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v1.1.0

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dr. M.S. (Matthijs) Berends
2020-04-17 19:16:30 +02:00
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33
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
<meta property="og:title" content="Deprecated functions — AMR-deprecated" />
<meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Deprecated functions</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<div class="hidden name"><code>AMR-deprecated.Rd</code></div>
</div>
@ -260,12 +264,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#retired-lifecycle">Retired lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
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@ -276,7 +277,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
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34
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@ -46,7 +50,7 @@
<meta property="og:title" content="The <code>AMR</code> Package — AMR" />
<meta property="og:description" content="Welcome to the AMR package." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
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<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<div class="hidden name"><code>AMR.Rd</code></div>
</div>
@ -276,13 +280,9 @@ The Netherlands</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#contact-us">Contact us</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -293,7 +293,7 @@ The Netherlands</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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</footer>

34
docs/reference/WHOCC.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
<meta property="og:description" content="All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
<div class="hidden name"><code>WHOCC.Rd</code></div>
</div>
@ -255,13 +259,9 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#whocc">WHOCC</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -272,7 +272,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

2
docs/reference/WHONET.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

39
docs/reference/ab_property.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Property of an antibiotic — ab_property" />
<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of an antibiotic</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<div class="hidden name"><code>ab_property.Rd</code></div>
</div>
@ -362,18 +366,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -384,7 +379,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Age in years of individuals — age" />
<meta property="og:description" content="Calculates age in years based on a reference date, which is the sytem date at default." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Age in years of individuals</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age.Rd</code></div>
</div>
@ -284,16 +288,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='no'>df</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -304,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</footer>

38
docs/reference/age_groups.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Split ages into age groups — age_groups" />
<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Split ages into age groups</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age_groups.Rd</code></div>
</div>
@ -316,17 +320,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -337,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

2
docs/reference/antibiotics.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

40
docs/reference/as.ab.html
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@ -24,16 +24,20 @@
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
<meta property="og:title" content="Transform to antibiotic ID — as.ab" />
<meta property="og:description" content="Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to antibiotic ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
<div class="hidden name"><code>as.ab.Rd</code></div>
</div>
@ -311,19 +315,9 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#whocc">WHOCC</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -334,7 +328,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

38
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@ -24,16 +24,20 @@
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
<meta property="og:title" content="Class 'disk' — as.disk" />
<meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'disk'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<div class="hidden name"><code>as.disk.Rd</code></div>
</div>
@ -290,17 +294,9 @@ 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='no'>df</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -311,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
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38
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Class 'mic' — as.mic" />
<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'mic'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
<div class="hidden name"><code>as.mic.Rd</code></div>
</div>
@ -292,17 +296,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mic_data</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -313,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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40
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Transform to microorganism ID — as.mo" />
<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (like &quot;S. aureus&quot;), an abbreviation known in the field (like &quot;MRSA&quot;), or just a genus. Please see Examples." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to microorganism ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
@ -438,19 +442,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -461,7 +455,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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39
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@ -24,16 +24,20 @@
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
<meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'rsi'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<div class="hidden name"><code>as.rsi.Rd</code></div>
</div>
@ -413,18 +417,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.99</span>) <span class='co'># succeeds</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -435,7 +430,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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37
docs/reference/atc_online.html
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@ -24,16 +24,20 @@
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<!-- pkgdown -->
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@ -47,7 +51,7 @@
<meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
This function requires an internet connection." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -65,7 +69,7 @@ This function requires an internet connection." />
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -79,7 +83,7 @@ This function requires an internet connection." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -224,7 +228,7 @@ This function requires an internet connection." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get ATC properties from WHOCC website</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<div class="hidden name"><code>atc_online.Rd</code></div>
</div>
@ -325,16 +329,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -345,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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37
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@ -24,16 +24,20 @@
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@ -46,7 +50,7 @@
<meta property="og:title" content="Check availability of columns — availability" />
<meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Check availability of columns</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
<div class="hidden name"><code>availability.Rd</code></div>
</div>
@ -281,16 +285,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>availability</span>()</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -301,7 +298,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

38
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@ -24,16 +24,20 @@
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
<meta property="og:title" content="Determine bug-drug combinations — bug_drug_combinations" />
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine bug-drug combinations</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
</div>
@ -348,17 +352,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -369,7 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

36
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
<meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life.Rd</code></div>
</div>
@ -296,15 +300,9 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#included-taxa">Included taxa</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -315,7 +313,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

37
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View File

@ -24,16 +24,20 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
<meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Version info of included Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
</div>
@ -262,16 +266,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -282,7 +279,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

40
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@ -24,16 +24,20 @@
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@ -47,7 +51,7 @@
<meta property="og:title" content="Count available isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() and support grouped variables, see Examples.
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -65,7 +69,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -79,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -224,7 +228,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<div class="col-md-9 contents">
<div class="page-header">
<h1>Count available isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
<div class="hidden name"><code>count.Rd</code></div>
</div>
@ -420,19 +424,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
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@ -443,7 +437,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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39
docs/reference/eucast_rules.html
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@ -24,16 +24,20 @@
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@ -47,7 +51,7 @@
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -65,7 +69,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -79,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -224,7 +228,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<div class="col-md-9 contents">
<div class="page-header">
<h1>Apply EUCAST rules</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
<div class="hidden name"><code>eucast_rules.Rd</code></div>
</div>
@ -444,18 +448,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
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@ -466,7 +461,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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33
docs/reference/example_isolates.html
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@ -24,16 +24,20 @@
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
<meta property="og:title" content="Data set with 2,000 example isolates — example_isolates" />
<meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
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<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
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@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 2,000 example isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates.Rd</code></div>
</div>
@ -257,12 +261,9 @@
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#format">Format</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -273,7 +274,7 @@
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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33
docs/reference/example_isolates_unclean.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
<meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with unclean data</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
</div>
@ -252,12 +256,9 @@
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#format">Format</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
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<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -268,7 +269,7 @@
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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33
docs/reference/extended-functions.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Extended functions — extended-functions" />
<meta property="og:description" content="These functions are extensions of functions in other packages." />
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@ -64,7 +68,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
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</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Extended functions</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/extended.R'><code>R/extended.R</code></a></small>
<div class="hidden name"><code>extended-functions.Rd</code></div>
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@ -251,12 +255,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@ -267,7 +268,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@ -46,7 +50,7 @@
<meta property="og:title" content="Filter isolates on result in antibiotic class — filter_ab_class" />
<meta property="og:description" content="Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
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@ -78,7 +82,7 @@
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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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Filter isolates on result in antibiotic class</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
<div class="hidden name"><code>filter_ab_class.Rd</code></div>
</div>
@ -324,14 +328,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)</pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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@ -342,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@ -82,7 +82,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="<em>G</em>-test for Count Data — g.test" />
<meta property="og:description" content="g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable (1). A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence)." />
<meta property="og:image" content="/logo.svg" />
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@ -64,7 +68,7 @@
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@ -78,7 +82,7 @@
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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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1><em>G</em>-test for Count Data</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
<div class="hidden name"><code>g.test.Rd</code></div>
</div>
@ -376,19 +380,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># Meaning: there are significantly more left-billed birds.</span></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#references">References</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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@ -399,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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@ -46,7 +50,7 @@
<meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot2 functions." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
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@ -78,7 +82,7 @@
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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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>AMR plots with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div>
@ -507,15 +511,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
}</pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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@ -526,7 +524,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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@ -46,7 +50,7 @@
<meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Guess antibiotic column</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
<div class="hidden name"><code>guess_ab_col.Rd</code></div>
</div>
@ -298,16 +302,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># [1] "AMP_ED20"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -318,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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2
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

36
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Join a table with <a href='microorganisms.html'>microorganisms</a> — join" />
<meta property="og:description" content="Join the data set microorganisms easily to an existing table or character vector." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Join a table with <a href='microorganisms.html'>microorganisms</a></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
<div class="hidden name"><code>join.Rd</code></div>
</div>
@ -298,15 +302,9 @@ 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='no'>df_joined</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -317,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

38
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Key antibiotics for first <em>weighted</em> isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/key_antibiotics.R'><code>R/key_antibiotics.R</code></a></small>
<div class="hidden name"><code>key_antibiotics.Rd</code></div>
</div>
@ -410,17 +414,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#key-antibiotics">Key antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -431,7 +427,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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35
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Kurtosis of the sample — kurtosis" />
<meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Kurtosis of the sample</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
<div class="hidden name"><code>kurtosis.Rd</code></div>
</div>
@ -272,14 +276,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -290,7 +289,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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@ -24,16 +24,20 @@
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@ -48,7 +52,7 @@
<meta property="og:description" content="Our functions are categorised using the lifecycle circle of the tidyverse as found on www.tidyverse.org/lifecycle.
This page contains a section for every lifecycle (with text borrowed from the aforementioned tidyverse website), so they can be used in the manual pages of our functions." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -66,7 +70,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -80,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
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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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -225,7 +229,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
<div class="col-md-9 contents">
<div class="page-header">
<h1>Lifecycles of functions in the <code>AMR</code> package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
<div class="hidden name"><code>lifecycle.Rd</code></div>
</div>
@ -283,17 +287,9 @@ The lifecycle of this function is <strong>questioning</strong>. We are no longer
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#experimental-lifecycle">Experimental lifecycle</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#retired-lifecycle">Retired lifecycle</a></li>
<li><a href="#archived-lifecycle">Archived lifecycle</a></li>
<li><a href="#dormant-lifecycle">Dormant lifecycle</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -304,7 +300,7 @@ The lifecycle of this function is <strong>questioning</strong>. We are no longer
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine multidrug-resistant organisms (MDRO)</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mdro.R'><code>R/mdro.R</code></a></small>
<div class="hidden name"><code>mdro.Rd</code></div>
</div>
@ -450,19 +454,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -473,7 +467,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

39
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Property of a microorganism — mo_property" />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
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<div class="container template-reference-topic">
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of a microorganism</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<div class="hidden name"><code>mo_property.Rd</code></div>
</div>
@ -437,18 +441,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -459,7 +454,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@ -24,16 +24,20 @@
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@ -47,7 +51,7 @@
<meta property="og:title" content="Use predefined reference data set — mo_source" />
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -65,7 +69,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -79,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -224,7 +228,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<div class="col-md-9 contents">
<div class="page-header">
<h1>Use predefined reference data set</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>
@ -313,14 +317,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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@ -331,7 +330,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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35
docs/reference/p_symbol.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Symbol of a p-value — p_symbol" />
<meta property="og:description" content="Return the symbol related to the p-value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above p = 1 will return NA." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
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<body>
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Symbol of a p-value</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/p_symbol.R'><code>R/p_symbol.R</code></a></small>
<div class="hidden name"><code>p_symbol.Rd</code></div>
</div>
@ -263,14 +267,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
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@ -281,7 +280,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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36
docs/reference/pca.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Principal Component Analysis (for AMR) — pca" />
<meta property="og:description" content="Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
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<body>
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<div class="container template-reference-topic">
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Principal Component Analysis (for AMR)</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
<div class="hidden name"><code>pca.Rd</code></div>
</div>
@ -328,15 +332,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='no'>pca_result</span>) <span class='co'># a new and convenient plot function</span></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
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@ -347,7 +345,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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41
docs/reference/proportion.html
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@ -24,16 +24,20 @@
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@ -47,7 +51,7 @@
<meta property="og:title" content="Calculate microbial resistance — proportion" />
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise()][dplyr::summarise()] and also support grouped variables, please see Examples.
resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -65,7 +69,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -79,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -224,7 +228,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<div class="col-md-9 contents">
<div class="page-header">
<h1>Calculate microbial resistance</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
<div class="hidden name"><code>proportion.Rd</code></div>
</div>
@ -463,20 +467,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
}</pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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@ -487,7 +480,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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35
docs/reference/read.4D.html
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Read data from 4D database — read.4D" />
<meta property="og:description" content="This function is only useful for the MMB department of the UMCG. Use this function to import data by just defining the file parameter. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with as.mo() and transform all antimicrobial columns with as.rsi()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
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<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Read data from 4D database</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/read.4d.R'><code>R/read.4d.R</code></a></small>
<div class="hidden name"><code>read.4D.Rd</code></div>
</div>
@ -401,14 +405,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#dormant-lifecycle">Dormant lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
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</div>
@ -419,7 +418,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</
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<!-- pkgdown -->
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@ -51,7 +55,7 @@ below to see their documentation.
cleanerfreq
" />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -69,7 +73,7 @@ below to see their documentation.
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -83,7 +87,7 @@ below to see their documentation.
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -228,14 +232,14 @@ below to see their documentation.
<div class="col-md-9 contents">
<div class="page-header">
<h1>Objects exported from other packages</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/freq.R'><code>R/freq.R</code></a></small>
<div class="hidden name"><code>reexports.Rd</code></div>
</div>
<div class="ref-description">
<p>These objects are imported from other packages. Follow the links
below to see their documentation.</p>
<dl class='dl-horizontal'>
<dl'>
<dt>cleaner</dt><dd><p><code><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></code></p></dd>
</dl>
@ -246,10 +250,9 @@ below to see their documentation.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
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</div>
</div>
@ -260,7 +263,7 @@ below to see their documentation.</p>
</div>
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39
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Predict antimicrobial resistance — resistance_predict" />
<meta property="og:description" content="Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Predict antimicrobial resistance</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
<div class="hidden name"><code>resistance_predict.Rd</code></div>
</div>
@ -434,18 +438,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -456,7 +451,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>

35
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@ -24,16 +24,20 @@
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@ -47,7 +51,7 @@
<meta property="og:title" content="Skewness of the sample — skewness" />
<meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -65,7 +69,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -79,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -224,7 +228,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<div class="col-md-9 contents">
<div class="page-header">
<h1>Skewness of the sample</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/skewness.R'><code>R/skewness.R</code></a></small>
<div class="hidden name"><code>skewness.Rd</code></div>
</div>
@ -274,14 +278,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -292,7 +291,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
<meta property="og:title" content="Translate strings from AMR package — translate" />
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_name(), mo_type() and ab_name()." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Translate strings from AMR package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/translate.R'><code>R/translate.R</code></a></small>
<div class="hidden name"><code>translate.Rd</code></div>
</div>
@ -284,14 +288,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -302,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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