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(v1.3.0) remove vignettes from CRAN
This commit is contained in:
parent
c5f7294381
commit
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^public$
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^data-raw$
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^\.lintr$
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^vignettes$
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^vignettes/AMR.Rmd$
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^vignettes/benchmarks.Rmd$
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^vignettes/EUCAST.Rmd$
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^vignettes/MDR.Rmd$
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^vignettes/PCA.Rmd$
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^vignettes/resistance_predict.Rmd$
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^vignettes/SPSS.Rmd$
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^vignettes/WHONET.Rmd$
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@ -249,6 +249,8 @@
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<dd></dt>
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<dt><a href="resistance_predict.html">How to predict antimicrobial resistance</a></dt>
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<dd></dt>
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<dt><a href="welcome_to_AMR.html">Welcome to the AMR package</a></dt>
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<dd></dt>
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</dl>
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</div>
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</div>
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256
docs/articles/welcome_to_AMR.html
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256
docs/articles/welcome_to_AMR.html
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@ -0,0 +1,256 @@
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<!DOCTYPE html>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>Welcome to the AMR package • AMR (for R)</title>
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<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
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<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
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<!-- 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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<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><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
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||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
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<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
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<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script><meta property="og:title" content="Welcome to the AMR package">
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<meta property="og:description" content="AMR">
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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<![endif]-->
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</head>
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<body data-spy="scroll" data-target="#toc">
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<div class="container template-article">
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<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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<div class="navbar-header">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
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<span class="sr-only">Toggle navigation</span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
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</span>
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</div>
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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<li>
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<a href="../index.html">
|
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<span class="fa fa-home"></span>
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Home
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</a>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fa fa-question-circle"></span>
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How to
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<span class="caret"></span>
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</a>
|
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<ul class="dropdown-menu" role="menu">
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<li>
|
||||
<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
|
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|
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Conduct AMR analysis
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</a>
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</li>
|
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<li>
|
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<a href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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</a>
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</li>
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<li>
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<a href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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|
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Conduct principal component analysis for AMR
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</a>
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</li>
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<li>
|
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<a href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
|
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|
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Determine multi-drug resistance (MDR)
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</a>
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</li>
|
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<li>
|
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<a href="../articles/WHONET.html">
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<span class="fa fa-globe-americas"></span>
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Work with WHONET data
|
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</a>
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</li>
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<li>
|
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<a href="../articles/SPSS.html">
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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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</a>
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</li>
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<li>
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<a href="../articles/EUCAST.html">
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<span class="fa fa-exchange-alt"></span>
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Apply EUCAST rules
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</a>
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</li>
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<li>
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<a href="../reference/mo_property.html">
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<span class="fa fa-bug"></span>
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Get properties of a microorganism
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</a>
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</li>
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<li>
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<a href="../reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antibiotic
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</a>
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</li>
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<li>
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<a href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
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Other: benchmarks
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</a>
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</li>
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</ul>
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</li>
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<li>
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<a href="../reference/index.html">
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<span class="fa fa-book-open"></span>
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Manual
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</a>
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</li>
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<li>
|
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<a href="../authors.html">
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<span class="fa fa-users"></span>
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Authors
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||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../news/index.html">
|
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<span class="far fa far fa-newspaper"></span>
|
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Changelog
|
||||
</a>
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</li>
|
||||
</ul>
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<ul class="nav navbar-nav navbar-right">
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<li>
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||||
<a href="https://github.com/msberends/AMR">
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||||
<span class="fab fa fab fa-github"></span>
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Source Code
|
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</a>
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</li>
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||||
<li>
|
||||
<a href="../survey.html">
|
||||
<span class="fa fa-clipboard-list"></span>
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||||
|
||||
Survey
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||||
</a>
|
||||
</li>
|
||||
</ul>
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||||
</div>
|
||||
<!--/.nav-collapse -->
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</div>
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<!--/.container -->
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||||
</div>
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||||
<!--/.navbar -->
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||||
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||||
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||||
|
||||
</header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Welcome to the AMR package</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">31 July 2020</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
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<div class="hidden name"><code>welcome_to_AMR.Rmd</code></div>
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</div>
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<div id="welcome-to-the-amr-package" class="section level1">
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<h1 class="hasAnchor">
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<a href="#welcome-to-the-amr-package" class="anchor"></a>Welcome to the AMR package</h1>
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<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. <strong>Our aim is to provide a standard</strong> 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>
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<p>After installing this package, R knows <strong>~70,000 distinct microbial species</strong> and all <strong>~550 antibiotic, antimycotic and antiviral drugs</strong> 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>
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<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). <strong>It was designed to work in any setting, including those with very limited resources</strong>. 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 (see Changelog) and is free software (see Copyright).</p>
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<p>Since its first public release in early 2018, this package has been downloaded from more than 100 countries.</p>
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<div id="usage-examples" class="section level2">
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<h2 class="hasAnchor">
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<a href="#usage-examples" class="anchor"></a>Usage examples</h2>
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<p>This package can be used for:</p>
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<ul>
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<li>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</li>
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<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</li>
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<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</li>
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<li>Determining first isolates to be used for AMR analysis</li>
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<li>Calculating antimicrobial resistance</li>
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<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</li>
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<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies</li>
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<li>Predicting future antimicrobial resistance using regression models</li>
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<li>Getting properties for any microorganism (like Gram stain, species, genus or family)</li>
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<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
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<li>Plotting antimicrobial resistance</li>
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<li>Applying EUCAST expert rules</li>
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<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code</li>
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<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code</li>
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<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</li>
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<li>Principal component analysis for AMR</li>
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</ul>
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</div>
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||||
</div>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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||||
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
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</nav>
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||||
</div>
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</div>
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|
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|
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<footer><div class="copyright">
|
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
</div>
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||||
|
||||
|
||||
|
||||
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||||
</body>
|
||||
</html>
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@ -0,0 +1,15 @@
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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
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// v0.0.1
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// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
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|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
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}
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}
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}
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});
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@ -10,7 +10,8 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-07-31T08:49Z
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-07-31T09:39Z
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urls:
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reference: https://msberends.github.io/AMR/reference
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article: https://msberends.github.io/AMR/articles
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@ -171,4 +171,7 @@
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<url>
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<loc>https://msberends.github.io/AMR/articles/resistance_predict.html</loc>
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</url>
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<url>
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<loc>https://msberends.github.io/AMR/articles/welcome_to_AMR.html</loc>
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</url>
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</urlset>
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56
vignettes/welcome_to_AMR.Rmd
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56
vignettes/welcome_to_AMR.Rmd
Normal file
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---
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title: "Welcome to the AMR package"
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author: "Matthijs S. Berends"
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date: '`r format(Sys.Date(), "%d %B %Y")`'
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output:
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rmarkdown::html_vignette:
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toc: true
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toc_depth: 3
|
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vignette: >
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%\VignetteIndexEntry{Welcome to the AMR package}
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%\VignetteEncoding{UTF-8}
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%\VignetteEngine{knitr::rmarkdown}
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editor_options:
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chunk_output_type: console
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---
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```{r setup, include = FALSE, results = 'markup'}
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knitr::opts_chunk$set(
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warning = FALSE,
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collapse = TRUE,
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comment = "#",
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fig.width = 7.5,
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fig.height = 5
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)
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```
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# Welcome to the AMR package
|
||||
|
||||
`AMR` 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.
|
||||
|
||||
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.
|
||||
|
||||
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 (see Changelog) and is free software (see Copyright).
|
||||
|
||||
Since its first public release in early 2018, this package has been downloaded from more than 100 countries.
|
||||
|
||||
## Usage examples
|
||||
|
||||
This package can be used for:
|
||||
|
||||
* 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
|
||||
* Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
|
||||
* Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
|
||||
* Determining first isolates to be used for AMR analysis
|
||||
* Calculating antimicrobial resistance
|
||||
* Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)
|
||||
* Calculating (empirical) susceptibility of both mono therapy and combination therapies
|
||||
* Predicting future antimicrobial resistance using regression models
|
||||
* Getting properties for any microorganism (like Gram stain, species, genus or family)
|
||||
* Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
|
||||
* Plotting antimicrobial resistance
|
||||
* Applying EUCAST expert rules
|
||||
* Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code
|
||||
* Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code
|
||||
* Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
|
||||
* Principal component analysis for AMR
|
||||
Loading…
Reference in New Issue
Block a user