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dr. M.S. (Matthijs) Berends
2020-12-21 22:46:29 +01:00
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commit ee70883246
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75
docs/reference/AMR-deprecated.html
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Deprecated functions — AMR-deprecated • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -272,7 +303,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

45
docs/reference/AMR.html
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>The AMR Package — AMR • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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>
<!-- Flatly Theme - Light -->
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
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<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -246,9 +277,9 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><code>AMR</code> is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p><code>AMR</code> is a free, open-source and independent <span style="R">R</span> package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, <span style="R">R</span> knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other <span style="R">R</span> package and works on Windows, macOS and Linux with all versions of <span style="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <span style="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>
<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
@@ -310,7 +341,7 @@ The Netherlands
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

75
docs/reference/WHOCC.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -280,7 +311,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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</footer>

75
docs/reference/WHONET.html
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with 500 isolates - WHONET example — WHONET • AMR (for R)</title>
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@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -302,7 +333,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

39
docs/reference/ab_from_text.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Retrieve antimicrobial drug names and doses from clinical text — ab_from_text • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -363,7 +394,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

75
docs/reference/ab_property.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Get properties of an antibiotic — ab_property • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -401,7 +432,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
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75
docs/reference/age.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Age in years of individuals — age • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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>
<!-- Flatly Theme - Light -->
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
<!-- preferably CSS -->
<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
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Work with WHONET data
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@@ -341,7 +372,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -6,6 +6,22 @@
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</script>
<title>Antibiotic class selectors — antibiotic_class_selectors • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
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@@ -82,7 +112,7 @@
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@@ -90,14 +120,14 @@
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Import data from SPSS/SAS/Stata
</a>
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Get properties of an antibiotic
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@@ -342,7 +373,7 @@
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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43
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@@ -6,6 +6,22 @@
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// i.e. In this case, inject the `light` CSS before the others, with
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if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>
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@@ -19,11 +35,22 @@
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@@ -59,6 +86,9 @@
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@@ -82,7 +112,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9041</span>
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@@ -206,6 +236,7 @@
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@@ -297,12 +328,12 @@
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
<p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
<p>These data sets are available as 'flat files' for use even without <span style="R">R</span> - you can find the files here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
</ul>
<p>Files in R format (with preserved data structure) can be found here:</p><ul>
<p>Files in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://github.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antivirals.rda'>https://github.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
</ul>
@@ -346,7 +377,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<meta name="color-scheme" content="dark light">
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// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to an antibiotic ID — as.ab • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -363,7 +394,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
docs/reference/as.disk.html
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@@ -6,6 +6,22 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to disk diffusion diameters — as.disk • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
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<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
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Home
</a>
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How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
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<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
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<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
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<a href="../authors.html">
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<span class="fas fa-users"></span>
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</a>
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<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -317,7 +348,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to minimum inhibitory concentrations (MIC) — as.mic • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -316,7 +347,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/as.mo.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to a microorganism ID — as.mo • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -475,7 +506,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Interpret MIC and disk values, or clean raw R/SI data — as.rsi • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
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<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
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<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -515,7 +546,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
docs/reference/atc_online.html
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Get ATC properties from WHOCC website — atc_online_property • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -352,7 +383,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

75
docs/reference/availability.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Check availability of columns — availability • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<!-- preferably CSS -->
<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -301,7 +332,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

39
docs/reference/bug_drug_combinations.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
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@@ -206,6 +236,7 @@
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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">1.4.0.9041</span>
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@@ -206,6 +236,7 @@
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@@ -265,7 +296,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
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@@ -82,7 +112,7 @@
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@@ -282,7 +313,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -60,6 +87,9 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -83,7 +113,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -207,6 +237,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -60,6 +87,9 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -83,7 +113,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -91,14 +121,14 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -186,37 +216,38 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -404,7 +435,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<!-- favicons -->
@@ -19,11 +35,22 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
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@@ -90,14 +120,14 @@
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@@ -106,77 +136,77 @@
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<a href="../articles/AMR.html">
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Predict antimicrobial resistance
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Data sets for download / own use
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
</a>
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<a href="../reference/ab_property.html">
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Get properties of an antibiotic
</a>
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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@@ -185,37 +215,38 @@
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<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
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<a href="../survey.html">
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Survey
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@@ -286,7 +317,7 @@
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<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
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@@ -6,6 +6,22 @@
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// i.e. In this case, inject the `light` CSS before the others, with
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if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with unclean data — example_isolates_unclean • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
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@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
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<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
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<a href="../authors.html">
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<span class="fas fa-users"></span>
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</a>
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</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
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@@ -281,7 +312,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Filter isolates on result in antimicrobial class — filter_ab_class • AMR (for R)</title>
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@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
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@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
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</a>
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<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
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Conduct principal component analysis for AMR
</a>
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Import data from SPSS/SAS/Stata
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
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Get properties of an antibiotic
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@@ -185,37 +215,38 @@
</li>
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<a href="../reference/index.html">
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</a>
</li>
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<a href="../survey.html">
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<span class="fas fa-clipboard-list"></span>
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</a>
@@ -364,7 +395,7 @@ 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> 1.6.1.</p>
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
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// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
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</script>
<title>Determine first (weighted) isolates — first_isolate • AMR (for R)</title>
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@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
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@@ -206,6 +236,7 @@
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<ul class="nav navbar-nav navbar-right">
<li>
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<span class="fab fa-github"></span>
@@ -476,7 +507,7 @@ 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> 1.6.1.</p>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>G-test for Count Data — g.test • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -403,7 +434,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,6 +6,22 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>PCA biplot with ggplot2 — ggplot_pca • AMR (for R)</title>
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@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
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<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
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Work with WHONET data
</a>
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<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
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<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
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</a>
</li>
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<a href="../survey.html">
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<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -431,7 +462,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,6 +6,22 @@
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<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
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</script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -517,7 +548,7 @@ 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> 1.6.1.</p>
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@@ -6,6 +6,22 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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document.head.insertAdjacentHTML(
"beforeend",
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<title>Guess antibiotic column — guess_ab_col • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
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Home
</a>
</li>
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@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
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<a href="../articles/resistance_predict.html">
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Predict antimicrobial resistance
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Data sets for download / own use
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<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
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<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
</a>
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<a href="../articles/EUCAST.html">
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<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
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<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
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<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
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<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
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<li>
<a href="https://github.com/msberends/AMR">
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</a>
</li>
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<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -324,7 +355,7 @@ 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> 1.6.1.</p>
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39
docs/reference/index.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Function reference • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -58,6 +85,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -81,7 +111,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -205,6 +235,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -677,7 +708,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
docs/reference/intrinsic_resistant.html
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with bacterial intrinsic resistance — intrinsic_resistant • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
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<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
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<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
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<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
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<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
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Authors
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Changelog
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Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -290,7 +321,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
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View File

@@ -6,6 +6,22 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Determine (new) episodes for patients — is_new_episode • AMR (for R)</title>
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@@ -19,11 +35,22 @@
<!-- jquery -->
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<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9039</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -341,7 +372,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

39
docs/reference/join.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Join microorganisms to a data set — join • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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>
<!-- Flatly Theme - Light -->
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<!-- Darkly Theme - Dark -->
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
<!-- preferably CSS -->
<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -329,7 +360,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

75
docs/reference/key_antibiotics.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Key antibiotics for first weighted isolates — key_antibiotics • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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>
<!-- Flatly Theme - Light -->
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<!-- Darkly Theme - Dark -->
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
<!-- preferably CSS -->
<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -440,7 +471,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>

75
docs/reference/kurtosis.html
View File

@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Kurtosis of the sample — kurtosis • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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>
<!-- Flatly Theme - Light -->
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<!-- Darkly Theme - Dark -->
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
<!-- preferably CSS -->
<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
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@@ -301,7 +332,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<title>Lifecycles of functions in the AMR package — lifecycle • AMR (for R)</title>
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@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -61,6 +88,9 @@ This page contains a section for every lifecycle (with text borrowed from the af
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -84,7 +114,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -92,14 +122,14 @@ This page contains a section for every lifecycle (with text borrowed from the af
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@@ -108,77 +138,77 @@ This page contains a section for every lifecycle (with text borrowed from the af
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
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Conduct AMR analysis
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Conduct principal component analysis for AMR
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Import data from SPSS/SAS/Stata
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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@@ -187,37 +217,38 @@ This page contains a section for every lifecycle (with text borrowed from the af
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@@ -295,7 +326,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
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@@ -6,6 +6,22 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
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</script>
<title>Pattern matching with keyboard shortcut — like • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
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@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
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<a href="../authors.html">
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<span class="fas fa-users"></span>
Authors
</a>
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Changelog
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<a href="https://github.com/msberends/AMR">
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</a>
</li>
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<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -335,7 +366,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Determine multidrug-resistant organisms (MDRO) — mdro • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
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<a href="../news/index.html">
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<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
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Survey
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@@ -405,7 +436,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
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// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with 5,583 common microorganism codes — microorganisms.codes • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<link rel="stylesheet" href="../bootstrap-toc.css">
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
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@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
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Conduct principal component analysis for AMR
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Get properties of an antibiotic
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@@ -185,37 +215,38 @@
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Survey
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@@ -288,7 +319,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with 67,151 microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -279,11 +310,11 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
<p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
</ul>
<p>The file in R format (with preserved data structure) can be found here:</p><ul>
<p>The file in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://github.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
</ul>
@@ -331,7 +362,7 @@ 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> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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75
docs/reference/microorganisms.old.html
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set with previously accepted taxonomic names — microorganisms.old • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,37 +215,38 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
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<span class="fas fa-users"></span>
Authors
</a>
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Changelog
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</ul>
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@@ -294,7 +325,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -82,7 +112,7 @@
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@@ -90,14 +120,14 @@
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@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
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@@ -307,7 +338,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -82,7 +112,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9041</span>
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@@ -206,6 +236,7 @@
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@@ -519,7 +550,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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43
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@@ -60,6 +87,9 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -83,7 +113,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -207,6 +237,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -266,8 +297,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into R and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> parameter and defaults to the user's home directory. It can also be set as an <span style="R">R</span> option, using <code>options(AMR_mo_source = "my/location/file.rds)</code>.</p>
<p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an <span style="R">R</span> object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> parameter and defaults to the user's home directory. It can also be set as an <span style="R">R</span> option, using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_mo_source = "my/location/file.rds")</a></code>.</p>
<p>The created compressed data file <code>"mo_source.rds"</code> will be used at default for MO determination (function <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>). The location and timestamp of the original file will be saved as an attribute to the compressed data file.</p>
<p>The function <code>get_mo_source()</code> will return the data set by reading <code>"mo_source.rds"</code> with <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>. If the original file has changed (by checking the location and timestamp of the original file), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</p>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p>
@@ -359,7 +390,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -90,14 +120,14 @@
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@@ -106,77 +136,77 @@
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@@ -206,6 +236,7 @@
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@@ -60,6 +87,9 @@ resistance() should be used to calculate resistance, susceptibility() should be
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -83,7 +113,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -207,6 +237,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -480,7 +511,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
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@@ -19,11 +35,22 @@
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@@ -59,6 +86,9 @@
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@@ -82,7 +112,7 @@
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@@ -90,14 +120,14 @@
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@@ -106,77 +136,77 @@
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<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
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</a>
</li>
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<a href="../articles/resistance_predict.html">
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Predict antimicrobial resistance
</a>
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<a href="../articles/datasets.html">
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Data sets for download / own use
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Conduct principal component analysis for AMR
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Import data from SPSS/SAS/Stata
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Get properties of an antibiotic
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
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@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -460,7 +491,7 @@ 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> 1.6.1.</p>
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
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// i.e. In this case, inject the `light` CSS before the others, with
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document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data set for R/SI interpretation — rsi_translation • AMR (for R)</title>
<!-- favicons -->
@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -90,14 +120,14 @@
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<li>
<a href="../index.html">
<span class="fa fa-home"></span>
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@@ -106,77 +136,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
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<a href="../articles/resistance_predict.html">
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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<a href="../articles/MDR.html">
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<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
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Work with WHONET data
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<span class="fa fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
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Get properties of an antibiotic
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@@ -185,37 +215,38 @@
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</a>
</li>
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<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
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</a>
@@ -292,7 +323,7 @@
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<meta name="color-scheme" content="dark light">
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// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
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if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -60,6 +87,9 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -83,7 +113,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -91,14 +121,14 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<ul class="nav navbar-nav">
<li>
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@@ -107,77 +137,77 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
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<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -186,37 +216,38 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
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<a href="../authors.html">
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Authors
</a>
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</a>
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</ul>
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<a href="https://github.com/msberends/AMR">
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</a>
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<a href="../survey.html">
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<span class="fas fa-clipboard-list"></span>
Survey
</a>
@@ -299,7 +330,7 @@ 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> 1.6.1.</p>
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39
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@@ -6,6 +6,22 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
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// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Translate strings from AMR package — translate • AMR (for R)</title>
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@@ -19,11 +35,22 @@
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -59,6 +86,9 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -82,7 +112,7 @@
</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">1.4.0.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@@ -206,6 +236,7 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -316,7 +347,7 @@ 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> 1.6.1.</p>
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