCode r'><code><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
</code></pre></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
</ol>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported Guidelines</h3>
<h3 class='hasAnchor' id='supported-guidelines'><a class='anchor' aria-hidden='true' href='#supported-guidelines'></a>Supported Guidelines</h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2020"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After Interpretation</h3>
<h3 class='hasAnchor' id='after-interpretation'><a class='anchor' aria-hidden='true' href='#after-interpretation'></a>After Interpretation</h3>
<p>After using <code>as.rsi()</code>, you can use the <code><a href='eucast_rules.html'>eucast_rules()</a></code> defined by EUCAST 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>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine-Readable Interpretation Guidelines</h3>
<h3 class='hasAnchor' id='machine-readable-interpretation-guidelines'><a class='anchor' aria-hidden='true' href='#machine-readable-interpretation-guidelines'></a>Machine-Readable Interpretation Guidelines</h3>
<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 22,000 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. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
<h3 class='hasAnchor' id='other'><a class='anchor' aria-hidden='true' href='#other'></a>Other</h3>
<p>The function <code>is.rsi()</code> detects if the input contains class <code>&lt;rsi&gt;</code>. If the input is a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, it iterates over all columns and returns a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector.</p>
@@ -418,7 +426,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr/'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># class &lt;rsi&gt; supported in skim() too:</span>
@@ -501,7 +509,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># mutate(across(where(is.rsi.eligible), as.rsi))</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -513,11 +521,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -526,6 +534,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

56
docs/reference/atc_online.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
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</li>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
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<a href="../authors.html">
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<span class="fa fa-users"></span>
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@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
</div>
<pre class="usage"><span class='fu'>atc_online_property</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>atc_online_property</span><span class='op'>(</span>
<span class='va'>atc_code</span>,
<span class='va'>property</span>,
administration <span class='op'>=</span> <span class='st'>"O"</span>,
@@ -252,7 +260,7 @@
<span class='fu'>atc_online_groups</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -327,7 +335,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"curl"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"rvest"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"xml2"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span><span class='op'>)</span>
@@ -338,7 +346,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, property <span class='op'>=</span> <span class='st'>"groups"</span><span class='op'>)</span> <span class='co'># search hierarchical groups of amoxicillin</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -350,11 +358,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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</footer>
@@ -363,6 +371,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

54
docs/reference/availability.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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<a href="../index.html">
<span class="fas fa-home"></span>
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Home
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How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
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<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
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<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
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@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>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. <code><a href='proportion.html'>susceptibility()</a></code> and <code><a href='proportion.html'>resistance()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>tbl</span>, width <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>availability</span><span class='op'>(</span><span class='va'>tbl</span>, width <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -277,7 +285,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>availability</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
@@ -286,7 +294,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>availability</span><span class='op'>(</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -298,11 +306,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -311,6 +319,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

24
docs/reference/bug_drug_combinations.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publishable/printable format, see <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for bug_drug_combinations</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span>
@@ -257,7 +265,7 @@
decimal.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"OutDec"</span><span class='op'>)</span>,
big.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>decimal.mark</span> <span class='op'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -342,7 +350,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<span class='va'>x</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='va'>x</span>, translate_ab <span class='op'>=</span> <span class='st'>"name (atc)"</span><span class='op'>)</span>
@@ -356,7 +364,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -368,11 +376,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -381,6 +389,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

52
docs/reference/catalogue_of_life.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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<a href="../index.html">
<span class="fas fa-home"></span>
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
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<a href="../articles/resistance_predict.html">
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -277,7 +285,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># Get version info of included data set</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># Get version info of included data set</span>
<span class='fu'><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></span><span class='op'>(</span><span class='op'>)</span>
@@ -305,7 +313,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<span class='co'>#&gt; [1] "Fungi" # Fungi?!</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
<span class='co'>#&gt; [1] "Cladosporium elegans" # Because a microorganism was found</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -317,11 +325,11 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -330,6 +338,8 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</body>
</html>

50
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View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
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<span class="fas fa-dice"></span>
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Predict antimicrobial resistance
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Data sets for download / own use
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Conduct principal component analysis for AMR
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<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
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Get properties of an antibiotic
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<a href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
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@@ -242,7 +250,7 @@
<p>This function returns information about the included data from the Catalogue of Life.</p>
</div>
<pre class="usage"><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -278,11 +286,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -291,6 +299,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -56,6 +56,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -67,9 +69,15 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -83,7 +91,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -91,14 +99,14 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -107,77 +115,77 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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Other: benchmarks
</a>
@@ -186,14 +194,14 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -216,7 +224,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -244,7 +252,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</p>
</div>
<pre class="usage"><span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@@ -268,7 +276,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -337,7 +345,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre><code>--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
@@ -353,15 +361,15 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</pre>
</code></pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</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>
@@ -374,7 +382,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<div class='dont-index'><p><code><a href='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># example_isolates is a data set available in the AMR package.</span>
<span class='op'>?</span><span class='va'>example_isolates</span>
<span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "R"</span>
@@ -440,7 +448,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>count_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -452,11 +460,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@@ -465,6 +473,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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44
docs/reference/custom_eucast_rules.html
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in <code><a href='eucast_rules.html'>eucast_rules()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -263,14 +271,14 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Basics</h3>
<h3 class='hasAnchor' id='basics'><a class='anchor' aria-hidden='true' href='#basics'></a>Basics</h3>
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
</pre>
</code></pre>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p><pre><span class='va'>x</span>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p><pre class='sourceCode r'><code><span class='va'>x</span>
<span class='co'>#&gt; A set of custom EUCAST rules:</span>
<span class='co'>#&gt; </span>
<span class='co'>#&gt; 1. If TZP is S then set to S:</span>
@@ -278,9 +286,9 @@
<span class='co'>#&gt; </span>
<span class='co'>#&gt; 2. If TZP is R then set to R:</span>
<span class='co'>#&gt; amoxicillin (AMX), ampicillin (AMP)</span>
</pre>
</code></pre>
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p><pre><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"K. pneumoniae"</span><span class='op'>)</span>,
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p><pre class='sourceCode r'><code><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"K. pneumoniae"</span><span class='op'>)</span>,
TZP <span class='op'>=</span> <span class='st'>"R"</span>,
amox <span class='op'>=</span> <span class='st'>""</span>,
AMP <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span>
@@ -293,23 +301,23 @@
<span class='co'>#&gt; mo TZP amox AMP</span>
<span class='co'>#&gt; 1 E. coli R R R </span>
<span class='co'>#&gt; 2 K. pneumoniae R R R </span>
</pre>
</code></pre>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Using taxonomic properties in rules</h3>
<h3 class='hasAnchor' id='using-taxonomic-properties-in-rules'><a class='anchor' aria-hidden='true' href='#using-taxonomic-properties-in-rules'></a>Using taxonomic properties in rules</h3>
<p>There is one exception in variables used for the rules: all column names of the <a href='microorganisms.html'>microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>mo</code>, <code>fullname</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code>, <code>rank</code>, <code>ref</code>, <code>species_id</code>, <code>source</code>, <code>prevalence</code> and <code>snomed</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p><pre><span class='va'>y</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<p>There is one exception in variables used for the rules: all column names of the <a href='microorganisms.html'>microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>mo</code>, <code>fullname</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code>, <code>rank</code>, <code>ref</code>, <code>species_id</code>, <code>source</code>, <code>prevalence</code> and <code>snomed</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p><pre class='sourceCode r'><code><span class='va'>y</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>df</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>y</span><span class='op'>)</span>
<span class='co'>#&gt; mo TZP amox AMP</span>
<span class='co'>#&gt; 1 E. coli R </span>
<span class='co'>#&gt; 2 K. pneumoniae R R R</span>
</pre>
</code></pre>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage of antibiotic group names</h3>
<h3 class='hasAnchor' id='usage-of-antibiotic-group-names'><a class='anchor' aria-hidden='true' href='#usage-of-antibiotic-group-names'></a>Usage of antibiotic group names</h3>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.</p><ul>
@@ -354,7 +362,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>example_isolates</span>,
rules <span class='op'>=</span> <span class='st'>"custom"</span>,
@@ -365,7 +373,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='va'>x2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>x</span>,
<span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>carbapenems</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>x2</span>
</pre>
</code></pre></div>
</div>
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@@ -377,11 +385,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -390,6 +398,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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50
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with <code><a href='eucast_rules.html'>eucast_dosage()</a></code>.</p>
</div>
<pre class="usage"><span class='va'>dosage</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>dosage</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -284,11 +292,11 @@
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -297,6 +305,8 @@
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@@ -56,6 +56,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -67,9 +69,15 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -83,7 +91,7 @@ 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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -244,7 +252,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
</div>
<pre class="usage"><span class='fu'>eucast_rules</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>eucast_rules</span><span class='op'>(</span>
<span class='va'>x</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
@@ -258,7 +266,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='va'>ab</span>, administration <span class='op'>=</span> <span class='st'>"iv"</span>, version_breakpoints <span class='op'>=</span> <span class='fl'>11</span><span class='op'>)</span></pre>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='va'>ab</span>, administration <span class='op'>=</span> <span class='st'>"iv"</span>, version_breakpoints <span class='op'>=</span> <span class='fl'>11</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -337,17 +345,17 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br /></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>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>March 2021</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Custom Rules</h3>
<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>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>March 2021</a>.</p><h3 class='hasAnchor' id='custom-rules'><a class='anchor' aria-hidden='true' href='#custom-rules'></a>Custom Rules</h3>
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>example_isolates</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>x</span><span class='op'>)</span>
</pre>
</code></pre>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
<h3 class='hasAnchor' id='-other-rules'><a class='anchor' aria-hidden='true' href='#-other-rules'></a>'Other' Rules</h3>
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
@@ -384,7 +392,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='va'>a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
@@ -426,7 +434,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># }</span>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"tobra"</span>, <span class='st'>"genta"</span>, <span class='st'>"cipro"</span><span class='op'>)</span>, <span class='st'>"iv"</span><span class='op'>)</span>
</pre>
</code></pre></div>
</div>
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<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -438,11 +446,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -451,6 +459,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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50
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View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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<body data-spy="scroll" data-target="#toc">
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@@ -82,7 +90,7 @@
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<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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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<a href="../articles/SPSS.html">
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Get properties of a microorganism
</a>
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
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Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<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 data 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='va'>example_isolates</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>example_isolates</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -282,11 +290,11 @@
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -295,6 +303,8 @@
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50
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
</button>
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<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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -242,7 +250,7 @@
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
</div>
<pre class="usage"><span class='va'>example_isolates_unclean</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>example_isolates_unclean</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -277,11 +285,11 @@
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -290,6 +298,8 @@
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@@ -56,6 +56,8 @@
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@@ -67,9 +69,15 @@
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@@ -83,7 +91,7 @@
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@@ -244,7 +252,7 @@
). To determine patient episodes not necessarily based on microorganisms, use <code><a href='get_episode.html'>is_new_episode()</a></code> that also supports grouping with the <code>dplyr</code> package.</p>
</div>
<pre class="usage"><span class='fu'>first_isolate</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>first_isolate</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -275,7 +283,7 @@
episode_days <span class='op'>=</span> <span class='fl'>365</span>,
method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenotype-based"</span>, <span class='st'>"episode-based"</span>, <span class='st'>"patient-based"</span>, <span class='st'>"isolate-based"</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -377,7 +385,7 @@
<p>To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.</p>
<p>These functions are context-aware. This means that the <code>x</code> argument can be left blank if used inside a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> call, see <em>Examples</em>.</p>
<p>The <code>first_isolate()</code> function is a wrapper around the <code><a href='get_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Different methods</h3>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='different-methods'><a class='anchor' aria-hidden='true' href='#different-methods'></a>Different methods</h3>
<p>According to Hindler <em>et al.</em> (2007, doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
@@ -405,23 +413,23 @@
</table>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Isolate-based</h4>
<h4 class='hasAnchor' id='isolate-based'><a class='anchor' aria-hidden='true' href='#isolate-based'></a>Isolate-based</h4>
<p>This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the <code>first_isolate()</code> function. For example, the default setting for <code>include_unknown</code> (<code>FALSE</code>) will omit selection of rows without a microbial ID.</p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Patient-based</h4>
<h4 class='hasAnchor' id='patient-based'><a class='anchor' aria-hidden='true' href='#patient-based'></a>Patient-based</h4>
<p>To include every genus-species combination per patient once, set the <code>episode_days</code> to <code>Inf</code>. Although often inappropriate, this method makes sure that no duplicate isolates are selected from the same patient. In a large longitudinal data set, this could mean that isolates are <em>excluded</em> that were found years after the initial isolate.</p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Episode-based</h4>
<h4 class='hasAnchor' id='episode-based'><a class='anchor' aria-hidden='true' href='#episode-based'></a>Episode-based</h4>
<p>To include every genus-species combination per patient episode once, set the <code>episode_days</code> to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data, long episodes are common for analysing regional and national data.</p>
<p>This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) isolate cannot be differentiated from a wildtype <em>Staphylococcus aureus</em> isolate.</p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Phenotype-based</h4>
<h4 class='hasAnchor' id='phenotype-based'><a class='anchor' aria-hidden='true' href='#phenotype-based'></a>Phenotype-based</h4>
<p>This is a more reliable method, since it also <em>weighs</em> the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:</p><ol>
@@ -454,7 +462,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code></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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>]</span>
@@ -494,7 +502,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># when you (erroneously) would have used all isolates for analysis.</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -506,11 +514,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -519,6 +527,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -242,7 +250,7 @@
<p><code>g.test()</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code> but is more reliable (1). A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
</div>
<pre class="usage"><span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, y <span class='op'>=</span> <span class='cn'>NULL</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, rescale.p <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, y <span class='op'>=</span> <span class='cn'>NULL</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, rescale.p <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -305,14 +313,25 @@
<p>If <code>x</code> is a <a href='https://rdrr.io/r/base/matrix.html'>matrix</a> with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of <code>x</code> must be non-negative integers. Otherwise, <code>x</code> and <code>y</code> must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.</p>
<p>The p-value is computed from the asymptotic chi-squared distribution of the test statistic.</p>
<p>In the contingency table case simulation is done by random sampling from the set of all contingency tables with given marginals, and works only if the marginals are strictly positive. Note that this is not the usual sampling situation assumed for a chi-squared test (such as the <em>G</em>-test) but rather that for Fisher's exact test.</p>
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><h3 class='hasAnchor' id='list-g-'><a class='anchor' aria-hidden='true' href='#list-g-'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>).</p>
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p><h3 class='hasAnchor' id='-test-of-goodness-of-fit-likelihood-ratio-test-'><a class='anchor' aria-hidden='true' href='#-test-of-goodness-of-fit-likelihood-ratio-test-'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>).</p>
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a><em>G</em>-test of Independence</h3>
<h3 class='hasAnchor' id='list-g-'><a class='anchor' aria-hidden='true' href='#list-g-'></a><em>G</em>-test of Independence</h3>
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
<p>It is also possible to do a <em>G</em>-test of independence with more than two nominal variables. For example, Jackson et al. (2013) also had data for children under 3, so you could do an analysis of old vs. young, thigh vs. arm, and reaction vs. no reaction, all analyzed together.</p>
<p>Fisher's exact test (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>), and they will give approximately the same results.</p><h3 class='hasAnchor' id='-test-of-independence'><a class='anchor' aria-hidden='true' href='#-test-of-independence'></a><em>G</em>-test of Independence</h3>
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
@@ -320,14 +339,14 @@
<p>Fisher's exact test (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>), and they will give approximately the same results.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How the Test Works</h3>
<h3 class='hasAnchor' id='how-the-test-works'><a class='anchor' aria-hidden='true' href='#how-the-test-works'></a>How the Test Works</h3>
<p>Unlike the exact test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
<p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
<p>\(G = 2 * sum(x * log(x / E))\)</p>
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre><span class='va'>p</span> <span class='op'>&lt;-</span> <span class='fu'>stats</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span><span class='op'>(</span><span class='va'>G</span>, <span class='va'>df</span>, lower.tail <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
</pre>
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre class='sourceCode r'><code><span class='va'>p</span> <span class='op'>&lt;-</span> <span class='fu'>stats</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span><span class='op'>(</span><span class='va'>G</span>, <span class='va'>df</span>, lower.tail <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
</code></pre>
<p>where <code>df</code> are the degrees of freedom.</p>
<p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
@@ -355,7 +374,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<div class='dont-index'><p><code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># = EXAMPLE 1 =</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># = EXAMPLE 1 =</span>
<span class='co'># Shivrain et al. (2006) crossed clearfield rice (which are resistant</span>
<span class='co'># to the herbicide imazethapyr) with red rice (which are susceptible to</span>
<span class='co'># imazethapyr). They then crossed the hybrid offspring and examined the</span>
@@ -387,7 +406,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># There is a significant difference from a 1:1 ratio.</span>
<span class='co'># Meaning: there are significantly more left-billed birds.</span>
</pre>
</code></pre></div>
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -412,6 +431,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -242,9 +250,9 @@
<p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while the <code>is_new_episode()</code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode.</p>
</div>
<pre class="usage"><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -293,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span> <span class='co'># indices</span>
@@ -353,7 +361,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>flag_episode <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
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Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
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<a href="../articles/SPSS.html">
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
</a>
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<a href="../reference/ab_property.html">
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<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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Survey
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@@ -242,7 +250,7 @@
<p>Produces a <code>ggplot2</code> variant of a so-called <a href='https://en.wikipedia.org/wiki/Biplot'>biplot</a> for PCA (principal component analysis), but is more flexible and more appealing than the base <span style="R">R</span> <code><a href='https://rdrr.io/r/stats/biplot.html'>biplot()</a></code> function.</p>
</div>
<pre class="usage"><span class='fu'>ggplot_pca</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ggplot_pca</span><span class='op'>(</span>
<span class='va'>x</span>,
choices <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>,
scale <span class='op'>=</span> <span class='fl'>1</span>,
@@ -265,7 +273,7 @@
arrows_alpha <span class='op'>=</span> <span class='fl'>0.75</span>,
base_textsize <span class='op'>=</span> <span class='fl'>10</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -393,7 +401,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
@@ -418,7 +426,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='op'>}</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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@@ -430,11 +438,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -443,6 +451,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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58
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
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</a>
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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<a href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
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<a href="../articles/SPSS.html">
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<a href="../reference/ab_property.html">
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Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>Use these functions to create bar plots for AMR data 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><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ggplot_rsi</span><span class='op'>(</span>
<span class='va'>data</span>,
position <span class='op'>=</span> <span class='cn'>NULL</span>,
x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
@@ -299,7 +307,7 @@
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
datalabels.size <span class='op'>=</span> <span class='fl'>3</span>,
datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -404,7 +412,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>The Functions</h3>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='the-functions'><a class='anchor' aria-hidden='true' href='#the-functions'></a>The Functions</h3>
<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>
@@ -429,7 +437,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
@@ -507,7 +515,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -519,11 +527,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -532,6 +540,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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56
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View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
</head>
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@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
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<a href="../articles/resistance_predict.html">
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Predict antimicrobial resistance
</a>
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Data sets for download / own use
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Conduct principal component analysis for AMR
</a>
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<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
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<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
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Apply EUCAST rules
</a>
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<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
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<a href="../reference/index.html">
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@@ -215,7 +223,7 @@
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@@ -242,12 +250,12 @@
<p>This tries to find a column name in a data set based on information from the <a href='antibiotics.html'>antibiotics</a> data set. Also supports WHONET abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>guess_ab_col</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>guess_ab_col</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
search_string <span class='op'>=</span> <span class='cn'>NULL</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -290,7 +298,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>amox <span class='op'>=</span> <span class='st'>"S"</span>,
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>amox <span class='op'>=</span> <span class='st'>"S"</span>,
tetr <span class='op'>=</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>
@@ -317,7 +325,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
AMP_ED20 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span>
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span>
<span class='co'># [1] "AMP_ED20"</span>
</pre>
</code></pre></div>
</div>
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@@ -329,11 +337,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -342,6 +350,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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18
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@@ -54,6 +54,8 @@
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@@ -65,9 +67,15 @@
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@@ -81,7 +89,7 @@
</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">1.7.1.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -418,7 +426,7 @@
<tr>
<th colspan="2">
<h2 id="section-preparing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-preparing-data-antimicrobial-resistance" class="anchor"></a>Preparing data: antimicrobial resistance</h2>
<p class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
<p class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
</th>
</tr>
@@ -685,11 +693,11 @@
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -698,6 +706,8 @@
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54
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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<div class="container template-reference-topic">
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@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
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Predict antimicrobial resistance
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Data sets for download / own use
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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<a href="../articles/WHONET.html">
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Work with WHONET data
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<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
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Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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<a href="../survey.html">
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<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
</div>
<pre class="usage"><span class='va'>intrinsic_resistant</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>intrinsic_resistant</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -268,7 +276,7 @@
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>intrinsic_resistant</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>antibiotic</span> <span class='op'>==</span> <span class='st'>"Vancomycin"</span>, <span class='va'>microorganism</span> <span class='op'>%like%</span> <span class='st'>"Enterococcus"</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
@@ -276,7 +284,7 @@
<span class='co'># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -288,11 +296,11 @@
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -301,6 +309,8 @@
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
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<a href="../articles/AMR.html">
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
</a>
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<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
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<a href="../articles/WHONET.html">
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Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,9 +250,9 @@
<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.</p>
</div>
<pre class="usage"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></pre>
<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -277,21 +285,21 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
<span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/cat.html'>cat</a></span><span class='op'>(</span><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span>, type <span class='op'>=</span> <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># since ggplot2 supports no markdown (yet), use</span>
<span class='co'># italicise_taxonomy() and the `ggtext` pkg for titles:</span>
<span class='co'># italicise_taxonomy() and the `ggtext` package for titles:</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://wilkelab.org/ggtext/'>"ggtext"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMC</span>,
title <span class='op'>=</span> <span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"Amoxi/clav in E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMC</span>,
title <span class='op'>=</span> <span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"Amoxi/clav in E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></span><span class='op'>(</span>plot.title <span class='op'>=</span> <span class='fu'>ggtext</span><span class='fu'>::</span><span class='fu'><a href='https://wilkelab.org/ggtext/reference/element_markdown.html'>element_markdown</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -303,11 +311,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -316,6 +324,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</body>
</html>

24
docs/reference/join.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Join the data set <a href='microorganisms.html'>microorganisms</a> easily to an existing data set or to a <a href='https://rdrr.io/r/base/character.html'>character</a> vector.</p>
</div>
<pre class="usage"><span class='fu'>inner_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>inner_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -252,7 +260,7 @@
<span class='fu'>semi_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>anti_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>anti_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -296,7 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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='op'>(</span><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"K. pneumoniae"</span><span class='op'>)</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"K. pneumoniae"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='st'>"B_KLBSL_PNMN"</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
@@ -316,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='va'>df_joined</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -328,11 +336,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -341,6 +349,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

56
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View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
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</li>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
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<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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@@ -185,14 +193,14 @@
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<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
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Manual
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<span class="fa fa-users"></span>
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@@ -215,7 +223,7 @@
</li>
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<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see <code><a href='first_isolate.html'>first_isolate()</a></code>). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.</p>
</div>
<pre class="usage"><span class='fu'>key_antimicrobials</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>key_antimicrobials</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
universal <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ampicillin"</span>, <span class='st'>"amoxicillin/clavulanic acid"</span>, <span class='st'>"cefuroxime"</span>,
@@ -266,7 +274,7 @@
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -379,7 +387,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># output of the `key_antimicrobials()` function could be like this:</span>
@@ -410,7 +418,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>my_patients</span><span class='op'>$</span><span class='va'>first_weighted</span>, na.rm <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -422,11 +430,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -435,6 +443,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

52
docs/reference/kurtosis.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Conduct AMR analysis
</a>
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Import data from SPSS/SAS/Stata
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<span class="fas fa-exchange-alt"></span>
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Apply EUCAST rules
</a>
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<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
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<a href="../reference/ab_property.html">
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Get properties of an antibiotic
</a>
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.</p>
</div>
<pre class="usage"><span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># S3 method for default</span>
<span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@@ -251,7 +259,7 @@
<span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># S3 method for data.frame</span>
<span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -297,11 +305,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -310,6 +318,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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48
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@@ -57,6 +57,8 @@ This page contains a section for every lifecycle (with text borrowed from the af
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@@ -68,9 +70,15 @@ This page contains a section for every lifecycle (with text borrowed from the af
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@@ -84,7 +92,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
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<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">1.7.1</span>
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@@ -92,14 +100,14 @@ This page contains a section for every lifecycle (with text borrowed from the af
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@@ -108,77 +116,77 @@ This page contains a section for every lifecycle (with text borrowed from the af
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@@ -187,14 +195,14 @@ This page contains a section for every lifecycle (with text borrowed from the af
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@@ -217,7 +225,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
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Survey
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@@ -291,11 +299,11 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -304,6 +312,8 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
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56
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>Convenient wrapper around <code><a href='https://rdrr.io/r/base/grep.html'>grepl()</a></code> to match a pattern: <code>x %like% pattern</code>. It always returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector and is always case-insensitive (use <code>x %like_case% pattern</code> for case-sensitive matching). Also, <code>pattern</code> can be as long as <code>x</code> to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.</p>
</div>
<pre class="usage"><span class='fu'>like</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>pattern</span>, ignore.case <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>like</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>pattern</span>, ignore.case <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>x</span> <span class='op'>%like%</span> <span class='va'>pattern</span>
@@ -250,7 +258,7 @@
<span class='va'>x</span> <span class='op'>%like_case%</span> <span class='va'>pattern</span>
<span class='va'>x</span> <span class='op'>%unlike_case%</span> <span class='va'>pattern</span></pre>
<span class='va'>x</span> <span class='op'>%unlike_case%</span> <span class='va'>pattern</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -302,7 +310,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>grepl()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>a</span> <span class='op'>&lt;-</span> <span class='st'>"This is a test"</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>a</span> <span class='op'>&lt;-</span> <span class='st'>"This is a test"</span>
<span class='va'>b</span> <span class='op'>&lt;-</span> <span class='st'>"TEST"</span>
<span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span>
<span class='co'>#&gt; TRUE</span>
@@ -333,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -345,11 +353,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -358,6 +366,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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40
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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</div>
@@ -242,7 +250,7 @@
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.</p>
</div>
<pre class="usage"><span class='fu'>mdro</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>mdro</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"CMI2012"</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -264,7 +272,7 @@
<span class='fu'>mdr_cmi2012</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -360,34 +368,34 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
<p>Custom guidelines can be set with the <code>custom_mdro_guideline()</code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre><span class='va'>custom</span> <span class='op'>&lt;-</span> <span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>CIP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>60</span> <span class='op'>~</span> <span class='st'>"Elderly Type A"</span>,
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre class='sourceCode r'><code><span class='va'>custom</span> <span class='op'>&lt;-</span> <span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>CIP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>60</span> <span class='op'>~</span> <span class='st'>"Elderly Type A"</span>,
<span class='va'>ERY</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>60</span> <span class='op'>~</span> <span class='st'>"Elderly Type B"</span><span class='op'>)</span>
</pre>
</code></pre>
<p>If a row/an isolate matches the first rule, the value after the first <code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code> (in this case <em>'Elderly Type A'</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.</p>
<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p><pre><span class='va'>custom</span>
<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p><pre class='sourceCode r'><code><span class='va'>custom</span>
<span class='co'>#&gt; A set of custom MDRO rules:</span>
<span class='co'>#&gt; 1. CIP is "R" and age is higher than 60 -&gt; Elderly Type A</span>
<span class='co'>#&gt; 2. ERY is "R" and age is higher than 60 -&gt; Elderly Type B</span>
<span class='co'>#&gt; 3. Otherwise -&gt; Negative</span>
<span class='co'>#&gt; </span>
<span class='co'>#&gt; Unmatched rows will return NA.</span>
</pre>
</code></pre>
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
guideline <span class='op'>=</span> <span class='va'>custom</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'>#&gt; Negative Elderly Type A Elderly Type B</span>
<span class='co'>#&gt; 1070 198 732</span>
</pre>
</code></pre>
<p>Rules can also be combined with other custom rules by using <code><a href='https://rdrr.io/r/base/c.html'>c()</a></code>:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
<p>Rules can also be combined with other custom rules by using <code><a href='https://rdrr.io/r/base/c.html'>c()</a></code>:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
guideline <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>custom</span>,
<span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>ERY</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>age</span> <span class='op'>&gt;</span> <span class='fl'>50</span> <span class='op'>~</span> <span class='st'>"Elderly Type C"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='co'>#&gt; Negative Elderly Type A Elderly Type B Elderly Type C </span>
<span class='co'>#&gt; 961 198 732 109</span>
</pre>
</code></pre>
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@@ -425,7 +433,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
guideline <span class='op'>=</span> <span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>AMX</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='st'>"Custom MDRO 1"</span>,
@@ -445,7 +453,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
MRGN <span class='op'>=</span> <span class='fu'>mrgn</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
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@@ -457,11 +465,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -470,6 +478,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -242,7 +250,7 @@
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>. They will all be searched when using <code><a href='as.mo.html'>as.mo()</a></code> and consequently all the <code><a href='mo_property.html'>mo_*</a></code> functions.</p>
</div>
<pre class="usage"><span class='va'>microorganisms.codes</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>microorganisms.codes</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -284,11 +292,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -297,6 +305,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -242,7 +250,7 @@
<p>A data set containing the microbial taxonomy, last updated in March 2021, of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href='as.mo.html'>as.mo()</a></code>.</p>
</div>
<pre class="usage"><span class='va'>microorganisms</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>microorganisms</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -281,7 +289,7 @@
<p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi: <a href='https://doi.org/10.1016/s0732-8893(02)00399-1'>10.1016/s0732-8893(02)00399-1</a>
), but it was not before 2007 that a publication in IJSEM followed (doi: <a href='https://doi.org/10.1099/ijs.0.64381-0'>10.1099/ijs.0.64381-0</a>
). Consequently, the <code>AMR</code> package returns 2007 for <code><a href='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Manual additions</h3>
). Consequently, the <code>AMR</code> package returns 2007 for <code><a href='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3 class='hasAnchor' id='manual-additions'><a class='anchor' aria-hidden='true' href='#manual-additions'></a>Manual additions</h3>
<p>For convenience, some entries were added manually:</p><ul>
@@ -295,7 +303,7 @@
</ul>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
<h3 class='hasAnchor' id='direct-download'><a class='anchor' aria-hidden='true' href='#direct-download'></a>Direct download</h3>
<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here:</p><ul>
@@ -345,11 +353,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -358,6 +366,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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50
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href='as.mo.html'>as.mo()</a></code>.</p>
</div>
<pre class="usage"><span class='va'>microorganisms.old</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>microorganisms.old</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -290,11 +298,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -303,6 +311,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -55,6 +55,8 @@
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@@ -242,7 +250,7 @@
<p>This algorithm is used by <code><a href='as.mo.html'>as.mo()</a></code> and all the <code><a href='mo_property.html'>mo_*</a></code> functions to determine the most probable match of taxonomic records based on user input.</p>
</div>
<pre class="usage"><span class='fu'>mo_matching_score</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>n</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>mo_matching_score</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>n</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -296,12 +304,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>Matthijs S. Berends</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
<span class='fu'><a href='as.mo.html'>mo_uncertainties</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>mo_matching_score</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"E. coli"</span>,
n <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Escherichia coli"</span>, <span class='st'>"Entamoeba coli"</span><span class='op'>)</span><span class='op'>)</span>
</pre>
</code></pre></div>
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@@ -313,11 +321,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -326,6 +334,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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</span>
</div>
@@ -242,7 +250,7 @@
<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. See <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>mo_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>mo_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -296,7 +304,7 @@
<span class='fu'>mo_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mo_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"fullname"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>mo_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"fullname"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -414,7 +422,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># taxonomic tree -----------------------------------------------------------</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># taxonomic tree -----------------------------------------------------------</span>
<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria"</span>
<span class='fu'>mo_phylum</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Proteobacteria"</span>
<span class='fu'>mo_class</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Gammaproteobacteria"</span>
@@ -514,7 +522,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_info</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
<span class='co'># }</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -526,11 +534,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -539,6 +547,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -56,6 +56,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -67,9 +69,15 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -83,7 +91,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -91,14 +99,14 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -107,77 +115,77 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -244,12 +252,12 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.</p>
</div>
<pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>set_mo_source</span><span class='op'>(</span>
<span class='va'>path</span>,
destination <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_mo_source"</span>, <span class='st'>"~/mo_source.rds"</span><span class='op'>)</span>
<span class='op'>)</span>
<span class='fu'>get_mo_source</span><span class='op'>(</span>destination <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_mo_source"</span>, <span class='st'>"~/mo_source.rds"</span><span class='op'>)</span><span class='op'>)</span></pre>
<span class='fu'>get_mo_source</span><span class='op'>(</span>destination <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_mo_source"</span>, <span class='st'>"~/mo_source.rds"</span><span class='op'>)</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -276,22 +284,22 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the <a href='microorganisms.html'>microorganisms</a> data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre> | A | B |
<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the <a href='microorganisms.html'>microorganisms</a> data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre><code> | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
4 | | |
</pre>
</code></pre>
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='st'>"home/me/ourcodes.xlsx"</span><span class='op'>)</span>
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre class='sourceCode r'><code><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='st'>"home/me/ourcodes.xlsx"</span><span class='op'>)</span>
<span class='co'>#&gt; NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span>
<span class='co'>#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns </span>
<span class='co'>#&gt; "Organisation XYZ" and "mo"</span>
</pre>
</code></pre>
<p>It has now created a file <code>"~/mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
<p>And now we can use it in our functions:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<p>And now we can use it in our functions:</p><pre class='sourceCode r'><code><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<span class='co'>#&gt; Class &lt;mo&gt;</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI</span>
@@ -304,18 +312,18 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<span class='co'>#&gt; Use mo_uncertainties() to review it.</span>
<span class='co'>#&gt; Class &lt;mo&gt;</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span>
</pre>
</code></pre>
<p>If we edit the Excel file by, let's say, adding row 4 like this:</p><pre> | A | B |
<p>If we edit the Excel file by, let's say, adding row 4 like this:</p><pre><code> | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
4 | lab_Staph_aureus | B_STPHY_AURS |
5 | | |
</pre>
</code></pre>
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<p>...any new usage of an MO function in this package will update your data file:</p><pre class='sourceCode r'><code><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<span class='co'>#&gt; NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span>
<span class='co'>#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
<span class='co'>#&gt; "Organisation XYZ" and "mo"</span>
@@ -324,11 +332,11 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"lab_Staph_aureus"</span><span class='op'>)</span>
<span class='co'>#&gt; [1] "Staphylococcus"</span>
</pre>
</code></pre>
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='cn'>NULL</span><span class='op'>)</span>
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre class='sourceCode r'><code><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='cn'>NULL</span><span class='op'>)</span>
<span class='co'>#&gt; Removed mo_source file '/Users/me/mo_source.rds'</span>
</pre>
</code></pre>
<p>If the original file (in the previous case an Excel file) is moved or deleted, the <code>mo_source.rds</code> file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code> or any <code><a href='mo_property.html'>mo_*</a></code> function.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@@ -355,11 +363,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -368,6 +376,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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56
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>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.</p>
</div>
<pre class="usage"><span class='fu'>pca</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>pca</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>...</span>,
retx <span class='op'>=</span> <span class='cn'>TRUE</span>,
@@ -250,7 +258,7 @@
scale. <span class='op'>=</span> <span class='cn'>TRUE</span>,
tol <span class='op'>=</span> <span class='cn'>NULL</span>,
rank. <span class='op'>=</span> <span class='cn'>NULL</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -325,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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'># `example_isolates` is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># \donttest{</span>
@@ -346,7 +354,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span> <span class='co'># a new and convenient plot function</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -358,11 +366,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -371,6 +379,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
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30
docs/reference/plot.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base <span style="R">R</span> and <code>ggplot2</code>.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mic</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='co'># S3 method for mic</span>
<span class='fu'>plot</span><span class='op'>(</span>
<span class='va'>x</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -258,7 +266,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>object</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -288,7 +296,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>object</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -312,7 +320,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>object</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
@@ -320,7 +328,7 @@
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -388,7 +396,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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='va'>some_mic_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>some_mic_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>
<span class='va'>some_disk_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_disk</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='va'>some_rsi_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_rsi</a></span><span class='op'>(</span><span class='fl'>50</span>, prob_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.30</span>, <span class='fl'>0.55</span>, <span class='fl'>0.05</span><span class='op'>)</span><span class='op'>)</span>
@@ -407,7 +415,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
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@@ -419,11 +427,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -432,6 +440,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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68
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View File

@@ -56,6 +56,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -67,9 +69,15 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -83,7 +91,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -91,14 +99,14 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -107,77 +115,77 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -186,14 +194,14 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -216,7 +224,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -244,7 +252,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
</div>
<pre class="usage"><span class='fu'>resistance</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>resistance</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@@ -276,7 +284,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -335,7 +343,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p><pre><code>--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
@@ -351,15 +359,15 @@ resistance() should be used to calculate resistance, susceptibility() should be
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</pre>
</code></pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@@ -393,7 +401,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># example_isolates is a data set available in the AMR package.</span>
<span class='op'>?</span><span class='va'>example_isolates</span>
<span class='fu'>resistance</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># determines %R</span>
@@ -466,7 +474,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>proportion_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -478,11 +486,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -491,6 +499,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</body>
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28
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,18 +250,18 @@
<p>These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.</p>
</div>
<pre class="usage"><span class='fu'>random_mic</span><span class='op'>(</span><span class='va'>size</span>, mo <span class='op'>=</span> <span class='cn'>NULL</span>, ab <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>random_mic</span><span class='op'>(</span>size <span class='op'>=</span> <span class='cn'>NULL</span>, mo <span class='op'>=</span> <span class='cn'>NULL</span>, ab <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='va'>size</span>, mo <span class='op'>=</span> <span class='cn'>NULL</span>, ab <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>random_disk</span><span class='op'>(</span>size <span class='op'>=</span> <span class='cn'>NULL</span>, mo <span class='op'>=</span> <span class='cn'>NULL</span>, ab <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>random_rsi</span><span class='op'>(</span><span class='va'>size</span>, prob_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.33</span>, <span class='fl'>0.33</span>, <span class='fl'>0.33</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>random_rsi</span><span class='op'>(</span>size <span class='op'>=</span> <span class='cn'>NULL</span>, prob_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.33</span>, <span class='fl'>0.33</span>, <span class='fl'>0.33</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>size</th>
<td><p>desired size of the returned vector</p></td>
<td><p>desired size of the returned vector. If used in a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> call or <code>dplyr</code> verb, will get the current (group) size if left blank.</p></td>
</tr>
<tr>
<th>mo</th>
@@ -294,7 +302,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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'>random_mic</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<span class='fu'>random_rsi</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
@@ -308,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 11-17</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Streptococcus pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 12-27</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -320,11 +328,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -333,6 +341,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

24
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns <code>se_min</code> and <code>se_max</code>. See <em>Examples</em> for a real live example.</p>
</div>
<pre class="usage"><span class='fu'>resistance_predict</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>resistance_predict</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>col_ab</span>,
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -288,7 +296,7 @@
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -408,7 +416,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p>Models: <code><a href='https://rdrr.io/r/stats/lm.html'>lm()</a></code> <code><a href='https://rdrr.io/r/stats/glm.html'>glm()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>resistance_predict</span><span class='op'>(</span><span class='va'>example_isolates</span>,
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>resistance_predict</span><span class='op'>(</span><span class='va'>example_isolates</span>,
col_ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
year_min <span class='op'>=</span> <span class='fl'>2010</span>,
model <span class='op'>=</span> <span class='st'>"binomial"</span><span class='op'>)</span>
@@ -461,7 +469,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span><span class='op'>(</span>base_size <span class='op'>=</span> <span class='fl'>13</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -473,11 +481,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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</footer>
@@ -486,6 +494,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</body>
</html>

18
docs/reference/rsi_translation.html
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<pre class="usage"><span class='va'>rsi_translation</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>rsi_translation</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -288,11 +296,11 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -301,6 +309,8 @@
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52
docs/reference/skewness.html
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@@ -56,6 +56,8 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -67,9 +69,15 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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@@ -83,7 +91,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</button>
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<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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -91,14 +99,14 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<ul class="nav navbar-nav">
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@@ -107,77 +115,77 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
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Get properties of an antibiotic
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@@ -186,14 +194,14 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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@@ -216,7 +224,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<a href="../survey.html">
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<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -244,7 +252,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<p>When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.</p>
</div>
<pre class="usage"><span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># S3 method for default</span>
<span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@@ -253,7 +261,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># S3 method for data.frame</span>
<span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -295,11 +303,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -308,6 +316,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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56
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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<a href="../articles/WHONET.html">
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Work with WHONET data
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<a href="../articles/SPSS.html">
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Import data from SPSS/SAS/Stata
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,14 +250,14 @@
<p>For language-dependent output of AMR functions, like <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> and <code><a href='ab_property.html'>ab_name()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>get_locale</span><span class='op'>(</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>get_locale</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<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://github.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>. This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <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.) and <code><a href='ab_property.html'>ab_*</a></code> functions (such as <code><a href='ab_property.html'>ab_name()</a></code>, <code><a href='ab_property.html'>ab_group()</a></code>, etc.).</p>
<p>Currently supported languages are: Dutch, English, French, German, Italian, Portuguese and 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><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Changing the Default Language</h3>
<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><h3 class='hasAnchor' id='changing-the-default-language'><a class='anchor' aria-hidden='true' href='#changing-the-default-language'></a>Changing the Default Language</h3>
<p>The system language will be used at default (as returned by <code><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><a href='https://rdrr.io/r/base/locales.html'>Sys.getlocale()</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol>
@@ -273,7 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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' argument of below functions</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># The 'language' argument of below functions</span>
<span class='co'># will be set automatically to your system language</span>
<span class='co'># with get_locale()</span>
@@ -300,7 +308,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># Portuguese</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"pt"</span><span class='op'>)</span>
<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span>
</pre>
</code></pre></div>
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@@ -312,11 +320,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -325,6 +333,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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