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(v1.2.0.9031) GitHub Actions
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Package: AMR
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Version: 1.2.0.9030
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Version: 1.2.0.9031
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Date: 2020-07-09
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.2.0.9030
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# AMR 1.2.0.9031
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## <small>Last updated: 09-Jul-2020</small>
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### New
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR/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">1.2.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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</span>
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@@ -81,7 +81,7 @@
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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">1.2.0.9030</span>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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</span>
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</div>
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@@ -81,7 +81,7 @@
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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">1.2.0.9030</span>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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</span>
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</div>
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@@ -81,7 +81,7 @@
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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>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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</span>
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</div>
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@@ -43,7 +43,7 @@
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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>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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</span>
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</div>
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@@ -81,7 +81,7 @@
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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>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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</span>
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||||
</div>
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@@ -229,9 +229,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1209030" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9030">
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<a href="#amr-1209030" class="anchor"></a>AMR 1.2.0.9030<small> Unreleased </small>
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<div id="amr-1209031" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9031">
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<a href="#amr-1209031" class="anchor"></a>AMR 1.2.0.9031<small> Unreleased </small>
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</h1>
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<div id="last-updated-09-jul-2020" class="section level2">
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<h2 class="hasAnchor">
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@@ -10,7 +10,7 @@ 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: 2020-07-09T12:07Z
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last_built: 2020-07-09T14:11Z
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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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@@ -81,7 +81,7 @@
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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>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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</span>
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</div>
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263
docs_/404.html
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<!-- Generated by pkgdown: do not edit by hand -->
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<!DOCTYPE html>
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<html lang="en">
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<head>
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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>Page not found (404) • AMR (for R)</title>
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<!-- favicons -->
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="https://msberends.github.io/AMR/apple-touch-icon-60x60.png" />
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<!-- jquery -->
|
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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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<!-- 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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|
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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>
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|
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<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="https://msberends.github.io/AMR/bootstrap-toc.css">
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<script src="https://msberends.github.io/AMR/bootstrap-toc.js"></script>
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|
||||
<!-- Font Awesome icons -->
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<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 -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
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|
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<!-- 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>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
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<link href="https://msberends.github.io/AMR/pkgdown.css" rel="stylesheet">
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
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<!-- mathjax -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<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>
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<![endif]-->
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</head>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR/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">1.2.0.9029</span>
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</span>
|
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</div>
|
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|
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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>
|
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<a href="articles/AMR.html">
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<span class="fa fa-directions"></span>
|
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Conduct AMR analysis
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</a>
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</li>
|
||||
<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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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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|
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Work with WHONET data
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</a>
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||||
</li>
|
||||
<li>
|
||||
<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
|
||||
</a>
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||||
</li>
|
||||
<li>
|
||||
<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>
|
||||
</li>
|
||||
<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>
|
||||
<li>
|
||||
<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/">
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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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Authors
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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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<!DOCTYPE html>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</span>
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Conduct principal component analysis for AMR
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Get properties of a microorganism
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Other: benchmarks
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</header>
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||||
<div class="row">
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<div class="contents col-md-9">
|
||||
<div class="page-header">
|
||||
<h1>License</h1>
|
||||
</div>
|
||||
|
||||
<pre>GNU GENERAL PUBLIC LICENSE
|
||||
Version 2, June 1991
|
||||
|
||||
Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
|
||||
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
|
||||
Everyone is permitted to copy and distribute verbatim copies
|
||||
of this license document, but changing it is not allowed.
|
||||
|
||||
A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
|
||||
|
||||
This R package, with package name 'AMR':
|
||||
- May be used for commercial purposes
|
||||
- May be used for private purposes
|
||||
- May NOT be used for patent purposes
|
||||
- May be modified, although:
|
||||
- Modifications MUST be released under the same license when distributing the package
|
||||
- Changes made to the code MUST be documented
|
||||
- May be distributed, although:
|
||||
- Source code MUST be made available when the package is distributed
|
||||
- A copy of the license and copyright notice MUST be included with the package.
|
||||
- Comes with a LIMITATION of liability
|
||||
- Comes with NO warranty
|
||||
|
||||
END OF THE SUMMARY
|
||||
|
||||
|
||||
GNU GENERAL PUBLIC LICENSE
|
||||
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
||||
|
||||
0. This License applies to any program or other work which contains
|
||||
a notice placed by the copyright holder saying it may be distributed
|
||||
under the terms of this General Public License. The "Program", below,
|
||||
refers to any such program or work, and a "work based on the Program"
|
||||
means either the Program or any derivative work under copyright law:
|
||||
that is to say, a work containing the Program or a portion of it,
|
||||
either verbatim or with modifications and/or translated into another
|
||||
language. (Hereinafter, translation is included without limitation in
|
||||
the term "modification".) Each licensee is addressed as "you".
|
||||
|
||||
Activities other than copying, distribution and modification are not
|
||||
covered by this License; they are outside its scope. The act of
|
||||
running the Program is not restricted, and the output from the Program
|
||||
is covered only if its contents constitute a work based on the
|
||||
Program (independent of having been made by running the Program).
|
||||
Whether that is true depends on what the Program does.
|
||||
|
||||
1. You may copy and distribute verbatim copies of the Program's
|
||||
source code as you receive it, in any medium, provided that you
|
||||
conspicuously and appropriately publish on each copy an appropriate
|
||||
copyright notice and disclaimer of warranty; keep intact all the
|
||||
notices that refer to this License and to the absence of any warranty;
|
||||
and give any other recipients of the Program a copy of this License
|
||||
along with the Program.
|
||||
|
||||
You may charge a fee for the physical act of transferring a copy, and
|
||||
you may at your option offer warranty protection in exchange for a fee.
|
||||
|
||||
2. You may modify your copy or copies of the Program or any portion
|
||||
of it, thus forming a work based on the Program, and copy and
|
||||
distribute such modifications or work under the terms of Section 1
|
||||
above, provided that you also meet all of these conditions:
|
||||
|
||||
a) You must cause the modified files to carry prominent notices
|
||||
stating that you changed the files and the date of any change.
|
||||
|
||||
b) You must cause any work that you distribute or publish, that in
|
||||
whole or in part contains or is derived from the Program or any
|
||||
part thereof, to be licensed as a whole at no charge to all third
|
||||
parties under the terms of this License.
|
||||
|
||||
c) If the modified program normally reads commands interactively
|
||||
when run, you must cause it, when started running for such
|
||||
interactive use in the most ordinary way, to print or display an
|
||||
announcement including an appropriate copyright notice and a
|
||||
notice that there is no warranty (or else, saying that you provide
|
||||
a warranty) and that users may redistribute the program under
|
||||
these conditions, and telling the user how to view a copy of this
|
||||
License. (Exception: if the Program itself is interactive but
|
||||
does not normally print such an announcement, your work based on
|
||||
the Program is not required to print an announcement.)
|
||||
|
||||
These requirements apply to the modified work as a whole. If
|
||||
identifiable sections of that work are not derived from the Program,
|
||||
and can be reasonably considered independent and separate works in
|
||||
themselves, then this License, and its terms, do not apply to those
|
||||
sections when you distribute them as separate works. But when you
|
||||
distribute the same sections as part of a whole which is a work based
|
||||
on the Program, the distribution of the whole must be on the terms of
|
||||
this License, whose permissions for other licensees extend to the
|
||||
entire whole, and thus to each and every part regardless of who wrote it.
|
||||
|
||||
Thus, it is not the intent of this section to claim rights or contest
|
||||
your rights to work written entirely by you; rather, the intent is to
|
||||
exercise the right to control the distribution of derivative or
|
||||
collective works based on the Program.
|
||||
|
||||
In addition, mere aggregation of another work not based on the Program
|
||||
with the Program (or with a work based on the Program) on a volume of
|
||||
a storage or distribution medium does not bring the other work under
|
||||
the scope of this License.
|
||||
|
||||
3. You may copy and distribute the Program (or a work based on it,
|
||||
under Section 2) in object code or executable form under the terms of
|
||||
Sections 1 and 2 above provided that you also do one of the following:
|
||||
|
||||
a) Accompany it with the complete corresponding machine-readable
|
||||
source code, which must be distributed under the terms of Sections
|
||||
1 and 2 above on a medium customarily used for software interchange; or,
|
||||
|
||||
b) Accompany it with a written offer, valid for at least three
|
||||
years, to give any third party, for a charge no more than your
|
||||
cost of physically performing source distribution, a complete
|
||||
machine-readable copy of the corresponding source code, to be
|
||||
distributed under the terms of Sections 1 and 2 above on a medium
|
||||
customarily used for software interchange; or,
|
||||
|
||||
c) Accompany it with the information you received as to the offer
|
||||
to distribute corresponding source code. (This alternative is
|
||||
allowed only for noncommercial distribution and only if you
|
||||
received the program in object code or executable form with such
|
||||
an offer, in accord with Subsection b above.)
|
||||
|
||||
The source code for a work means the preferred form of the work for
|
||||
making modifications to it. For an executable work, complete source
|
||||
code means all the source code for all modules it contains, plus any
|
||||
associated interface definition files, plus the scripts used to
|
||||
control compilation and installation of the executable. However, as a
|
||||
special exception, the source code distributed need not include
|
||||
anything that is normally distributed (in either source or binary
|
||||
form) with the major components (compiler, kernel, and so on) of the
|
||||
operating system on which the executable runs, unless that component
|
||||
itself accompanies the executable.
|
||||
|
||||
If distribution of executable or object code is made by offering
|
||||
access to copy from a designated place, then offering equivalent
|
||||
access to copy the source code from the same place counts as
|
||||
distribution of the source code, even though third parties are not
|
||||
compelled to copy the source along with the object code.
|
||||
|
||||
4. You may not copy, modify, sublicense, or distribute the Program
|
||||
except as expressly provided under this License. Any attempt
|
||||
otherwise to copy, modify, sublicense or distribute the Program is
|
||||
void, and will automatically terminate your rights under this License.
|
||||
However, parties who have received copies, or rights, from you under
|
||||
this License will not have their licenses terminated so long as such
|
||||
parties remain in full compliance.
|
||||
|
||||
5. You are not required to accept this License, since you have not
|
||||
signed it. However, nothing else grants you permission to modify or
|
||||
distribute the Program or its derivative works. These actions are
|
||||
prohibited by law if you do not accept this License. Therefore, by
|
||||
modifying or distributing the Program (or any work based on the
|
||||
Program), you indicate your acceptance of this License to do so, and
|
||||
all its terms and conditions for copying, distributing or modifying
|
||||
the Program or works based on it.
|
||||
|
||||
6. Each time you redistribute the Program (or any work based on the
|
||||
Program), the recipient automatically receives a license from the
|
||||
original licensor to copy, distribute or modify the Program subject to
|
||||
these terms and conditions. You may not impose any further
|
||||
restrictions on the recipients' exercise of the rights granted herein.
|
||||
You are not responsible for enforcing compliance by third parties to
|
||||
this License.
|
||||
|
||||
7. If, as a consequence of a court judgment or allegation of patent
|
||||
infringement or for any other reason (not limited to patent issues),
|
||||
conditions are imposed on you (whether by court order, agreement or
|
||||
otherwise) that contradict the conditions of this License, they do not
|
||||
excuse you from the conditions of this License. If you cannot
|
||||
distribute so as to satisfy simultaneously your obligations under this
|
||||
License and any other pertinent obligations, then as a consequence you
|
||||
may not distribute the Program at all. For example, if a patent
|
||||
license would not permit royalty-free redistribution of the Program by
|
||||
all those who receive copies directly or indirectly through you, then
|
||||
the only way you could satisfy both it and this License would be to
|
||||
refrain entirely from distribution of the Program.
|
||||
|
||||
If any portion of this section is held invalid or unenforceable under
|
||||
any particular circumstance, the balance of the section is intended to
|
||||
apply and the section as a whole is intended to apply in other
|
||||
circumstances.
|
||||
|
||||
It is not the purpose of this section to induce you to infringe any
|
||||
patents or other property right claims or to contest validity of any
|
||||
such claims; this section has the sole purpose of protecting the
|
||||
integrity of the free software distribution system, which is
|
||||
implemented by public license practices. Many people have made
|
||||
generous contributions to the wide range of software distributed
|
||||
through that system in reliance on consistent application of that
|
||||
system; it is up to the author/donor to decide if he or she is willing
|
||||
to distribute software through any other system and a licensee cannot
|
||||
impose that choice.
|
||||
|
||||
This section is intended to make thoroughly clear what is believed to
|
||||
be a consequence of the rest of this License.
|
||||
|
||||
8. If the distribution and/or use of the Program is restricted in
|
||||
certain countries either by patents or by copyrighted interfaces, the
|
||||
original copyright holder who places the Program under this License
|
||||
may add an explicit geographical distribution limitation excluding
|
||||
those countries, so that distribution is permitted only in or among
|
||||
countries not thus excluded. In such case, this License incorporates
|
||||
the limitation as if written in the body of this License.
|
||||
|
||||
9. The Free Software Foundation may publish revised and/or new versions
|
||||
of the General Public License from time to time. Such new versions will
|
||||
be similar in spirit to the present version, but may differ in detail to
|
||||
address new problems or concerns.
|
||||
|
||||
Each version is given a distinguishing version number. If the Program
|
||||
specifies a version number of this License which applies to it and "any
|
||||
later version", you have the option of following the terms and conditions
|
||||
either of that version or of any later version published by the Free
|
||||
Software Foundation. If the Program does not specify a version number of
|
||||
this License, you may choose any version ever published by the Free Software
|
||||
Foundation.
|
||||
|
||||
10. If you wish to incorporate parts of the Program into other free
|
||||
programs whose distribution conditions are different, write to the author
|
||||
to ask for permission. For software which is copyrighted by the Free
|
||||
Software Foundation, write to the Free Software Foundation; we sometimes
|
||||
make exceptions for this. Our decision will be guided by the two goals
|
||||
of preserving the free status of all derivatives of our free software and
|
||||
of promoting the sharing and reuse of software generally.
|
||||
|
||||
NO WARRANTY
|
||||
|
||||
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
|
||||
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
|
||||
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
|
||||
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
|
||||
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
|
||||
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
||||
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
||||
REPAIR OR CORRECTION.
|
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<h1 data-toc-skip>How to apply EUCAST rules</h1>
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<h4 class="author">Matthijs S. Berends</h4>
|
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|
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<h4 class="date">28 May 2020</h4>
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<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
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<div id="introduction" class="section level2">
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<h2 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor"></a>Introduction</h2>
|
||||
<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">on their website</a>:</p>
|
||||
<blockquote>
|
||||
<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
|
||||
</blockquote>
|
||||
<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 10.0, 2020). Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
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<div id="examples" class="section level2">
|
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<h2 class="hasAnchor">
|
||||
<a href="#examples" class="anchor"></a>Examples</h2>
|
||||
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
|
||||
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">oops</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>,
|
||||
<span class="st">"Escherichia"</span>),
|
||||
<span class="kw">ampicillin</span> <span class="kw">=</span> <span class="st">"S"</span>)
|
||||
<span class="no">oops</span>
|
||||
<span class="co"># mo ampicillin</span>
|
||||
<span class="co"># 1 Klebsiella S</span>
|
||||
<span class="co"># 2 Escherichia S</span>
|
||||
|
||||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">oops</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
|
||||
<span class="co"># mo ampicillin</span>
|
||||
<span class="co"># 1 Klebsiella R</span>
|
||||
<span class="co"># 2 Escherichia S</span></pre></body></html></div>
|
||||
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">data</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,
|
||||
<span class="st">"Enterococcus faecalis"</span>,
|
||||
<span class="st">"Escherichia coli"</span>,
|
||||
<span class="st">"Klebsiella pneumoniae"</span>,
|
||||
<span class="st">"Pseudomonas aeruginosa"</span>),
|
||||
<span class="kw">VAN</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
|
||||
<span class="kw">AMX</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
|
||||
<span class="kw">COL</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span>
|
||||
<span class="kw">CAZ</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
|
||||
<span class="kw">CXM</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
|
||||
<span class="kw">PEN</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Penicillin G</span>
|
||||
<span class="kw">FOX</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
|
||||
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
|
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<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">data</span></pre></body></html></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">mo</th>
|
||||
<th align="center">VAN</th>
|
||||
<th align="center">AMX</th>
|
||||
<th align="center">COL</th>
|
||||
<th align="center">CAZ</th>
|
||||
<th align="center">CXM</th>
|
||||
<th align="center">PEN</th>
|
||||
<th align="center">FOX</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Enterococcus faecalis</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Pseudomonas aeruginosa</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>)</pre></body></html></div>
|
||||
<pre><code># Warning: Not all columns with antimicrobial results are of class <rsi>.
|
||||
# Transform eligible columns to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)</code></pre>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">mo</th>
|
||||
<th align="center">VAN</th>
|
||||
<th align="center">AMX</th>
|
||||
<th align="center">COL</th>
|
||||
<th align="center">CAZ</th>
|
||||
<th align="center">CXM</th>
|
||||
<th align="center">PEN</th>
|
||||
<th align="center">FOX</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Enterococcus faecalis</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Pseudomonas aeruginosa</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
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<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">28 May 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>MDR.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine which micro-organisms are multi-drug resistant organisms (MDRO).</p>
|
||||
<div id="type-of-input" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#type-of-input" class="anchor"></a>Type of input</h4>
|
||||
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a regular <code>data.frame</code>. It tries to automatically determine the right columns for info about your isolates, like the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
|
||||
<p>For WHONET data (and most other data), all settings are automatically set correctly.</p>
|
||||
</div>
|
||||
<div id="guidelines" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#guidelines" class="anchor"></a>Guidelines</h4>
|
||||
<p>The function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
|
||||
<ul>
|
||||
<li>
|
||||
<p><code>guideline = "CMI2012"</code> (default)</p>
|
||||
Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</li>
|
||||
<li>
|
||||
<p><code>guideline = "EUCAST"</code></p>
|
||||
The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</li>
|
||||
<li>
|
||||
<p><code>guideline = "TB"</code></p>
|
||||
The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/">link</a>)</li>
|
||||
<li>
|
||||
<p><code>guideline = "MRGN"</code></p>
|
||||
The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. (<a href="https://doi.org/10.1186/s13756-015-0047-6">link</a>)</li>
|
||||
<li>
|
||||
<p><code>guideline = "BRMO"</code></p>
|
||||
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]” (<a href="https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH">link</a>)</p>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="examples" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#examples" class="anchor"></a>Examples</h4>
|
||||
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
|
||||
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <span class="co"># to support pipes: %>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">cleaner</span>) <span class="co"># to create frequency tables</span></pre></body></html></div>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>() <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>() <span class="co"># show frequency table of the result</span>
|
||||
<span class="co"># NOTE: Using column `mo` as input for `col_mo`.</span>
|
||||
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
|
||||
<span class="co"># NOTE: Reliability would be improved if these antimicrobial results would be available too: ceftaroline (CPT), fusidic acid (FUS), telavancin (TLV), daptomycin (DAP), quinupristin/dalfopristin (QDA), minocycline (MNO), gentamicin-high (GEH), streptomycin-high (STH), doripenem (DOR), levofloxacin (LVX), netilmicin (NET), ticarcillin/clavulanic acid (TCC), ertapenem (ETP), cefotetan (CTT), aztreonam (ATM), ampicillin/sulbactam (SAM), polymyxin B (PLB)</span>
|
||||
<span class="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span>
|
||||
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></pre></body></html></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
Length: 2,000<br>
|
||||
Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant …<br>
|
||||
Available: 1,711 (85.55%, NA: 289 = 14.45%)<br>
|
||||
Unique: 2</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left"></th>
|
||||
<th align="left">Item</th>
|
||||
<th align="right">Count</th>
|
||||
<th align="right">Percent</th>
|
||||
<th align="right">Cum. Count</th>
|
||||
<th align="right">Cum. Percent</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">1595</td>
|
||||
<td align="right">93.22%</td>
|
||||
<td align="right">1595</td>
|
||||
<td align="right">93.22%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Multi-drug-resistant (MDR)</td>
|
||||
<td align="right">116</td>
|
||||
<td align="right">6.78%</td>
|
||||
<td align="right">1711</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
|
||||
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># a helper function to get a random vector with values S, I and R</span>
|
||||
<span class="co"># with the probabilities 50% - 10% - 40%</span>
|
||||
<span class="no">sample_rsi</span> <span class="kw"><-</span> <span class="kw">function</span>() {
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),
|
||||
<span class="kw">size</span> <span class="kw">=</span> <span class="fl">5000</span>,
|
||||
<span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),
|
||||
<span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
|
||||
}
|
||||
|
||||
<span class="no">my_TB_data</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">rifampicin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">isoniazid</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">gatifloxacin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">ethambutol</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">pyrazinamide</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">moxifloxacin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">kanamycin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>())</pre></body></html></div>
|
||||
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">my_TB_data</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">RIF</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">INH</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">GAT</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">ETH</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">PZA</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">MFX</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
|
||||
<span class="kw">KAN</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>())</pre></body></html></div>
|
||||
<p>The data set now looks like this:</p>
|
||||
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 S R R S R R</span>
|
||||
<span class="co"># 2 R S R S R S</span>
|
||||
<span class="co"># 3 R R S S R S</span>
|
||||
<span class="co"># 4 S S S S R S</span>
|
||||
<span class="co"># 5 S R S S R S</span>
|
||||
<span class="co"># 6 R S R S S S</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 R</span>
|
||||
<span class="co"># 2 I</span>
|
||||
<span class="co"># 3 R</span>
|
||||
<span class="co"># 4 S</span>
|
||||
<span class="co"># 5 R</span>
|
||||
<span class="co"># 6 S</span></pre></body></html></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="no">my_TB_data</span>, <span class="kw">guideline</span> <span class="kw">=</span> <span class="st">"TB"</span>)</pre></body></html></div>
|
||||
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">my_TB_data</span>$<span class="no">mdr</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span>(<span class="no">my_TB_data</span>)
|
||||
<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span>
|
||||
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
|
||||
<span class="co"># NOTE: Reliability would be improved if these antimicrobial results would be available too: capreomycin (CAP), rifabutin (RIB), rifapentine (RFP)</span></pre></body></html></div>
|
||||
<p>Create a frequency table of the results:</p>
|
||||
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">my_TB_data</span>$<span class="no">mdr</span>)</pre></body></html></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
Length: 5,000<br>
|
||||
Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <…<br>
|
||||
Available: 5,000 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 5</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left"></th>
|
||||
<th align="left">Item</th>
|
||||
<th align="right">Count</th>
|
||||
<th align="right">Percent</th>
|
||||
<th align="right">Cum. Count</th>
|
||||
<th align="right">Cum. Percent</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3245</td>
|
||||
<td align="right">64.90%</td>
|
||||
<td align="right">3245</td>
|
||||
<td align="right">64.90%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">678</td>
|
||||
<td align="right">13.56%</td>
|
||||
<td align="right">3923</td>
|
||||
<td align="right">78.46%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">607</td>
|
||||
<td align="right">12.14%</td>
|
||||
<td align="right">4530</td>
|
||||
<td align="right">90.60%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">262</td>
|
||||
<td align="right">5.24%</td>
|
||||
<td align="right">4792</td>
|
||||
<td align="right">95.84%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">208</td>
|
||||
<td align="right">4.16%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
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Conduct AMR analysis
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Predict antimicrobial resistance
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<a href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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Conduct principal component analysis for AMR
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</a>
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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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Determine multi-drug resistance (MDR)
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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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<div class="page-header toc-ignore">
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<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">28 May 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>PCA.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
|
||||
<div id="introduction" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
||||
</div>
|
||||
<div id="transforming" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#transforming" class="anchor"></a>Transforming</h1>
|
||||
<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/reexports.html">glimpse</a></span>(<span class="no">example_isolates</span>)
|
||||
<span class="co"># Rows: 2,000</span>
|
||||
<span class="co"># Columns: 49</span>
|
||||
<span class="co"># $ date <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…</span>
|
||||
<span class="co"># $ hospital_id <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B,…</span>
|
||||
<span class="co"># $ ward_icu <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, T…</span>
|
||||
<span class="co"># $ ward_clinical <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, F…</span>
|
||||
<span class="co"># $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALS…</span>
|
||||
<span class="co"># $ age <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…</span>
|
||||
<span class="co"># $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span>
|
||||
<span class="co"># $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "06…</span>
|
||||
<span class="co"># $ mo <mo> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STP…</span>
|
||||
<span class="co"># $ PEN <ord> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ OXA <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FLC <ord> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ AMX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ AMC <ord> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
|
||||
<span class="co"># $ AMP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TZP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CZO <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FEP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CXM <ord> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
|
||||
<span class="co"># $ FOX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CTX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ CAZ <ord> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
|
||||
<span class="co"># $ CRO <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ GEN <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TOB <ord> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
|
||||
<span class="co"># $ AMK <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ KAN <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TMP <ord> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
|
||||
<span class="co"># $ SXT <ord> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
|
||||
<span class="co"># $ NIT <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FOS <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ LNZ <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ CIP <ord> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ MFX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ VAN <ord> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ TEC <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ TCY <ord> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
|
||||
<span class="co"># $ TGC <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ DOX <ord> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
|
||||
<span class="co"># $ ERY <ord> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ CLI <ord> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ AZM <ord> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ IPM <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ MEM <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ MTR <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CHL <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ COL <ord> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ MUP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ RIF <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></pre></body></html></div>
|
||||
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">resistance_data</span> <span class="kw"><-</span> <span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">order</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">mo</span>), <span class="co"># group on anything, like order</span>
|
||||
<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%>%</span> <span class="co"># and genus as we do here</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span>(<span class="no">is.rsi</span>, <span class="no">resistance</span>) <span class="kw">%>%</span> <span class="co"># then get resistance of all drugs</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">order</span>, <span class="no">genus</span>, <span class="no">AMC</span>, <span class="no">CXM</span>, <span class="no">CTX</span>,
|
||||
<span class="no">CAZ</span>, <span class="no">GEN</span>, <span class="no">TOB</span>, <span class="no">TMP</span>, <span class="no">SXT</span>) <span class="co"># and select only relevant columns</span>
|
||||
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">resistance_data</span>)
|
||||
<span class="co"># # A tibble: 6 x 10</span>
|
||||
<span class="co"># # Groups: order [2]</span>
|
||||
<span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span>
|
||||
<span class="co"># <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl></span>
|
||||
<span class="co"># 1 (unknown order) (unknown genu… NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 2 Actinomycetales Corynebacteri… NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 3 Actinomycetales Cutibacterium NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 4 Actinomycetales Dermabacter NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 5 Actinomycetales Micrococcus NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 6 Actinomycetales Rothia NA NA NA NA NA NA NA NA</span></pre></body></html></div>
|
||||
</div>
|
||||
<div id="perform-principal-component-analysis" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
|
||||
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
|
||||
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">pca_result</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span>(<span class="no">resistance_data</span>)
|
||||
<span class="co"># NOTE: Columns selected for PCA: AMC CXM CTX CAZ GEN TOB TMP SXT.</span>
|
||||
<span class="co"># Total observations available: 7.</span></pre></body></html></div>
|
||||
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">pca_result</span>)
|
||||
<span class="co"># Importance of components:</span>
|
||||
<span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span>
|
||||
<span class="co"># Standard deviation 2.154 1.6809 0.61305 0.33882 0.20755 0.03137 1.602e-16</span>
|
||||
<span class="co"># Proportion of Variance 0.580 0.3532 0.04698 0.01435 0.00538 0.00012 0.000e+00</span>
|
||||
<span class="co"># Cumulative Proportion 0.580 0.9332 0.98014 0.99449 0.99988 1.00000 1.000e+00</span></pre></body></html></div>
|
||||
<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
|
||||
</div>
|
||||
<div id="plotting-the-results" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#plotting-the-results" class="anchor"></a>Plotting the results</h1>
|
||||
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span>(<span class="no">pca_result</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
|
||||
<p>But we can’t see the explanation of the points. Perhaps this works better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-6-1.png" width="750"></p>
|
||||
<p>You can also print an ellipse per group, and edit the appearance:</p>
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>, <span class="kw">ellipse</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +
|
||||
<span class="kw pkg">ggplot2</span><span class="kw ns">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="kw">title</span> <span class="kw">=</span> <span class="st">"An AMR/PCA biplot!"</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
|
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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 class="page-header toc-ignore">
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<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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||||
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<h4 class="date">08 July 2020</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
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<div id="spss-sas-stata" class="section level2">
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<h2 class="hasAnchor">
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<a href="#spss-sas-stata" class="anchor"></a>SPSS / SAS / Stata</h2>
|
||||
<p>SPSS (Statistical Package for the Social Sciences) is probably the most well-known software package for statistical analysis. SPSS is easier to learn than R, because in SPSS you only have to click a menu to run parts of your analysis. Because of its user-friendliness, it is taught at universities and particularly useful for students who are new to statistics. From my experience, I would guess that pretty much all (bio)medical students know it at the time they graduate. SAS and Stata are comparable statistical packages popular in big industries.</p>
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<div id="compared-to-r" class="section level2">
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<h2 class="hasAnchor">
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<a href="#compared-to-r" class="anchor"></a>Compared to R</h2>
|
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<p>As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major downsides when comparing it with R:</p>
|
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<ul>
|
||||
<li>
|
||||
<p><strong>R is highly modular.</strong></p>
|
||||
<p>The <a href="https://cran.r-project.org/">official R network (CRAN)</a> features almost 14,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.</p>
|
||||
<p>Bottom line is, you can really extend it yourself or ask somebody to do this for you. Take for example our <code>AMR</code> package. Among other things, it adds reliable reference data to R to help you with the data cleaning and analysis. SPSS, SAS and Stata will never know what a valid MIC value is or what the Gram stain of <em>E. coli</em> is. Or that all species of <em>Klebiella</em> are resistant to amoxicillin and that Floxapen<sup>®</sup> is a trade name of flucloxacillin. These facts and properties are often needed to clean existing data, which would be very inconvenient in a software package without reliable reference data. See below for a demonstration.</p>
|
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|
||||
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|
||||
<p><strong>R is extremely flexible.</strong></p>
|
||||
<p>Because you write the syntax yourself, you can do anything you want. The flexibility in transforming, arranging, grouping and summarising data, or drawing plots, is endless - with SPSS, SAS or Stata you are bound to their algorithms and format styles. They may be a bit flexible, but you can probably never create that very specific publication-ready plot without using other (paid) software. If you sometimes write syntaxes in SPSS to run a complete analysis or to ‘automate’ some of your work, you could do this a lot less time in R. You will notice that writing syntaxes in R is a lot more nifty and clever than in SPSS. Still, as working with any statistical package, you will have to have knowledge about what you are doing (statistically) and what you are willing to accomplish.</p>
|
||||
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|
||||
<li>
|
||||
<p><strong>R can be easily automated.</strong></p>
|
||||
<p>Over the last years, <a href="https://rmarkdown.rstudio.com/">R Markdown</a> has really made an interesting development. With R Markdown, you can very easily produce reports, whether the format has to be Word, PowerPoint, a website, a PDF document or just the raw data to Excel. It even allows the use of a reference file containing the layout style (e.g. fonts and colours) of your organisation. I use this a lot to generate weekly and monthly reports automatically. Just write the code once and enjoy the automatically updated reports at any interval you like.</p>
|
||||
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
|
||||
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|
||||
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|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, more than <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">300,000 R-related questions</a> have already been asked on this platform (which covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||
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|
||||
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|
||||
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
||||
<p>And that’s not vice versa I’m afraid. You can import data from any source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/">link</a>), from Minitab, Epi Info and EpiData (<a href="https://cran.r-project.org/package=foreign">link</a>), from Excel (<a href="https://readxl.tidyverse.org/">link</a>), from flat files like CSV, TXT or TSV (<a href="https://readr.tidyverse.org/">link</a>), or directly from databases and datawarehouses from anywhere on the world (<a href="https://dbplyr.tidyverse.org/">link</a>). You can even scrape websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest">link</a>) or get the results of an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread">link</a>).</p>
|
||||
<p>And the best part - you can export from R to most data formats as well. So you can import an SPSS file, do your analysis neatly in R and export the resulting tables to Excel files for sharing.</p>
|
||||
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|
||||
<li>
|
||||
<p><strong>R is completely free and open-source.</strong></p>
|
||||
<p>No strings attached. It was created and is being maintained by volunteers who believe that (data) science should be open and publicly available to everybody. SPSS, SAS and Stata are quite expensive. IBM SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing">between USD 1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html">around USD 10,000</a> per computer. Stata also has a business model with subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/">between USD 600 and USD 2,800</a> per computer per year, but lower prices come with a limitation of the number of variables you can work with. And still they do not offer the above benefits of R.</p>
|
||||
<p>If you are working at a midsized or small company, you can save it tens of thousands of dollars by using R instead of e.g. SPSS - gaining even more functions and flexibility. And all R enthousiasts can do as much PR as they want (like I do here), because nobody is officially associated with or affiliated by R. It is really free.</p>
|
||||
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|
||||
<li>
|
||||
<p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
|
||||
<p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
|
||||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2020, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||||
</li>
|
||||
</ul>
|
||||
<p>To demonstrate the first point:</p>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="co"># not all values are valid MIC values:</span>
|
||||
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)
|
||||
<span class="co"># Class <mic></span>
|
||||
<span class="co"># [1] 0.125</span>
|
||||
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)
|
||||
<span class="co"># Class <mic></span>
|
||||
<span class="co"># [1] <NA></span>
|
||||
|
||||
<span class="co"># the Gram stain is avaiable for all bacteria:</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="co"># [1] "Gram-negative"</span>
|
||||
|
||||
<span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span>
|
||||
<span class="no">klebsiella_test</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="st">"klebsiella"</span>,
|
||||
<span class="kw">amox</span> <span class="kw">=</span> <span class="st">"S"</span>,
|
||||
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
|
||||
<span class="no">klebsiella_test</span> <span class="co"># (our original data)</span>
|
||||
<span class="co"># mo amox</span>
|
||||
<span class="co"># 1 klebsiella S</span>
|
||||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">klebsiella_test</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span>
|
||||
<span class="co"># mo amox</span>
|
||||
<span class="co"># 1 klebsiella R</span>
|
||||
|
||||
<span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)
|
||||
<span class="co"># [1] "Flucloxacillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)
|
||||
<span class="co"># [1] "floxacillin" "floxapen" "floxapen sodium salt"</span>
|
||||
<span class="co"># [4] "fluclox" "flucloxacilina" "flucloxacillin" </span>
|
||||
<span class="co"># [7] "flucloxacilline" "flucloxacillinum" "fluorochloroxacillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)
|
||||
<span class="co"># [1] "J01CF05"</span></pre></body></html></div>
|
||||
</div>
|
||||
<div id="import-data-from-spsssasstata" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#import-data-from-spsssasstata" class="anchor"></a>Import data from SPSS/SAS/Stata</h2>
|
||||
<div id="rstudio" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#rstudio" class="anchor"></a>RStudio</h3>
|
||||
<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
|
||||
<p>To import a data file, just click <em>Import Dataset</em> in the Environment tab:</p>
|
||||
<p><img src="https://github.com/msberends/AMR/raw/master/docs/import1.png"></p>
|
||||
<p>If additional packages are needed, RStudio will ask you if they should be installed on beforehand.</p>
|
||||
<p>In the the window that opens, you can define all options (parameters) that should be used for import and you’re ready to go:</p>
|
||||
<p><img src="https://github.com/msberends/AMR/raw/master/docs/import2.png"></p>
|
||||
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
|
||||
<p>The difference is this:</p>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">SPSS_data</span>
|
||||
<span class="co"># # A tibble: 4,203 x 4</span>
|
||||
<span class="co"># v001 sex status statusage</span>
|
||||
<span class="co"># <dbl> <dbl+lbl> <dbl+lbl> <dbl></span>
|
||||
<span class="co"># 1 10002 1 1 76.6</span>
|
||||
<span class="co"># 2 10004 0 1 59.1</span>
|
||||
<span class="co"># 3 10005 1 1 54.5</span>
|
||||
<span class="co"># 4 10006 1 1 54.1</span>
|
||||
<span class="co"># 5 10007 1 1 57.7</span>
|
||||
<span class="co"># 6 10008 1 1 62.8</span>
|
||||
<span class="co"># 7 10010 0 1 63.7</span>
|
||||
<span class="co"># 8 10011 1 1 73.1</span>
|
||||
<span class="co"># 9 10017 1 1 56.7</span>
|
||||
<span class="co"># 10 10018 0 1 66.6</span>
|
||||
<span class="co"># # … with 4,193 more rows</span>
|
||||
|
||||
<span class="fu">as_factor</span>(<span class="no">SPSS_data</span>)
|
||||
<span class="co"># # A tibble: 4,203 x 4</span>
|
||||
<span class="co"># v001 sex status statusage</span>
|
||||
<span class="co"># <dbl> <fct> <fct> <dbl></span>
|
||||
<span class="co"># 1 10002 Male alive 76.6</span>
|
||||
<span class="co"># 2 10004 Female alive 59.1</span>
|
||||
<span class="co"># 3 10005 Male alive 54.5</span>
|
||||
<span class="co"># 4 10006 Male alive 54.1</span>
|
||||
<span class="co"># 5 10007 Male alive 57.7</span>
|
||||
<span class="co"># 6 10008 Male alive 62.8</span>
|
||||
<span class="co"># 7 10010 Female alive 63.7</span>
|
||||
<span class="co"># 8 10011 Male alive 73.1</span>
|
||||
<span class="co"># 9 10017 Male alive 56.7</span>
|
||||
<span class="co"># 10 10018 Female alive 66.6</span>
|
||||
<span class="co"># # … with 4,193 more rows</span></pre></body></html></div>
|
||||
</div>
|
||||
<div id="base-r" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#base-r" class="anchor"></a>Base R</h3>
|
||||
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/">great <code>haven</code> package</a> yourself:</p>
|
||||
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># download and install the latest version:</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"haven"</span>)
|
||||
<span class="co"># load the package you just installed:</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">haven</span>)</pre></body></html></div>
|
||||
<p>You can now import files as follows:</p>
|
||||
<div id="spss" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#spss" class="anchor"></a>SPSS</h4>
|
||||
<p>To read files from SPSS into R:</p>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># read any SPSS file based on file extension (best way):</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
|
||||
|
||||
<span class="co"># read .sav or .zsav file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
|
||||
|
||||
<span class="co"># read .por file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></div>
|
||||
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>, as mentioned above.</p>
|
||||
<p>To export your R objects to the SPSS file format:</p>
|
||||
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="co"># save as .sav file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
|
||||
|
||||
<span class="co"># save as compressed .zsav file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">compress</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
|
||||
</div>
|
||||
<div id="sas" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#sas" class="anchor"></a>SAS</h4>
|
||||
<p>To read files from SAS into R:</p>
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="kw">data_file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">catalog_file</span> <span class="kw">=</span> <span class="kw">NULL</span>)
|
||||
|
||||
<span class="co"># read SAS transport files (version 5 and version 8):</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></div>
|
||||
<p>To export your R objects to the SAS file format:</p>
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="co"># save as regular SAS file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
|
||||
|
||||
<span class="co"># the SAS transport format is an open format </span>
|
||||
<span class="co"># (required for submission of the data to the FDA)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">8</span>)</pre></body></html></div>
|
||||
</div>
|
||||
<div id="stata" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#stata" class="anchor"></a>Stata</h4>
|
||||
<p>To read files from Stata into R:</p>
|
||||
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="co"># read .dta file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)
|
||||
|
||||
<span class="co"># works exactly the same:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)</pre></body></html></div>
|
||||
<p>To export your R objects to the Stata file format:</p>
|
||||
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="co"># save as .dta file, Stata version 14:</span>
|
||||
<span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">14</span>)</pre></body></html></div>
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Work with WHONET data
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Get properties of a microorganism
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Get properties of an antibiotic
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<h1 data-toc-skip>How to work with WHONET data</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">28 May 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
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<div class="hidden name"><code>WHONET.Rmd</code></div>
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<div id="import-of-data" class="section level3">
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||||
<h3 class="hasAnchor">
|
||||
<a href="#import-of-data" class="anchor"></a>Import of data</h3>
|
||||
<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
|
||||
<p>An example syntax could look like this:</p>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">readxl</span>)
|
||||
<span class="no">data</span> <span class="kw"><-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/your/file.xlsx"</span>)</pre></body></html></div>
|
||||
<p>This package comes with an <a href="https://msberends.gitlab.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
|
||||
</div>
|
||||
<div id="preparation" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#preparation" class="anchor"></a>Preparation</h3>
|
||||
<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="uri">https://www.tidyverse.org/</a>.</p>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <span class="co"># part of tidyverse</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">ggplot2</span>) <span class="co"># part of tidyverse</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>) <span class="co"># this package</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">cleaner</span>) <span class="co"># to create frequency tables</span></pre></body></html></div>
|
||||
<p>We will have to transform some variables to simplify and automate the analysis:</p>
|
||||
<ul>
|
||||
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.gitlab.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
|
||||
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
|
||||
</ul>
|
||||
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># transform variables</span>
|
||||
<span class="no">data</span> <span class="kw"><-</span> <span class="no">WHONET</span> <span class="kw">%>%</span>
|
||||
<span class="co"># get microbial ID based on given organism</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">Organism</span>)) <span class="kw">%>%</span>
|
||||
<span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">AMP_ND10</span>:<span class="no">CIP_EE</span>), <span class="no">as.rsi</span>)</pre></body></html></div>
|
||||
<p>No errors or warnings, so all values are transformed succesfully.</p>
|
||||
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. Its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function can be used to create frequency tables.</p>
|
||||
<p>So let’s check our data, with a couple of frequency tables:</p>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
|
||||
<span class="no">data</span> <span class="kw">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>), <span class="kw">nmax</span> <span class="kw">=</span> <span class="fl">10</span>)</pre></body></html></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 500<br>
|
||||
Available: 500 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 37</p>
|
||||
<p>Shortest: 11<br>
|
||||
Longest: 40</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left"></th>
|
||||
<th align="left">Item</th>
|
||||
<th align="right">Count</th>
|
||||
<th align="right">Percent</th>
|
||||
<th align="right">Cum. Count</th>
|
||||
<th align="right">Cum. Percent</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">245</td>
|
||||
<td align="right">49.0%</td>
|
||||
<td align="right">245</td>
|
||||
<td align="right">49.0%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Coagulase-negative Staphylococcus (CoNS)</td>
|
||||
<td align="right">74</td>
|
||||
<td align="right">14.8%</td>
|
||||
<td align="right">319</td>
|
||||
<td align="right">63.8%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Staphylococcus epidermidis</td>
|
||||
<td align="right">38</td>
|
||||
<td align="right">7.6%</td>
|
||||
<td align="right">357</td>
|
||||
<td align="right">71.4%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">31</td>
|
||||
<td align="right">6.2%</td>
|
||||
<td align="right">388</td>
|
||||
<td align="right">77.6%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Staphylococcus hominis</td>
|
||||
<td align="right">21</td>
|
||||
<td align="right">4.2%</td>
|
||||
<td align="right">409</td>
|
||||
<td align="right">81.8%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">6</td>
|
||||
<td align="left">Proteus mirabilis</td>
|
||||
<td align="right">9</td>
|
||||
<td align="right">1.8%</td>
|
||||
<td align="right">418</td>
|
||||
<td align="right">83.6%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">7</td>
|
||||
<td align="left">Enterococcus faecium</td>
|
||||
<td align="right">8</td>
|
||||
<td align="right">1.6%</td>
|
||||
<td align="right">426</td>
|
||||
<td align="right">85.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">8</td>
|
||||
<td align="left">Staphylococcus capitis</td>
|
||||
<td align="right">8</td>
|
||||
<td align="right">1.6%</td>
|
||||
<td align="right">434</td>
|
||||
<td align="right">86.8%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">9</td>
|
||||
<td align="left">Enterobacter cloacae</td>
|
||||
<td align="right">5</td>
|
||||
<td align="right">1.0%</td>
|
||||
<td align="right">439</td>
|
||||
<td align="right">87.8%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">10</td>
|
||||
<td align="left">Streptococcus anginosus</td>
|
||||
<td align="right">5</td>
|
||||
<td align="right">1.0%</td>
|
||||
<td align="right">444</td>
|
||||
<td align="right">88.8%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>(omitted 27 entries, n = 56 [11.20%])</p>
|
||||
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="co"># our transformed antibiotic columns</span>
|
||||
<span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
|
||||
<span class="no">data</span> <span class="kw">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">AMC_ND2</span>)</pre></body></html></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered > rsi (numeric)<br>
|
||||
Length: 500<br>
|
||||
Levels: 3: S < I < R<br>
|
||||
Available: 481 (96.2%, NA: 19 = 3.8%)<br>
|
||||
Unique: 3</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left"></th>
|
||||
<th align="left">Item</th>
|
||||
<th align="right">Count</th>
|
||||
<th align="right">Percent</th>
|
||||
<th align="right">Cum. Count</th>
|
||||
<th align="right">Cum. Percent</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">S</td>
|
||||
<td align="right">356</td>
|
||||
<td align="right">74.01%</td>
|
||||
<td align="right">356</td>
|
||||
<td align="right">74.01%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">R</td>
|
||||
<td align="right">103</td>
|
||||
<td align="right">21.41%</td>
|
||||
<td align="right">459</td>
|
||||
<td align="right">95.43%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">I</td>
|
||||
<td align="right">22</td>
|
||||
<td align="right">4.57%</td>
|
||||
<td align="right">481</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="a-first-glimpse-at-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#a-first-glimpse-at-results" class="anchor"></a>A first glimpse at results</h3>
|
||||
<p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">data</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">Country</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">Country</span>, <span class="no">AMP_ND2</span>, <span class="no">AMC_ED20</span>, <span class="no">CAZ_ED10</span>, <span class="no">CIP_ED5</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span>(<span class="kw">translate_ab</span> <span class="kw">=</span> <span class="st">'ab'</span>, <span class="kw">facet</span> <span class="kw">=</span> <span class="st">"Country"</span>, <span class="kw">datalabels</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
|
||||
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
</div>
|
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<a href="../articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine multi-drug resistance (MDR)
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET data
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/SPSS.html">
|
||||
<span class="fa 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>
|
||||
|
||||
Apply EUCAST rules
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get properties of a microorganism
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
Other: benchmarks
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/">
|
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<span class="fa fa-book-open"></span>
|
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|
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Manual
|
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</a>
|
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|
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|
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|
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<span class="fa fa-users"></span>
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|
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Authors
|
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|
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|
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|
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<a href="../news/">
|
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<span class="far fa far fa-newspaper"></span>
|
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|
||||
Changelog
|
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</a>
|
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|
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</ul>
|
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<ul class="nav navbar-nav navbar-right">
|
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<li>
|
||||
<a href="https://gitlab.com/msberends/AMR">
|
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<span class="fab fa fab fa-gitlab"></span>
|
||||
|
||||
Source Code
|
||||
</a>
|
||||
</li>
|
||||
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|
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<a href="../LICENSE-text.html">
|
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|
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|
||||
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|
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|
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|
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|
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|
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</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Benchmarks</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">28 May 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>benchmarks.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
|
||||
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code>microbenchmark()</code> runs different input expressions independently of each other and measures their time-to-result.</p>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">microbenchmark</span> <span class="kw"><-</span> <span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="no"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)</pre></body></html></div>
|
||||
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
|
||||
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
|
||||
<p>But the calculation time differs a lot:</p>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">S.aureus</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S aureus"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>), <span class="co"># official taxonomic name</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus (MRSA)"</span>), <span class="co"># additional text</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Sthafilokkockus aaureuz"</span>), <span class="co"># incorrect spelling</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fl">22242419</span>), <span class="co"># Catalogue of Life ID</span>
|
||||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">2</span>)
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max</span>
|
||||
<span class="co"># as.mo("sau") 8.5 11.0 17.0 12.0 12.0 43.0</span>
|
||||
<span class="co"># as.mo("stau") 120.0 130.0 150.0 140.0 160.0 180.0</span>
|
||||
<span class="co"># as.mo("STAU") 130.0 140.0 150.0 150.0 160.0 170.0</span>
|
||||
<span class="co"># as.mo("staaur") 7.7 9.1 13.0 11.0 12.0 38.0</span>
|
||||
<span class="co"># as.mo("STAAUR") 8.3 9.3 15.0 10.0 11.0 37.0</span>
|
||||
<span class="co"># as.mo("S. aureus") 11.0 12.0 18.0 13.0 14.0 41.0</span>
|
||||
<span class="co"># as.mo("S aureus") 8.8 11.0 17.0 12.0 13.0 41.0</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 6.4 6.6 7.4 7.6 7.8 9.1</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 810.0 870.0 890.0 890.0 900.0 1000.0</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 320.0 340.0 370.0 350.0 400.0 490.0</span>
|
||||
<span class="co"># as.mo("MRSA") 9.2 10.0 13.0 11.0 12.0 37.0</span>
|
||||
<span class="co"># as.mo("VISA") 12.0 12.0 22.0 13.0 43.0 44.0</span>
|
||||
<span class="co"># as.mo("VRSA") 11.0 13.0 21.0 14.0 38.0 41.0</span>
|
||||
<span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 170.0 200.0</span>
|
||||
<span class="co"># neval</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span></pre></body></html></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second.</p>
|
||||
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
|
||||
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">M.semesiae</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Methanosarcina semesiae"</span>),
|
||||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max</span>
|
||||
<span class="co"># as.mo("metsem") 143.400 146.300 156.10 155.400 164.900 176.40</span>
|
||||
<span class="co"># as.mo("METSEM") 141.600 146.900 167.00 170.700 185.000 188.00</span>
|
||||
<span class="co"># as.mo("M. semesiae") 9.665 9.879 16.50 10.090 11.960 44.29</span>
|
||||
<span class="co"># as.mo("M. semesiae") 10.000 10.080 14.46 11.660 13.140 42.01</span>
|
||||
<span class="co"># as.mo("Methanosarcina semesiae") 7.161 7.389 10.40 7.542 9.294 33.00</span>
|
||||
<span class="co"># neval</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span></pre></body></html></div>
|
||||
<p>Looking up arbitrary codes of less prevalent microorganisms costs the most time. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
|
||||
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></p>
|
||||
<p>Uncommon microorganisms take some more time than common microorganisms. To further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
<div id="repetitive-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
|
||||
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># take all MO codes from the example_isolates data set</span>
|
||||
<span class="no">x</span> <span class="kw"><-</span> <span class="no">example_isolates</span>$<span class="no">mo</span> <span class="kw">%>%</span>
|
||||
<span class="co"># keep only the unique ones</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/unique.html">unique</a></span>() <span class="kw">%>%</span>
|
||||
<span class="co"># pick 50 of them at random</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="fl">50</span>) <span class="kw">%>%</span>
|
||||
<span class="co"># paste that 10,000 times</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">10000</span>) <span class="kw">%>%</span>
|
||||
<span class="co"># scramble it</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()
|
||||
|
||||
<span class="co"># got indeed 50 times 10,000 = half a million?</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span>(<span class="no">x</span>)
|
||||
<span class="co"># [1] 500000</span>
|
||||
|
||||
<span class="co"># and how many unique values do we have?</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(<span class="no">x</span>)
|
||||
<span class="co"># [1] 50</span>
|
||||
|
||||
<span class="co"># now let's see:</span>
|
||||
<span class="no">run_it</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">x</span>),
|
||||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 1650 1730 1790 1790 1840 1900 10</span></pre></body></html></div>
|
||||
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.79 seconds. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
|
||||
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
|
||||
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),
|
||||
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
|
||||
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
|
||||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 5.680 5.820 9.61 6.36 6.850 39.500 10</span>
|
||||
<span class="co"># B 9.790 10.000 10.60 10.40 10.900 11.900 10</span>
|
||||
<span class="co"># C 0.229 0.259 0.27 0.27 0.286 0.311 10</span></pre></body></html></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0003 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
|
||||
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
|
||||
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
|
||||
<span class="kw">D</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),
|
||||
<span class="kw">E</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),
|
||||
<span class="kw">F</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),
|
||||
<span class="kw">G</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),
|
||||
<span class="kw">H</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),
|
||||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 0.209 0.221 0.236 0.225 0.244 0.311 10</span>
|
||||
<span class="co"># B 0.197 0.201 0.215 0.212 0.222 0.266 10</span>
|
||||
<span class="co"># C 0.205 0.224 0.243 0.229 0.242 0.383 10</span>
|
||||
<span class="co"># D 0.199 0.207 0.216 0.211 0.214 0.270 10</span>
|
||||
<span class="co"># E 0.196 0.206 0.218 0.215 0.221 0.270 10</span>
|
||||
<span class="co"># F 0.188 0.197 0.212 0.210 0.216 0.269 10</span>
|
||||
<span class="co"># G 0.195 0.198 0.213 0.203 0.215 0.299 10</span>
|
||||
<span class="co"># H 0.184 0.193 0.205 0.201 0.207 0.252 10</span></pre></body></html></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
|
||||
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span>
|
||||
<span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
|
||||
<span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
|
||||
<span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span>
|
||||
|
||||
<span class="no">run_it</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="kw">en</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>),
|
||||
<span class="kw">de</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>),
|
||||
<span class="kw">nl</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>),
|
||||
<span class="kw">es</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>),
|
||||
<span class="kw">it</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"it"</span>),
|
||||
<span class="kw">fr</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"fr"</span>),
|
||||
<span class="kw">pt</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>),
|
||||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 9.303 11.59 14.90 12.40 13.63 45.92 100</span>
|
||||
<span class="co"># de 10.080 12.39 15.77 13.11 14.45 46.27 100</span>
|
||||
<span class="co"># nl 13.200 16.26 20.88 17.80 19.52 49.93 100</span>
|
||||
<span class="co"># es 9.957 12.23 15.57 13.12 14.59 51.99 100</span>
|
||||
<span class="co"># it 10.210 12.44 19.02 13.34 14.74 52.96 100</span>
|
||||
<span class="co"># fr 10.040 12.40 18.90 13.26 15.07 54.40 100</span>
|
||||
<span class="co"># pt 10.450 12.67 16.91 13.46 14.68 51.47 100</span></pre></body></html></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
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Conduct principal component analysis for AMR
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||||
<a href="../articles/MDR.html">
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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||||
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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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||||
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<span class="fa fa-exchange-alt"></span>
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Apply EUCAST rules
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||||
<a href="../reference/mo_property.html">
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Get properties of a microorganism
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Get properties of an antibiotic
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||||
<dt><a href="AMR.html">How to conduct AMR analysis</a></dt>
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||||
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|
||||
<dt><a href="EUCAST.html">How to apply EUCAST rules</a></dt>
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||||
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||||
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<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">28 May 2020</h4>
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<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd"><code>vignettes/resistance_predict.Rmd</code></a></small>
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<div class="hidden name"><code>resistance_predict.Rmd</code></div>
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<div id="needed-r-packages" class="section level2">
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<h2 class="hasAnchor">
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<a href="#needed-r-packages" class="anchor"></a>Needed R packages</h2>
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<p>As with many uses in R, we need some additional packages for AMR analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
|
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<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">ggplot2</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
|
||||
|
||||
<span class="co"># (if not yet installed, install with:)</span>
|
||||
<span class="co"># install.packages(c("tidyverse", "AMR"))</span></pre></body></html></div>
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</div>
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<div id="prediction-analysis" class="section level2">
|
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<h2 class="hasAnchor">
|
||||
<a href="#prediction-analysis" class="anchor"></a>Prediction analysis</h2>
|
||||
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
|
||||
<p>It is basically as easy as:</p>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"># resistance prediction of piperacillin/tazobactam (TZP):
|
||||
resistance_predict(tbl = example_isolates, col_date = "date", col_ab = "TZP", model = "binomial")
|
||||
|
||||
# or:
|
||||
example_isolates %>%
|
||||
resistance_predict(col_ab = "TZP",
|
||||
model "binomial")
|
||||
|
||||
# to bind it to object 'predict_TZP' for example:
|
||||
predict_TZP <- example_isolates %>%
|
||||
resistance_predict(col_ab = "TZP",
|
||||
model = "binomial")</pre></body></html></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code><a href="../reference/resistance_predict.html">resistance_predict(..., info = FALSE)</a></code>.</p>
|
||||
<pre><code># NOTE: Using column `date` as input for `col_date`.</code></pre>
|
||||
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">predict_TZP</span>
|
||||
<span class="co"># year value se_min se_max observations observed estimated</span>
|
||||
<span class="co"># 1 2002 0.20000000 NA NA 15 0.20000000 0.05616378</span>
|
||||
<span class="co"># 2 2003 0.06250000 NA NA 32 0.06250000 0.06163839</span>
|
||||
<span class="co"># 3 2004 0.08536585 NA NA 82 0.08536585 0.06760841</span>
|
||||
<span class="co"># 4 2005 0.05000000 NA NA 60 0.05000000 0.07411100</span>
|
||||
<span class="co"># 5 2006 0.05084746 NA NA 59 0.05084746 0.08118454</span>
|
||||
<span class="co"># 6 2007 0.12121212 NA NA 66 0.12121212 0.08886843</span>
|
||||
<span class="co"># 7 2008 0.04166667 NA NA 72 0.04166667 0.09720264</span>
|
||||
<span class="co"># 8 2009 0.01639344 NA NA 61 0.01639344 0.10622731</span>
|
||||
<span class="co"># 9 2010 0.05660377 NA NA 53 0.05660377 0.11598223</span>
|
||||
<span class="co"># 10 2011 0.18279570 NA NA 93 0.18279570 0.12650615</span>
|
||||
<span class="co"># 11 2012 0.30769231 NA NA 65 0.30769231 0.13783610</span>
|
||||
<span class="co"># 12 2013 0.06896552 NA NA 58 0.06896552 0.15000651</span>
|
||||
<span class="co"># 13 2014 0.10000000 NA NA 60 0.10000000 0.16304829</span>
|
||||
<span class="co"># 14 2015 0.23636364 NA NA 55 0.23636364 0.17698785</span>
|
||||
<span class="co"># 15 2016 0.22619048 NA NA 84 0.22619048 0.19184597</span>
|
||||
<span class="co"># 16 2017 0.16279070 NA NA 86 0.16279070 0.20763675</span>
|
||||
<span class="co"># 17 2018 0.22436641 0.1938710 0.2548618 NA NA 0.22436641</span>
|
||||
<span class="co"># 18 2019 0.24203228 0.2062911 0.2777735 NA NA 0.24203228</span>
|
||||
<span class="co"># 19 2020 0.26062172 0.2191758 0.3020676 NA NA 0.26062172</span>
|
||||
<span class="co"># 20 2021 0.28011130 0.2325557 0.3276669 NA NA 0.28011130</span>
|
||||
<span class="co"># 21 2022 0.30046606 0.2464567 0.3544755 NA NA 0.30046606</span>
|
||||
<span class="co"># 22 2023 0.32163907 0.2609011 0.3823771 NA NA 0.32163907</span>
|
||||
<span class="co"># 23 2024 0.34357130 0.2759081 0.4112345 NA NA 0.34357130</span>
|
||||
<span class="co"># 24 2025 0.36619175 0.2914934 0.4408901 NA NA 0.36619175</span>
|
||||
<span class="co"># 25 2026 0.38941799 0.3076686 0.4711674 NA NA 0.38941799</span>
|
||||
<span class="co"># 26 2027 0.41315710 0.3244399 0.5018743 NA NA 0.41315710</span>
|
||||
<span class="co"># 27 2028 0.43730688 0.3418075 0.5328063 NA NA 0.43730688</span>
|
||||
<span class="co"># 28 2029 0.46175755 0.3597639 0.5637512 NA NA 0.46175755</span>
|
||||
<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span></pre></body></html></div>
|
||||
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
|
||||
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">predict_TZP</span>)</pre></body></html></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
|
||||
<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
|
||||
<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">predict_TZP</span>)</pre></body></html></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r">
|
||||
<span class="co"># choose for error bars instead of a ribbon</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">predict_TZP</span>, <span class="kw">ribbon</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
|
||||
<div id="choosing-the-right-model" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
|
||||
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
|
||||
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="no">mo</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="kw">==</span> <span class="st">"Gram-positive"</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"VAN"</span>, <span class="kw">year_min</span> <span class="kw">=</span> <span class="fl">2010</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"binomial"</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()
|
||||
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></body></html></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
|
||||
<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
|
||||
<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
|
||||
<p>Valid values are:</p>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="32%">
|
||||
<col width="25%">
|
||||
<col width="42%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th>Input values</th>
|
||||
<th>Function used by R</th>
|
||||
<th>Type of model</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>
|
||||
<code>"binomial"</code> or <code>"binom"</code> or <code>"logit"</code>
|
||||
</td>
|
||||
<td><code><a href="https://rdrr.io/r/stats/glm.html">glm(..., family = binomial)</a></code></td>
|
||||
<td>Generalised linear model with binomial distribution</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>
|
||||
<code>"loglin"</code> or <code>"poisson"</code>
|
||||
</td>
|
||||
<td><code><a href="https://rdrr.io/r/stats/glm.html">glm(..., family = poisson)</a></code></td>
|
||||
<td>Generalised linear model with poisson distribution</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>
|
||||
<code>"lin"</code> or <code>"linear"</code>
|
||||
</td>
|
||||
<td><code><a href="https://rdrr.io/r/stats/lm.html">lm()</a></code></td>
|
||||
<td>Linear model</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
|
||||
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="no">mo</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="kw">==</span> <span class="st">"Gram-positive"</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"VAN"</span>, <span class="kw">year_min</span> <span class="kw">=</span> <span class="fl">2010</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"linear"</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()
|
||||
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></body></html></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
<p>This seems more likely, doesn’t it?</p>
|
||||
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
|
||||
<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">model</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span>(<span class="no">predict_TZP</span>)$<span class="no">model</span>
|
||||
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">model</span>)$<span class="no">family</span>
|
||||
<span class="co"># </span>
|
||||
<span class="co"># Family: binomial </span>
|
||||
<span class="co"># Link function: logit</span>
|
||||
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">model</span>)$<span class="no">coefficients</span>
|
||||
<span class="co"># Estimate Std. Error z value Pr(>|z|)</span>
|
||||
<span class="co"># (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span>
|
||||
<span class="co"># year 0.09883005 0.02295317 4.305725 1.664395e-05</span></pre></body></html></div>
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Conduct principal component analysis for AMR
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Import data from SPSS/SAS/Stata
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<h1>Citation</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
|
||||
</div>
|
||||
|
||||
<p>Berends MS, Luz CF et al. (2019). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622</p>
|
||||
<pre>@Article{,
|
||||
title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
|
||||
author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
|
||||
journal = {bioRxiv},
|
||||
publisher = {Cold Spring Harbor Laboratory},
|
||||
year = {2019},
|
||||
url = {https://doi.org/10.1101/810622},
|
||||
}</pre>
|
||||
|
||||
<div class="page-header">
|
||||
<h1>Authors</h1>
|
||||
</div>
|
||||
|
||||
<ul class="list-unstyled">
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a></strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
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||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
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|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
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|
||||
<p><strong>Judith M. Fonville</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Erwin E. A. Hassing</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Eric H. L. C. M. Hazenberg</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Annick Lenglet</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Bart C. Meijer</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Sofia Ny</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Dennis Souverein</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
</div>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
|
||||
60
docs_/bootstrap-toc.css
vendored
60
docs_/bootstrap-toc.css
vendored
@@ -1,60 +0,0 @@
|
||||
/*!
|
||||
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
|
||||
* Copyright 2015 Aidan Feldman
|
||||
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
|
||||
|
||||
/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
|
||||
|
||||
/* All levels of nav */
|
||||
nav[data-toggle='toc'] .nav > li > a {
|
||||
display: block;
|
||||
padding: 4px 20px;
|
||||
font-size: 13px;
|
||||
font-weight: 500;
|
||||
color: #767676;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav > li > a:hover,
|
||||
nav[data-toggle='toc'] .nav > li > a:focus {
|
||||
padding-left: 19px;
|
||||
color: #563d7c;
|
||||
text-decoration: none;
|
||||
background-color: transparent;
|
||||
border-left: 1px solid #563d7c;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav > .active > a,
|
||||
nav[data-toggle='toc'] .nav > .active:hover > a,
|
||||
nav[data-toggle='toc'] .nav > .active:focus > a {
|
||||
padding-left: 18px;
|
||||
font-weight: bold;
|
||||
color: #563d7c;
|
||||
background-color: transparent;
|
||||
border-left: 2px solid #563d7c;
|
||||
}
|
||||
|
||||
/* Nav: second level (shown on .active) */
|
||||
nav[data-toggle='toc'] .nav .nav {
|
||||
display: none; /* Hide by default, but at >768px, show it */
|
||||
padding-bottom: 10px;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav .nav > li > a {
|
||||
padding-top: 1px;
|
||||
padding-bottom: 1px;
|
||||
padding-left: 30px;
|
||||
font-size: 12px;
|
||||
font-weight: normal;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:hover,
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:focus {
|
||||
padding-left: 29px;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav .nav > .active > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:hover > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:focus > a {
|
||||
padding-left: 28px;
|
||||
font-weight: 500;
|
||||
}
|
||||
|
||||
/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
|
||||
nav[data-toggle='toc'] .nav > .active > ul {
|
||||
display: block;
|
||||
}
|
||||
159
docs_/bootstrap-toc.js
vendored
159
docs_/bootstrap-toc.js
vendored
@@ -1,159 +0,0 @@
|
||||
/*!
|
||||
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
|
||||
* Copyright 2015 Aidan Feldman
|
||||
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
|
||||
(function() {
|
||||
'use strict';
|
||||
|
||||
window.Toc = {
|
||||
helpers: {
|
||||
// return all matching elements in the set, or their descendants
|
||||
findOrFilter: function($el, selector) {
|
||||
// http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
|
||||
// http://stackoverflow.com/a/12731439/358804
|
||||
var $descendants = $el.find(selector);
|
||||
return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
|
||||
},
|
||||
|
||||
generateUniqueIdBase: function(el) {
|
||||
var text = $(el).text();
|
||||
var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
|
||||
return anchor || el.tagName.toLowerCase();
|
||||
},
|
||||
|
||||
generateUniqueId: function(el) {
|
||||
var anchorBase = this.generateUniqueIdBase(el);
|
||||
for (var i = 0; ; i++) {
|
||||
var anchor = anchorBase;
|
||||
if (i > 0) {
|
||||
// add suffix
|
||||
anchor += '-' + i;
|
||||
}
|
||||
// check if ID already exists
|
||||
if (!document.getElementById(anchor)) {
|
||||
return anchor;
|
||||
}
|
||||
}
|
||||
},
|
||||
|
||||
generateAnchor: function(el) {
|
||||
if (el.id) {
|
||||
return el.id;
|
||||
} else {
|
||||
var anchor = this.generateUniqueId(el);
|
||||
el.id = anchor;
|
||||
return anchor;
|
||||
}
|
||||
},
|
||||
|
||||
createNavList: function() {
|
||||
return $('<ul class="nav"></ul>');
|
||||
},
|
||||
|
||||
createChildNavList: function($parent) {
|
||||
var $childList = this.createNavList();
|
||||
$parent.append($childList);
|
||||
return $childList;
|
||||
},
|
||||
|
||||
generateNavEl: function(anchor, text) {
|
||||
var $a = $('<a></a>');
|
||||
$a.attr('href', '#' + anchor);
|
||||
$a.text(text);
|
||||
var $li = $('<li></li>');
|
||||
$li.append($a);
|
||||
return $li;
|
||||
},
|
||||
|
||||
generateNavItem: function(headingEl) {
|
||||
var anchor = this.generateAnchor(headingEl);
|
||||
var $heading = $(headingEl);
|
||||
var text = $heading.data('toc-text') || $heading.text();
|
||||
return this.generateNavEl(anchor, text);
|
||||
},
|
||||
|
||||
// Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
|
||||
getTopLevel: function($scope) {
|
||||
for (var i = 1; i <= 6; i++) {
|
||||
var $headings = this.findOrFilter($scope, 'h' + i);
|
||||
if ($headings.length > 1) {
|
||||
return i;
|
||||
}
|
||||
}
|
||||
|
||||
return 1;
|
||||
},
|
||||
|
||||
// returns the elements for the top level, and the next below it
|
||||
getHeadings: function($scope, topLevel) {
|
||||
var topSelector = 'h' + topLevel;
|
||||
|
||||
var secondaryLevel = topLevel + 1;
|
||||
var secondarySelector = 'h' + secondaryLevel;
|
||||
|
||||
return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
|
||||
},
|
||||
|
||||
getNavLevel: function(el) {
|
||||
return parseInt(el.tagName.charAt(1), 10);
|
||||
},
|
||||
|
||||
populateNav: function($topContext, topLevel, $headings) {
|
||||
var $context = $topContext;
|
||||
var $prevNav;
|
||||
|
||||
var helpers = this;
|
||||
$headings.each(function(i, el) {
|
||||
var $newNav = helpers.generateNavItem(el);
|
||||
var navLevel = helpers.getNavLevel(el);
|
||||
|
||||
// determine the proper $context
|
||||
if (navLevel === topLevel) {
|
||||
// use top level
|
||||
$context = $topContext;
|
||||
} else if ($prevNav && $context === $topContext) {
|
||||
// create a new level of the tree and switch to it
|
||||
$context = helpers.createChildNavList($prevNav);
|
||||
} // else use the current $context
|
||||
|
||||
$context.append($newNav);
|
||||
|
||||
$prevNav = $newNav;
|
||||
});
|
||||
},
|
||||
|
||||
parseOps: function(arg) {
|
||||
var opts;
|
||||
if (arg.jquery) {
|
||||
opts = {
|
||||
$nav: arg
|
||||
};
|
||||
} else {
|
||||
opts = arg;
|
||||
}
|
||||
opts.$scope = opts.$scope || $(document.body);
|
||||
return opts;
|
||||
}
|
||||
},
|
||||
|
||||
// accepts a jQuery object, or an options object
|
||||
init: function(opts) {
|
||||
opts = this.helpers.parseOps(opts);
|
||||
|
||||
// ensure that the data attribute is in place for styling
|
||||
opts.$nav.attr('data-toggle', 'toc');
|
||||
|
||||
var $topContext = this.helpers.createChildNavList(opts.$nav);
|
||||
var topLevel = this.helpers.getTopLevel(opts.$scope);
|
||||
var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
|
||||
this.helpers.populateNav($topContext, topLevel, $headings);
|
||||
}
|
||||
};
|
||||
|
||||
$(function() {
|
||||
$('nav[data-toggle="toc"]').each(function(i, el) {
|
||||
var $nav = $(el);
|
||||
Toc.init($nav);
|
||||
});
|
||||
});
|
||||
})();
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 60 KiB |
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|
Before Width: | Height: | Size: 1.4 MiB |
Binary file not shown.
|
Before Width: | Height: | Size: 334 KiB |
File diff suppressed because one or more lines are too long
@@ -1,85 +0,0 @@
|
||||
$(function() {
|
||||
|
||||
// register a handler to move the focus to the search bar
|
||||
// upon pressing shift + "/" (i.e. "?")
|
||||
$(document).on('keydown', function(e) {
|
||||
if (e.shiftKey && e.keyCode == 191) {
|
||||
e.preventDefault();
|
||||
$("#search-input").focus();
|
||||
}
|
||||
});
|
||||
|
||||
$(document).ready(function() {
|
||||
// do keyword highlighting
|
||||
/* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
|
||||
var mark = function() {
|
||||
|
||||
var referrer = document.URL ;
|
||||
var paramKey = "q" ;
|
||||
|
||||
if (referrer.indexOf("?") !== -1) {
|
||||
var qs = referrer.substr(referrer.indexOf('?') + 1);
|
||||
var qs_noanchor = qs.split('#')[0];
|
||||
var qsa = qs_noanchor.split('&');
|
||||
var keyword = "";
|
||||
|
||||
for (var i = 0; i < qsa.length; i++) {
|
||||
var currentParam = qsa[i].split('=');
|
||||
|
||||
if (currentParam.length !== 2) {
|
||||
continue;
|
||||
}
|
||||
|
||||
if (currentParam[0] == paramKey) {
|
||||
keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
|
||||
}
|
||||
}
|
||||
|
||||
if (keyword !== "") {
|
||||
$(".contents").unmark({
|
||||
done: function() {
|
||||
$(".contents").mark(keyword);
|
||||
}
|
||||
});
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
mark();
|
||||
});
|
||||
});
|
||||
|
||||
/* Search term highlighting ------------------------------*/
|
||||
|
||||
function matchedWords(hit) {
|
||||
var words = [];
|
||||
|
||||
var hierarchy = hit._highlightResult.hierarchy;
|
||||
// loop to fetch from lvl0, lvl1, etc.
|
||||
for (var idx in hierarchy) {
|
||||
words = words.concat(hierarchy[idx].matchedWords);
|
||||
}
|
||||
|
||||
var content = hit._highlightResult.content;
|
||||
if (content) {
|
||||
words = words.concat(content.matchedWords);
|
||||
}
|
||||
|
||||
// return unique words
|
||||
var words_uniq = [...new Set(words)];
|
||||
return words_uniq;
|
||||
}
|
||||
|
||||
function updateHitURL(hit) {
|
||||
|
||||
var words = matchedWords(hit);
|
||||
var url = "";
|
||||
|
||||
if (hit.anchor) {
|
||||
url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
|
||||
} else {
|
||||
url = hit.url + '?q=' + escape(words.join(" "));
|
||||
}
|
||||
|
||||
return url;
|
||||
}
|
||||
@@ -1,95 +0,0 @@
|
||||
{
|
||||
"index_name": "amr",
|
||||
"start_urls": [
|
||||
{
|
||||
"url": "https://msberends.gitlab.io/AMR/index.html",
|
||||
"selectors_key": "homepage",
|
||||
"tags": [
|
||||
"homepage"
|
||||
]
|
||||
},
|
||||
{
|
||||
"url": "https://msberends.gitlab.io/AMR/reference",
|
||||
"selectors_key": "reference",
|
||||
"tags": [
|
||||
"reference"
|
||||
]
|
||||
},
|
||||
{
|
||||
"url": "https://msberends.gitlab.io/AMR/articles",
|
||||
"selectors_key": "articles",
|
||||
"tags": [
|
||||
"articles"
|
||||
]
|
||||
}
|
||||
],
|
||||
"stop_urls": [
|
||||
"/reference/$",
|
||||
"/reference/index.html",
|
||||
"/articles/$",
|
||||
"/articles/index.html"
|
||||
],
|
||||
"sitemap_urls": [
|
||||
"https://msberends.gitlab.io/AMR/sitemap.xml"
|
||||
],
|
||||
"selectors": {
|
||||
"homepage": {
|
||||
"lvl0": {
|
||||
"selector": ".contents h1",
|
||||
"default_value": "AMR Home page"
|
||||
},
|
||||
"lvl1": {
|
||||
"selector": ".contents h2"
|
||||
},
|
||||
"lvl2": {
|
||||
"selector": ".contents h3",
|
||||
"default_value": "Context"
|
||||
},
|
||||
"lvl3": ".ref-arguments td, .ref-description",
|
||||
"text": ".contents p, .contents li, .contents .pre"
|
||||
},
|
||||
"reference": {
|
||||
"lvl0": {
|
||||
"selector": ".contents h1"
|
||||
},
|
||||
"lvl1": {
|
||||
"selector": ".contents .name",
|
||||
"default_value": "Argument"
|
||||
},
|
||||
"lvl2": {
|
||||
"selector": ".ref-arguments th",
|
||||
"default_value": "Description"
|
||||
},
|
||||
"lvl3": ".ref-arguments td, .ref-description",
|
||||
"text": ".contents p, .contents li"
|
||||
},
|
||||
"articles": {
|
||||
"lvl0": {
|
||||
"selector": ".contents h1"
|
||||
},
|
||||
"lvl1": {
|
||||
"selector": ".contents .name"
|
||||
},
|
||||
"lvl2": {
|
||||
"selector": ".contents h2, .contents h3",
|
||||
"default_value": "Context"
|
||||
},
|
||||
"text": ".contents p, .contents li, .tempate-article .contents .pre"
|
||||
}
|
||||
},
|
||||
"selectors_exclude": [
|
||||
".dont-index"
|
||||
],
|
||||
"min_indexed_level": 2,
|
||||
"custom_settings": {
|
||||
"separatorsToIndex": "_",
|
||||
"attributesToRetrieve": [
|
||||
"hierarchy",
|
||||
"content",
|
||||
"anchor",
|
||||
"url",
|
||||
"url_without_anchor"
|
||||
]
|
||||
}
|
||||
}
|
||||
|
||||
233
docs_/extra.css
233
docs_/extra.css
@@ -1,233 +0,0 @@
|
||||
/*
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.github.io/AMR. #
|
||||
# ==================================================================== #
|
||||
*/
|
||||
|
||||
/* R for Data Science (r4ds) */
|
||||
#r4ds a {
|
||||
display: inline-flex;
|
||||
align-items: center;
|
||||
text-align: right;
|
||||
}
|
||||
#r4ds img {
|
||||
margin-left: 10px;
|
||||
}
|
||||
|
||||
/* class for footer */
|
||||
.footer_logo {
|
||||
float: right;
|
||||
height: 43px;
|
||||
margin-top: 2px;
|
||||
}
|
||||
.partner_logo {
|
||||
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|
||||
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|
||||
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|
||||
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|
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||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
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|
||||
|
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/* Remove the 'Read more on our website!' part from the manual pages */
|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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}
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104
docs_/extra.js
104
docs_/extra.js
@@ -1,104 +0,0 @@
|
||||
/*
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.github.io/AMR. #
|
||||
# ==================================================================== #
|
||||
*/
|
||||
|
||||
// Add updated Font Awesome 5.8.2 library
|
||||
$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.2/css/all.css">');
|
||||
|
||||
// Email template for new GitLab issues
|
||||
//https://stackoverflow.com/a/33190494/4575331
|
||||
//incoming+msberends-amr-9011429-5miwzuo1xo70wbz9r6fwv4dmg-issue@incoming.gitlab.com
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||||
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$( document ).ready(function() {
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// add SurveyMonkey
|
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// $('body').append('<script>(function(t,e,s,o){var n,a,c;t.SMCX=t.SMCX||[],e.getElementById(o)||(n=e.getElementsByTagName(s),a=n[n.length-1],c=e.createElement(s),c.type="text/javascript",c.async=!0,c.id=o,c.src=["https:"===location.protocol?"https://":"http://","widget.surveymonkey.com/collect/website/js/tRaiETqnLgj758hTBazgd_2BrwaGaWbg59AiLjNGdPaaJiBHKqgXKIw46VauwBvZ67.js"].join(""),a.parentNode.insertBefore(c,a))})(window,document,"script","smcx-sdk");</script>');
|
||||
// add link to survey at home sidebar
|
||||
// $('.template-home #sidebar .list-unstyled:first').append('<li><strong>Please fill in our survey at</strong> <br><a href="https://www.surveymonkey.com/r/AMR_for_R" target="_blank">https://www.surveymonkey.com/r/AMR_for_R</a></li>');
|
||||
|
||||
|
||||
// remove version label from header
|
||||
$(".version.label").remove();
|
||||
|
||||
// redirect to GitLab
|
||||
var url_old = window.location.href;
|
||||
var url_new = url_old.replace("gitlab", "github");
|
||||
if (url_old != url_new) {
|
||||
window.location.replace(url_new);
|
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|
||||
|
||||
// Replace 'Value' in manual to 'Returned value'
|
||||
$(".template-reference-topic h2#value").text("Returned value");
|
||||
|
||||
// PR for 'R for Data Science' on How To pages
|
||||
if ($(".template-article").length > 0) {
|
||||
$('#sidebar').prepend(
|
||||
'<div id="r4ds">' +
|
||||
' <a target="_blank" href="https://r4ds.had.co.nz/">' +
|
||||
' Learn R reading this great book: R for Data Science.' +
|
||||
' <br><br>' +
|
||||
' Click to read it online - it was published for free.' +
|
||||
' <img src="https://gitlab.com/msberends/AMR/raw/master/docs/cover_r4ds.png" height="100px">' +
|
||||
' </a> ' +
|
||||
' <hr>' +
|
||||
'</div>');
|
||||
}
|
||||
|
||||
// edit footer
|
||||
$('footer').html(
|
||||
'<div>' +
|
||||
'<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
|
||||
'<a href="https://www.rug.nl"><img src="https://gitlab.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' +
|
||||
'</div>');
|
||||
// all links should open in new tab/window
|
||||
$('footer').html($('footer').html().replace(/href/g, 'target="_blank" href'));
|
||||
|
||||
// doctoral titles of authors
|
||||
function doct_tit(x) {
|
||||
if (typeof(x) != "undefined") {
|
||||
// authors
|
||||
x = x.replace(/Author, maintainer/g, "Main developer");
|
||||
x = x.replace(/Author, contributor/g, "Main contributor");
|
||||
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
|
||||
x = x.replace("Alex", "Prof. Dr. Alex");
|
||||
x = x.replace("Bhanu", "Prof. Dr. Bhanu");
|
||||
x = x.replace("Casper", "Prof. Dr. Casper");
|
||||
x = x.replace("Corinna", "Dr. Corinna");
|
||||
// others
|
||||
x = x.replace("Bart", "Dr. Bart");
|
||||
x = x.replace("Sofia", "Dr. Sofia");
|
||||
x = x.replace("Dennis", "Dr. Dennis");
|
||||
x = x.replace("Judith", "Dr. Judith");
|
||||
x = x.replace("Gwen", "Dr. Gwen");
|
||||
}
|
||||
return(x);
|
||||
}
|
||||
$(".template-authors").html(doct_tit($(".template-authors").html()));
|
||||
$(".template-citation-authors").html(doct_tit($(".template-citation-authors").html()));
|
||||
$(".developers").html(doct_tit($(".developers").html()));
|
||||
// $("footer").html(doct_tit($("footer").html()));
|
||||
|
||||
// Edit title of manual
|
||||
$('.template-reference-index h1').text('Manual');
|
||||
});
|
||||
|
||||
$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");
|
||||
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432
docs_/index.html
432
docs_/index.html
@@ -1,432 +0,0 @@
|
||||
<!DOCTYPE html>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<title>Antimicrobial Resistance Analysis • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
|
||||
<!-- 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><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<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">
|
||||
<script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
|
||||
<script src="extra.js"></script><meta property="og:title" content="Antimicrobial Resistance Analysis">
|
||||
<meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial
|
||||
Resistance (AMR) and to work with microbial and antimicrobial properties by
|
||||
using evidence-based methods, like those defined by Leclercq et al. (2013)
|
||||
<doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory
|
||||
Standards Institute (2014) <isbn: 1-56238-899-1>.">
|
||||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
|
||||
<!-- 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]>
|
||||
<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>
|
||||
<![endif]-->
|
||||
</head>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-home">
|
||||
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
<div class="container">
|
||||
<div class="navbar-header">
|
||||
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
|
||||
<span class="sr-only">Toggle navigation</span>
|
||||
<span class="icon-bar"></span>
|
||||
<span class="icon-bar"></span>
|
||||
<span class="icon-bar"></span>
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
<div id="navbar" class="navbar-collapse collapse">
|
||||
<ul class="nav navbar-nav">
|
||||
<li>
|
||||
<a href="index.html">
|
||||
<span class="fa fa-home"></span>
|
||||
|
||||
Home
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="articles/AMR.html">
|
||||
<span class="fa fa-directions"></span>
|
||||
|
||||
Conduct AMR analysis
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine multi-drug resistance (MDR)
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET data
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/SPSS.html">
|
||||
<span class="fa 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>
|
||||
|
||||
Apply EUCAST rules
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get properties of a microorganism
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
Other: benchmarks
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/">
|
||||
<span class="fa fa-book-open"></span>
|
||||
|
||||
Manual
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="authors.html">
|
||||
<span class="fa fa-users"></span>
|
||||
|
||||
Authors
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="news/">
|
||||
<span class="far fa 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>
|
||||
|
||||
Source Code
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="LICENSE-text.html">
|
||||
<span class="fa fa-book"></span>
|
||||
|
||||
Licence
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<!--/.nav-collapse -->
|
||||
</div>
|
||||
<!--/.container -->
|
||||
</div>
|
||||
<!--/.navbar -->
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
<div class="contents col-md-9">
|
||||
<div id="amr-for-r-" class="section level1">
|
||||
<div class="page-header"><h1 class="hasAnchor">
|
||||
<a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
|
||||
</h1></div>
|
||||
<blockquote>
|
||||
<p><strong>METHODS PAPER PREPRINTED</strong><br>
|
||||
A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/810622). Please click <a href="https://doi.org/10.1101/810622">here for the paper on bioRxiv’s publishers page</a>.</p>
|
||||
</blockquote>
|
||||
<div id="what-is-amr-for-r" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
|
||||
<p><em>(To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p>
|
||||
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org">R package</a> 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>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> 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). <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 <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
|
||||
<div class="main-content">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in more than 100 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(source: <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.
|
||||
</p>
|
||||
<br><br>
|
||||
</div>
|
||||
<div id="partners" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#partners" class="anchor"></a>Partners</h4>
|
||||
<p>The development of this package is part of, related to, or made possible by:</p>
|
||||
<div align="center">
|
||||
<a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="what-can-you-do-with-this-package" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#what-can-you-do-with-this-package" class="anchor"></a>What can you do with this package?</h3>
|
||||
<p>This package can be used for:</p>
|
||||
<ul>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
|
||||
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
|
||||
<li>Determining first isolates to be used for AMR analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
|
||||
<li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
|
||||
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
|
||||
<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
|
||||
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
|
||||
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="get-this-package" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#get-this-package" class="anchor"></a>Get this package</h3>
|
||||
<div id="latest-released-version" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
|
||||
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)</pre></div>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> > <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
|
||||
</div>
|
||||
<div id="latest-development-version" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
|
||||
<p>The latest and unpublished development version can be installed from GitHub using:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)
|
||||
<span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span>(<span class="st">"msberends/AMR"</span>)</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="get-started" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#get-started" class="anchor"></a>Get started</h3>
|
||||
<p>To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the links in the ‘How to’ menu.</p>
|
||||
</div>
|
||||
<div id="short-introduction" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#short-introduction" class="anchor"></a>Short introduction</h3>
|
||||
<div id="microbial-taxonomic-reference-data" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
|
||||
<p>This package contains the complete taxonomic tree of almost all ~70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
|
||||
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div id="antimicrobial-reference-data" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</h4>
|
||||
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div id="whonet--ears-net" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#whonet--ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
|
||||
<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
|
||||
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
|
||||
</div>
|
||||
<div id="overview-of-functions" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#overview-of-functions" class="anchor"></a>Overview of functions</h4>
|
||||
<p>The <code>AMR</code> package basically does four important things:</p>
|
||||
<ol>
|
||||
<li>
|
||||
<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
|
||||
<ul>
|
||||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||||
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
|
||||
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
|
||||
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
|
||||
<ul>
|
||||
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
|
||||
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
|
||||
<ul>
|
||||
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
|
||||
<ul>
|
||||
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise()</code>)</li>
|
||||
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
|
||||
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
|
||||
<ul>
|
||||
<li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
|
||||
<li>The package also contains example data sets:
|
||||
<ul>
|
||||
<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> data set</a>. This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis.</li>
|
||||
<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data set</a>. This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ol>
|
||||
</div>
|
||||
</div>
|
||||
<div id="copyright" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#copyright" class="anchor"></a>Copyright</h3>
|
||||
<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
|
||||
<ul>
|
||||
<li><p>May be used for commercial purposes</p></li>
|
||||
<li><p>May be used for private purposes</p></li>
|
||||
<li><p>May <strong>not</strong> be used for patent purposes</p></li>
|
||||
<li>
|
||||
<p>May be modified, although:</p>
|
||||
<ul>
|
||||
<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
|
||||
<li>Changes made to the code <strong>must</strong> be documented</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>May be distributed, although:</p>
|
||||
<ul>
|
||||
<li>Source code <strong>must</strong> be made available when the package is distributed</li>
|
||||
<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><p>Comes with a LIMITATION of liability</p></li>
|
||||
<li><p>Comes with NO warranty</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<div class="links">
|
||||
<h2>Links</h2>
|
||||
<ul class="list-unstyled">
|
||||
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://cloud.r-project.org/package=AMR</a>
|
||||
</li>
|
||||
<li>Browse source code at <br><a href="https://github.com/msberends/AMR/">https://github.com/msberends/AMR/</a>
|
||||
</li>
|
||||
<li>Report a bug at <br><a href="https://github.com/msberends/AMR/issues">https://github.com/msberends/AMR/issues</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="license">
|
||||
<h2>License</h2>
|
||||
<ul class="list-unstyled">
|
||||
<li>
|
||||
<a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="citation">
|
||||
<h2>Citation</h2>
|
||||
<ul class="list-unstyled">
|
||||
<li><a href="authors.html">Citing AMR</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="developers">
|
||||
<h2>Developers</h2>
|
||||
<ul class="list-unstyled">
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li><a href="authors.html">All authors...</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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169.19774 87.361075 143.238715 94.26646" marker-end="url(#FilledArrow_Marker)"
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font-family="Helvetica Neue" font-size="16" font-weight="500" x="20.887573"
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y1="136.29211" x2="696.1446" y2="136.29211"
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stroke-linejoin="round" stroke-width="1"/></g></g></svg>
|
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<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
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viewBox="0 0 20 20" style="enable-background:new 0 0 20 20;" xml:space="preserve">
|
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<style type="text/css">
|
||||
.st0{fill:#75AADB;}
|
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</style>
|
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<path class="st0" d="M4,11.3h1.3v1.3H4c-2,0-4-2.3-4-4.7s2.1-4.7,4-4.7h5.3c1.9,0,4,2.3,4,4.7c0,1.9-1.2,3.6-2.7,4.3v-1.5
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||||
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|
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|
||||
/* Sticky footer */
|
||||
|
||||
/**
|
||||
* Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
|
||||
* Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
|
||||
*
|
||||
* .Site -> body > .container
|
||||
* .Site-content -> body > .container .row
|
||||
* .footer -> footer
|
||||
*
|
||||
* Key idea seems to be to ensure that .container and __all its parents__
|
||||
* have height set to 100%
|
||||
*
|
||||
*/
|
||||
|
||||
html, body {
|
||||
height: 100%;
|
||||
}
|
||||
|
||||
body {
|
||||
position: relative;
|
||||
}
|
||||
|
||||
body > .container {
|
||||
display: flex;
|
||||
height: 100%;
|
||||
flex-direction: column;
|
||||
}
|
||||
|
||||
body > .container .row {
|
||||
flex: 1 0 auto;
|
||||
}
|
||||
|
||||
footer {
|
||||
margin-top: 45px;
|
||||
padding: 35px 0 36px;
|
||||
border-top: 1px solid #e5e5e5;
|
||||
color: #666;
|
||||
display: flex;
|
||||
flex-shrink: 0;
|
||||
}
|
||||
footer p {
|
||||
margin-bottom: 0;
|
||||
}
|
||||
footer div {
|
||||
flex: 1;
|
||||
}
|
||||
footer .pkgdown {
|
||||
text-align: right;
|
||||
}
|
||||
footer p {
|
||||
margin-bottom: 0;
|
||||
}
|
||||
|
||||
img.icon {
|
||||
float: right;
|
||||
}
|
||||
|
||||
img {
|
||||
max-width: 100%;
|
||||
}
|
||||
|
||||
/* Fix bug in bootstrap (only seen in firefox) */
|
||||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
|
||||
/* Typographic tweaking ---------------------------------*/
|
||||
|
||||
.contents .page-header {
|
||||
margin-top: calc(-60px + 1em);
|
||||
}
|
||||
|
||||
dd {
|
||||
margin-left: 3em;
|
||||
}
|
||||
|
||||
/* Section anchors ---------------------------------*/
|
||||
|
||||
a.anchor {
|
||||
margin-left: -30px;
|
||||
display:inline-block;
|
||||
width: 30px;
|
||||
height: 30px;
|
||||
visibility: hidden;
|
||||
|
||||
background-image: url(./link.svg);
|
||||
background-repeat: no-repeat;
|
||||
background-size: 20px 20px;
|
||||
background-position: center center;
|
||||
}
|
||||
|
||||
.hasAnchor:hover a.anchor {
|
||||
visibility: visible;
|
||||
}
|
||||
|
||||
@media (max-width: 767px) {
|
||||
.hasAnchor:hover a.anchor {
|
||||
visibility: hidden;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* Fixes for fixed navbar --------------------------*/
|
||||
|
||||
.contents h1, .contents h2, .contents h3, .contents h4 {
|
||||
padding-top: 60px;
|
||||
margin-top: -40px;
|
||||
}
|
||||
|
||||
/* Navbar submenu --------------------------*/
|
||||
|
||||
.dropdown-submenu {
|
||||
position: relative;
|
||||
}
|
||||
|
||||
.dropdown-submenu>.dropdown-menu {
|
||||
top: 0;
|
||||
left: 100%;
|
||||
margin-top: -6px;
|
||||
margin-left: -1px;
|
||||
border-radius: 0 6px 6px 6px;
|
||||
}
|
||||
|
||||
.dropdown-submenu:hover>.dropdown-menu {
|
||||
display: block;
|
||||
}
|
||||
|
||||
.dropdown-submenu>a:after {
|
||||
display: block;
|
||||
content: " ";
|
||||
float: right;
|
||||
width: 0;
|
||||
height: 0;
|
||||
border-color: transparent;
|
||||
border-style: solid;
|
||||
border-width: 5px 0 5px 5px;
|
||||
border-left-color: #cccccc;
|
||||
margin-top: 5px;
|
||||
margin-right: -10px;
|
||||
}
|
||||
|
||||
.dropdown-submenu:hover>a:after {
|
||||
border-left-color: #ffffff;
|
||||
}
|
||||
|
||||
.dropdown-submenu.pull-left {
|
||||
float: none;
|
||||
}
|
||||
|
||||
.dropdown-submenu.pull-left>.dropdown-menu {
|
||||
left: -100%;
|
||||
margin-left: 10px;
|
||||
border-radius: 6px 0 6px 6px;
|
||||
}
|
||||
|
||||
/* Sidebar --------------------------*/
|
||||
|
||||
#pkgdown-sidebar {
|
||||
margin-top: 30px;
|
||||
position: -webkit-sticky;
|
||||
position: sticky;
|
||||
top: 70px;
|
||||
}
|
||||
|
||||
#pkgdown-sidebar h2 {
|
||||
font-size: 1.5em;
|
||||
margin-top: 1em;
|
||||
}
|
||||
|
||||
#pkgdown-sidebar h2:first-child {
|
||||
margin-top: 0;
|
||||
}
|
||||
|
||||
#pkgdown-sidebar .list-unstyled li {
|
||||
margin-bottom: 0.5em;
|
||||
}
|
||||
|
||||
/* bootstrap-toc tweaks ------------------------------------------------------*/
|
||||
|
||||
/* All levels of nav */
|
||||
|
||||
nav[data-toggle='toc'] .nav > li > a {
|
||||
padding: 4px 20px 4px 6px;
|
||||
font-size: 1.5rem;
|
||||
font-weight: 400;
|
||||
color: inherit;
|
||||
}
|
||||
|
||||
nav[data-toggle='toc'] .nav > li > a:hover,
|
||||
nav[data-toggle='toc'] .nav > li > a:focus {
|
||||
padding-left: 5px;
|
||||
color: inherit;
|
||||
border-left: 1px solid #878787;
|
||||
}
|
||||
|
||||
nav[data-toggle='toc'] .nav > .active > a,
|
||||
nav[data-toggle='toc'] .nav > .active:hover > a,
|
||||
nav[data-toggle='toc'] .nav > .active:focus > a {
|
||||
padding-left: 5px;
|
||||
font-size: 1.5rem;
|
||||
font-weight: 400;
|
||||
color: inherit;
|
||||
border-left: 2px solid #878787;
|
||||
}
|
||||
|
||||
/* Nav: second level (shown on .active) */
|
||||
|
||||
nav[data-toggle='toc'] .nav .nav {
|
||||
display: none; /* Hide by default, but at >768px, show it */
|
||||
padding-bottom: 10px;
|
||||
}
|
||||
|
||||
nav[data-toggle='toc'] .nav .nav > li > a {
|
||||
padding-left: 16px;
|
||||
font-size: 1.35rem;
|
||||
}
|
||||
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:hover,
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:focus {
|
||||
padding-left: 15px;
|
||||
}
|
||||
|
||||
nav[data-toggle='toc'] .nav .nav > .active > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:hover > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:focus > a {
|
||||
padding-left: 15px;
|
||||
font-weight: 500;
|
||||
font-size: 1.35rem;
|
||||
}
|
||||
|
||||
/* orcid ------------------------------------------------------------------- */
|
||||
|
||||
.orcid {
|
||||
font-size: 16px;
|
||||
color: #A6CE39;
|
||||
/* margins are required by official ORCID trademark and display guidelines */
|
||||
margin-left:4px;
|
||||
margin-right:4px;
|
||||
vertical-align: middle;
|
||||
}
|
||||
|
||||
/* Reference index & topics ----------------------------------------------- */
|
||||
|
||||
.ref-index th {font-weight: normal;}
|
||||
|
||||
.ref-index td {vertical-align: top;}
|
||||
.ref-index .icon {width: 40px;}
|
||||
.ref-index .alias {width: 40%;}
|
||||
.ref-index-icons .alias {width: calc(40% - 40px);}
|
||||
.ref-index .title {width: 60%;}
|
||||
|
||||
.ref-arguments th {text-align: right; padding-right: 10px;}
|
||||
.ref-arguments th, .ref-arguments td {vertical-align: top;}
|
||||
.ref-arguments .name {width: 20%;}
|
||||
.ref-arguments .desc {width: 80%;}
|
||||
|
||||
/* Nice scrolling for wide elements --------------------------------------- */
|
||||
|
||||
table {
|
||||
display: block;
|
||||
overflow: auto;
|
||||
}
|
||||
|
||||
/* Syntax highlighting ---------------------------------------------------- */
|
||||
|
||||
pre {
|
||||
word-wrap: normal;
|
||||
word-break: normal;
|
||||
border: 1px solid #eee;
|
||||
}
|
||||
|
||||
pre, code {
|
||||
background-color: #f8f8f8;
|
||||
color: #333;
|
||||
}
|
||||
|
||||
pre code {
|
||||
overflow: auto;
|
||||
word-wrap: normal;
|
||||
white-space: pre;
|
||||
}
|
||||
|
||||
pre .img {
|
||||
margin: 5px 0;
|
||||
}
|
||||
|
||||
pre .img img {
|
||||
background-color: #fff;
|
||||
display: block;
|
||||
height: auto;
|
||||
}
|
||||
|
||||
code a, pre a {
|
||||
color: #375f84;
|
||||
}
|
||||
|
||||
a.sourceLine:hover {
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
.fl {color: #1514b5;}
|
||||
.fu {color: #000000;} /* function */
|
||||
.ch,.st {color: #036a07;} /* string */
|
||||
.kw {color: #264D66;} /* keyword */
|
||||
.co {color: #888888;} /* comment */
|
||||
|
||||
.message { color: black; font-weight: bolder;}
|
||||
.error { color: orange; font-weight: bolder;}
|
||||
.warning { color: #6A0366; font-weight: bolder;}
|
||||
|
||||
/* Clipboard --------------------------*/
|
||||
|
||||
.hasCopyButton {
|
||||
position: relative;
|
||||
}
|
||||
|
||||
.btn-copy-ex {
|
||||
position: absolute;
|
||||
right: 0;
|
||||
top: 0;
|
||||
visibility: hidden;
|
||||
}
|
||||
|
||||
.hasCopyButton:hover button.btn-copy-ex {
|
||||
visibility: visible;
|
||||
}
|
||||
|
||||
/* headroom.js ------------------------ */
|
||||
|
||||
.headroom {
|
||||
will-change: transform;
|
||||
transition: transform 200ms linear;
|
||||
}
|
||||
.headroom--pinned {
|
||||
transform: translateY(0%);
|
||||
}
|
||||
.headroom--unpinned {
|
||||
transform: translateY(-100%);
|
||||
}
|
||||
|
||||
/* mark.js ----------------------------*/
|
||||
|
||||
mark {
|
||||
background-color: rgba(255, 255, 51, 0.5);
|
||||
border-bottom: 2px solid rgba(255, 153, 51, 0.3);
|
||||
padding: 1px;
|
||||
}
|
||||
|
||||
/* vertical spacing after htmlwidgets */
|
||||
.html-widget {
|
||||
margin-bottom: 10px;
|
||||
}
|
||||
|
||||
/* fontawesome ------------------------ */
|
||||
|
||||
.fab {
|
||||
font-family: "Font Awesome 5 Brands" !important;
|
||||
}
|
||||
|
||||
/* don't display links in code chunks when printing */
|
||||
/* source: https://stackoverflow.com/a/10781533 */
|
||||
@media print {
|
||||
code a:link:after, code a:visited:after {
|
||||
content: "";
|
||||
}
|
||||
}
|
||||
108
docs_/pkgdown.js
108
docs_/pkgdown.js
@@ -1,108 +0,0 @@
|
||||
/* http://gregfranko.com/blog/jquery-best-practices/ */
|
||||
(function($) {
|
||||
$(function() {
|
||||
|
||||
$('.navbar-fixed-top').headroom();
|
||||
|
||||
$('body').css('padding-top', $('.navbar').height() + 10);
|
||||
$(window).resize(function(){
|
||||
$('body').css('padding-top', $('.navbar').height() + 10);
|
||||
});
|
||||
|
||||
$('[data-toggle="tooltip"]').tooltip();
|
||||
|
||||
var cur_path = paths(location.pathname);
|
||||
var links = $("#navbar ul li a");
|
||||
var max_length = -1;
|
||||
var pos = -1;
|
||||
for (var i = 0; i < links.length; i++) {
|
||||
if (links[i].getAttribute("href") === "#")
|
||||
continue;
|
||||
// Ignore external links
|
||||
if (links[i].host !== location.host)
|
||||
continue;
|
||||
|
||||
var nav_path = paths(links[i].pathname);
|
||||
|
||||
var length = prefix_length(nav_path, cur_path);
|
||||
if (length > max_length) {
|
||||
max_length = length;
|
||||
pos = i;
|
||||
}
|
||||
}
|
||||
|
||||
// Add class to parent <li>, and enclosing <li> if in dropdown
|
||||
if (pos >= 0) {
|
||||
var menu_anchor = $(links[pos]);
|
||||
menu_anchor.parent().addClass("active");
|
||||
menu_anchor.closest("li.dropdown").addClass("active");
|
||||
}
|
||||
});
|
||||
|
||||
function paths(pathname) {
|
||||
var pieces = pathname.split("/");
|
||||
pieces.shift(); // always starts with /
|
||||
|
||||
var end = pieces[pieces.length - 1];
|
||||
if (end === "index.html" || end === "")
|
||||
pieces.pop();
|
||||
return(pieces);
|
||||
}
|
||||
|
||||
// Returns -1 if not found
|
||||
function prefix_length(needle, haystack) {
|
||||
if (needle.length > haystack.length)
|
||||
return(-1);
|
||||
|
||||
// Special case for length-0 haystack, since for loop won't run
|
||||
if (haystack.length === 0) {
|
||||
return(needle.length === 0 ? 0 : -1);
|
||||
}
|
||||
|
||||
for (var i = 0; i < haystack.length; i++) {
|
||||
if (needle[i] != haystack[i])
|
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pandoc: 2.7.3
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pkgdown_sha: ~
|
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articles:
|
||||
AMR: AMR.html
|
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EUCAST: EUCAST.html
|
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|
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PCA: PCA.html
|
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SPSS: SPSS.html
|
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WHONET: WHONET.html
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|
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reference: https://msberends.github.io/AMR/reference
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||||
<h1>Deprecated functions</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
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|
||||
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|
||||
|
||||
<div class="ref-description">
|
||||
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>portion_R</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>portion_IR</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>portion_I</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>portion_SI</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>portion_S</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>portion_df</span>(<span class='no'>...</span>)</pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_retired.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
|
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
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||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
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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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<h1>The <code>AMR</code> Package</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
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<div class="hidden name"><code>AMR.Rd</code></div>
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||||
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||||
<p>Welcome to the <code>AMR</code> package.</p>
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||||
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||||
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||||
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||||
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||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p><code>AMR</code> is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.</p>
|
||||
<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). 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>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 <a href='http://www.catalogueoflife.org'>Catalogue of Life</a></p></li>
|
||||
<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
|
||||
<li><p>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</p></li>
|
||||
<li><p>Determining first isolates to be used for AMR analysis</p></li>
|
||||
<li><p>Calculating antimicrobial resistance</p></li>
|
||||
<li><p>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</p></li>
|
||||
<li><p>Calculating (empirical) susceptibility of both mono therapy and combination therapies</p></li>
|
||||
<li><p>Predicting future antimicrobial resistance using regression models</p></li>
|
||||
<li><p>Getting properties for any microorganism (like Gram stain, species, genus or family)</p></li>
|
||||
<li><p>Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)</p></li>
|
||||
<li><p>Plotting antimicrobial resistance</p></li>
|
||||
<li><p>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code</p></li>
|
||||
<li><p>Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code</p></li>
|
||||
<li><p>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</p></li>
|
||||
<li><p>Principal component analysis for AMR</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
|
||||
|
||||
|
||||
|
||||
<p>For suggestions, comments or questions, please contact us at:</p>
|
||||
<p>Matthijs S. Berends <br />
|
||||
m.s.berends [at] umcg [dot] nl <br />
|
||||
University of Groningen
|
||||
Department of Medical Microbiology
|
||||
University Medical Center Groningen <br />
|
||||
Post Office Box 30001 <br />
|
||||
9700 RB Groningen <br />
|
||||
The Netherlands</p>
|
||||
<p>If you have found a bug, please file a new issue at: <br />
|
||||
<a href='https://github.com/msberends/AMR/issues'>https://github.com/msberends/AMR/issues</a></p>
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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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<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine multi-drug resistance (MDR)
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET data
|
||||
</a>
|
||||
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|
||||
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|
||||
<a href="../articles/SPSS.html">
|
||||
<span class="fa fa-file-upload"></span>
|
||||
|
||||
Import data from SPSS/SAS/Stata
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
<a href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get properties of a microorganism
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
</a>
|
||||
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|
||||
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|
||||
<a href="../articles/benchmarks.html">
|
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|
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|
||||
<div class="page-header">
|
||||
<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
|
||||
<div class="hidden name"><code>WHOCC.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.</p>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01DH02"</span>)
|
||||
|
||||
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)</pre>
|
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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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Import data from SPSS/SAS/Stata
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||||
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|
||||
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|
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Get properties of an antibiotic
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<div class="page-header">
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||||
<h1>Data set with 500 isolates - WHONET example</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
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<div class="hidden name"><code>WHONET.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our <a href='example_isolates.html'>example_isolates</a> data set.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='no'>WHONET</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 500 observations and 53 variables:</p><ul>
|
||||
<li><p><code>Identification number</code><br /> ID of the sample</p></li>
|
||||
<li><p><code>Specimen number</code><br /> ID of the specimen</p></li>
|
||||
<li><p><code>Organism</code><br /> Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using <code><a href='as.mo.html'>as.mo()</a></code>.</p></li>
|
||||
<li><p><code>Country</code><br /> Country of origin</p></li>
|
||||
<li><p><code>Laboratory</code><br /> Name of laboratory</p></li>
|
||||
<li><p><code>Last name</code><br /> Last name of patient</p></li>
|
||||
<li><p><code>First name</code><br /> Initial of patient</p></li>
|
||||
<li><p><code>Sex</code><br /> Gender of patient</p></li>
|
||||
<li><p><code>Age</code><br /> Age of patient</p></li>
|
||||
<li><p><code>Age category</code><br /> Age group, can also be looked up using <code><a href='age_groups.html'>age_groups()</a></code></p></li>
|
||||
<li><p><code>Date of admission</code><br /> Date of hospital admission</p></li>
|
||||
<li><p><code>Specimen date</code><br /> Date when specimen was received at laboratory</p></li>
|
||||
<li><p><code>Specimen type</code><br /> Specimen type or group</p></li>
|
||||
<li><p><code>Specimen type (Numeric)</code><br /> Translation of <code>"Specimen type"</code></p></li>
|
||||
<li><p><code>Reason</code><br /> Reason of request with Differential Diagnosis</p></li>
|
||||
<li><p><code>Isolate number</code><br /> ID of isolate</p></li>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<li><p><code>Inducible clindamycin resistance</code><br /> Clindamycin can be induced?</p></li>
|
||||
<li><p><code>Comment</code><br /> Other comments</p></li>
|
||||
<li><p><code>Date of data entry</code><br /> Date this data was entered in WHONET</p></li>
|
||||
<li><p><code>AMP_ND10:CIP_EE</code><br /> 28 different antibiotics. You can lookup the abbreviations in the <a href='antibiotics.html'>antibiotics</a> data set, or use e.g. <code><a href='ab_property.html'>ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href='as.rsi.html'>as.rsi()</a></code>.</p></li>
|
||||
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|
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<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h1>Retrieve antimicrobial drug names and doses from clinical text</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
|
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<div class="hidden name"><code>ab_from_text.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href='https://rdrr.io/r/base/list.html'>list</a> with all antimicrobial drugs, doses and forms of administration found in the texts.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ab_from_text</span>(
|
||||
<span class='no'>text</span>,
|
||||
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
|
||||
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
||||
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>thorough_search</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
||||
<span class='no'>...</span>
|
||||
)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>text</th>
|
||||
<td><p>text to analyse</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>type</th>
|
||||
<td><p>type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>collapse</th>
|
||||
<td><p>character to pass on to <code><a href='https://rdrr.io/r/base/paste.html'>paste(..., collapse = ...)</a></code> to only return one character per element of <code>text</code>, see <em>Examples</em></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>translate_ab</th>
|
||||
<td><p>if <code>type = "drug"</code>: a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>thorough_search</th>
|
||||
<td><p>logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.</p><h3>Parameter <code>type</code></h3>
|
||||
|
||||
|
||||
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
|
||||
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
|
||||
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
|
||||
|
||||
<h3>Parameter <code>collapse</code></h3>
|
||||
|
||||
|
||||
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
|
||||
<code>df %>% mutate(abx = ab_from_text(clinical_text))</code></p>
|
||||
<p>The returned AB codes can be transformed to official names, groups, etc. with all <code><a href='ab_property.html'>ab_property()</a></code> functions like <code><a href='ab_property.html'>ab_name()</a></code> and <code><a href='ab_property.html'>ab_group()</a></code>, or by using the <code>translate_ab</code> parameter.</p>
|
||||
<p>With using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/character.html'>character</a>:<br />
|
||||
<code>df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))</code></p>
|
||||
|
||||
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>
|
||||
<span class='co'># straight from a true health care record:</span>
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span>)
|
||||
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"dose"</span>)
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>)
|
||||
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>", "</span>)
|
||||
|
||||
<span class='co'># if you want to know which antibiotic groups were administered, do e.g.:</span>
|
||||
<span class='no'>abx</span> <span class='kw'><-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
|
||||
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='no'>abx</span><span class='kw'>[[</span><span class='fl'>1</span>]])
|
||||
|
||||
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>dplyr</span>)) {
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/reexports.html'>tibble</a></span>(<span class='kw'>clinical_text</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
|
||||
<span class='st'>"started on doxy iv today"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>abx_codes</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>),
|
||||
<span class='kw'>abx_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>),
|
||||
<span class='kw'>abx_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>),
|
||||
<span class='kw'>abx_coll</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
|
||||
<span class='kw'>abx_coll_names</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
|
||||
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>,
|
||||
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>),
|
||||
<span class='kw'>abx_coll_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
|
||||
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>,
|
||||
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
|
||||
<span class='kw'>abx_coll_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
|
||||
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>,
|
||||
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>))
|
||||
|
||||
}</pre>
|
||||
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|
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<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." />
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|
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<h1>Property of an antibiotic</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
|
||||
<div class="hidden name"><code>ab_property.Rd</code></div>
|
||||
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|
||||
|
||||
<div class="ref-description">
|
||||
<p>Use these functions to return a specific property of an antibiotic from the <a href='antibiotics.html'>antibiotics</a> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ab_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_atc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_cid</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_synonyms</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_tradenames</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_group</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_atc_group1</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_loinc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_ddd</span>(<span class='no'>x</span>, <span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>language</th>
|
||||
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption("AMR_locale")</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>tolower</th>
|
||||
<td><p>logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>other parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>administration</th>
|
||||
<td><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>units</th>
|
||||
<td><p>a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>open</th>
|
||||
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>utils::browseURL()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
<td><p>one of the column names of one of the <a href='antibiotics.html'>antibiotics</a> data set</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
|
||||
<ul>
|
||||
<li><p>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> in case of <code>ab_cid()</code></p></li>
|
||||
<li><p>A named <code><a href='https://rdrr.io/r/base/list.html'>list</a></code> in case of <code>ab_info()</code> and multiple <code>ab_synonyms()</code>/<code>ab_tradenames()</code></p></li>
|
||||
<li><p>A <code><a href='https://rdrr.io/r/base/double.html'>double</a></code> in case of <code>ab_ddd()</code></p></li>
|
||||
<li><p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in all other cases</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
|
||||
<p>The function <code>ab_url()</code> will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
||||
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># all properties:</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"AMX"</span>) <span class='co'># "Amoxicillin"</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"AMX"</span>) <span class='co'># J01CA04 (ATC code from the WHO)</span>
|
||||
<span class='fu'>ab_cid</span>(<span class='st'>"AMX"</span>) <span class='co'># 33613 (Compound ID from PubChem)</span>
|
||||
<span class='fu'>ab_synonyms</span>(<span class='st'>"AMX"</span>) <span class='co'># a list with brand names of amoxicillin</span>
|
||||
<span class='fu'>ab_tradenames</span>(<span class='st'>"AMX"</span>) <span class='co'># same</span>
|
||||
<span class='fu'>ab_group</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactams/penicillins"</span>
|
||||
<span class='fu'>ab_atc_group1</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactam antibacterials, penicillins"</span>
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='st'>"AMX"</span>) <span class='co'># "Penicillins with extended spectrum"</span>
|
||||
<span class='fu'>ab_url</span>(<span class='st'>"AMX"</span>) <span class='co'># link to the official WHO page</span>
|
||||
|
||||
<span class='co'># smart lowercase tranformation</span>
|
||||
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>)) <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>),
|
||||
<span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
|
||||
|
||||
<span class='co'># defined daily doses (DDD)</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>) <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>) <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
|
||||
|
||||
<span class='fu'>ab_info</span>(<span class='st'>"AMX"</span>) <span class='co'># all properties as a list</span>
|
||||
|
||||
<span class='co'># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"AMP"</span>) <span class='co'># ATC code of AMP (ampicillin)</span>
|
||||
<span class='fu'>ab_group</span>(<span class='st'>"J01CA01"</span>) <span class='co'># Drug group of ampicillins ATC code</span>
|
||||
<span class='fu'>ab_loinc</span>(<span class='st'>"ampicillin"</span>) <span class='co'># LOINC codes of ampicillin</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"21066-6"</span>) <span class='co'># "Ampicillin" (using LOINC)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='fl'>6249</span>) <span class='co'># "Ampicillin" (using CID)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"J01CA01"</span>) <span class='co'># "Ampicillin" (using ATC)</span>
|
||||
|
||||
<span class='co'># spelling from different languages and dyslexia are no problem</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
|
||||
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|
||||
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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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<h1>Age in years of individuals</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
|
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<div class="hidden name"><code>age.Rd</code></div>
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|
||||
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||||
<div class="ref-description">
|
||||
<p>Calculates age in years based on a reference date, which is the sytem date at default.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>age</span>(<span class='no'>x</span>, <span class='kw'>reference</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), <span class='kw'>exact</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
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||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>date(s), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>reference</th>
|
||||
<td><p>reference date(s) (defaults to today), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code> and cannot be lower than <code>x</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>exact</th>
|
||||
<td><p>a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of <a href='https://en.wikipedia.org/wiki/Year-to-date'>year-to-date</a> (YTD) of <code>x</code> by the number of days in the year of <code>reference</code> (either 365 or 366).</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>na.rm</th>
|
||||
<td><p>a logical to indicate whether missing values should be removed</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>An <a href='https://rdrr.io/r/base/integer.html'>integer</a> (no decimals) if <code>exact = FALSE</code>, a <a href='https://rdrr.io/r/base/double.html'>double</a> (with decimals) otherwise</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
||||
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
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||||
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||||
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||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># 10 random birth dates</span>
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>birth_date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>() - <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span>(<span class='fl'>10</span>) * <span class='fl'>25000</span>)
|
||||
<span class='co'># add ages</span>
|
||||
<span class='no'>df</span>$<span class='no'>age</span> <span class='kw'><-</span> <span class='fu'>age</span>(<span class='no'>df</span>$<span class='no'>birth_date</span>)
|
||||
<span class='co'># add exact ages</span>
|
||||
<span class='no'>df</span>$<span class='no'>age_exact</span> <span class='kw'><-</span> <span class='fu'>age</span>(<span class='no'>df</span>$<span class='no'>birth_date</span>, <span class='kw'>exact</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
|
||||
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||||
<span class='no'>df</span></pre>
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<h1>Split ages into age groups</h1>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
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||||
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||||
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<p>Split ages into age groups defined by the <code>split</code> parameter. This allows for easier demographic (antimicrobial resistance) analysis.</p>
|
||||
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|
||||
|
||||
<pre class="usage"><span class='fu'>age_groups</span>(<span class='no'>x</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>age, e.g. calculated with <code><a href='age.html'>age()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>split_at</th>
|
||||
<td><p>values to split <code>x</code> at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See Details.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>na.rm</th>
|
||||
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether missing values should be removed</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>To split ages, the input for the <code>split_at</code> parameter can be:</p><ul>
|
||||
<li><p>A numeric vector. A vector of e.g. <code><a href='https://rdrr.io/r/base/c.html'>c(10, 20)</a></code> will split on 0-9, 10-19 and 20+. A value of only <code>50</code> will split on 0-49 and 50+.
|
||||
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).</p></li>
|
||||
<li><p>A character:</p><ul>
|
||||
<li><p><code>"children"</code> or <code>"kids"</code>, equivalent of: <code><a href='https://rdrr.io/r/base/c.html'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
|
||||
<li><p><code>"elderly"</code> or <code>"seniors"</code>, equivalent of: <code><a href='https://rdrr.io/r/base/c.html'>c(65, 75, 85)</a></code>. This will split on 0-64, 65-74, 75-84, 85+.</p></li>
|
||||
<li><p><code>"fives"</code>, equivalent of: <code>1:20 * 5</code>. This will split on 0-4, 5-9, 10-14, ..., 90-94, 95-99, 100+.</p></li>
|
||||
<li><p><code>"tens"</code>, equivalent of: <code>1:10 * 10</code>. This will split on 0-9, 10-19, 20-29, ..., 80-89, 90-99, 100+.</p></li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
||||
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='no'>ages</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
|
||||
|
||||
<span class='co'># split into 0-49 and 50+</span>
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)
|
||||
|
||||
<span class='co'># split into 0-19, 20-49 and 50+</span>
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
|
||||
|
||||
<span class='co'># split into groups of ten years</span>
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)
|
||||
|
||||
<span class='co'># split into groups of five years</span>
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)
|
||||
|
||||
<span class='co'># split specifically for children</span>
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)
|
||||
<span class='co'># same:</span>
|
||||
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
|
||||
|
||||
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
|
||||
<span class='co'># resistance of ciprofloxacine per age group</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
|
||||
}</pre>
|
||||
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<meta property="og:description" content="Use these selection helpers inside any function that allows Tidyverse selections, like dplyr::select() or tidyr::pivot_longer(). They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations." />
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<div class="row">
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<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Antibiotic class selectors</h1>
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_class_selectors.R'><code>R/ab_class_selectors.R</code></a></small>
|
||||
<div class="hidden name"><code>antibiotic_class_selectors.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>Use these selection helpers inside any function that allows <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selections</a>, like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>dplyr::select()</a></code> or <code><a href='https://tidyr.tidyverse.org/reference/pivot_longer.html'>tidyr::pivot_longer()</a></code>. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ab_class</span>(<span class='no'>ab_class</span>)
|
||||
|
||||
<span class='fu'>aminoglycosides</span>()
|
||||
|
||||
<span class='fu'>carbapenems</span>()
|
||||
|
||||
<span class='fu'>cephalosporins</span>()
|
||||
|
||||
<span class='fu'>cephalosporins_1st</span>()
|
||||
|
||||
<span class='fu'>cephalosporins_2nd</span>()
|
||||
|
||||
<span class='fu'>cephalosporins_3rd</span>()
|
||||
|
||||
<span class='fu'>cephalosporins_4th</span>()
|
||||
|
||||
<span class='fu'>cephalosporins_5th</span>()
|
||||
|
||||
<span class='fu'>fluoroquinolones</span>()
|
||||
|
||||
<span class='fu'>glycopeptides</span>()
|
||||
|
||||
<span class='fu'>macrolides</span>()
|
||||
|
||||
<span class='fu'>penicillins</span>()
|
||||
|
||||
<span class='fu'>tetracyclines</span>()</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>ab_class</th>
|
||||
<td><p>an antimicrobial class, like <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
|
||||
<p>These functions only work if the <code>tidyselect</code> package is installed, that comes with the <code>dplyr</code> package. An error will be thrown if <code>tidyselect</code> package is not installed, or if the functions are used outside a function that allows Tidyverse selections like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> or <code>pivot_longer()</code>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
|
||||
|
||||
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>carbapenems</span>())
|
||||
|
||||
<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>aminoglycosides</span>())
|
||||
|
||||
<span class='co'># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>ab_class</span>(<span class='st'>"mycobact"</span>))
|
||||
|
||||
|
||||
<span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>"pos"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>macrolides</span>()) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span>() <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>()
|
||||
|
||||
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>irrelevant</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
|
||||
<span class='kw'>J01CA01</span> <span class='kw'>=</span> <span class='st'>"S"</span>) <span class='kw'>%>%</span> <span class='co'># ATC code of ampicillin</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>()) <span class='co'># so the 'J01CA01' column is selected</span>
|
||||
|
||||
}</pre>
|
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<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
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<h1>Data sets with 558 antimicrobials</h1>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
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<div class="hidden name"><code>antibiotics.Rd</code></div>
|
||||
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|
||||
|
||||
<div class="ref-description">
|
||||
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href='as.ab.html'>as.ab()</a></code> or one of the <code><a href='ab_property.html'>ab_property()</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes.</p>
|
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||||
<pre class="usage"><span class='no'>antibiotics</span>
|
||||
|
||||
<span class='no'>antivirals</span></pre>
|
||||
|
||||
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||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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||||
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||||
|
||||
<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 456 observations and 14 variables:</h3>
|
||||
|
||||
<ul>
|
||||
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
|
||||
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
|
||||
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
|
||||
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
|
||||
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
|
||||
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
|
||||
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
|
||||
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
|
||||
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
|
||||
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
|
||||
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
|
||||
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
|
||||
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
|
||||
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
<h3>For the antivirals data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 102 observations and 9 variables:</h3>
|
||||
|
||||
<ul>
|
||||
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
|
||||
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
|
||||
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
|
||||
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
|
||||
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
|
||||
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
|
||||
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
|
||||
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
|
||||
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
<p>An object of class <code>data.frame</code> with 102 rows and 9 columns.</p>
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
|
||||
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3>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>
|
||||
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
|
||||
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
|
||||
</ul>
|
||||
|
||||
<p>Files in R format (with preserved data structure) can be found here:</p><ul>
|
||||
<li><p><a href='https://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>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
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<h1>Transform to antibiotic ID</h1>
|
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
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|
||||
|
||||
<div class="ref-description">
|
||||
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.ab</span>(<span class='no'>x</span>, <span class='kw'>flag_multiple_results</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>is.ab</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>character vector to determine to antibiotic ID</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>flag_multiple_results</th>
|
||||
<td><p>logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>arguments passed on to internal functions</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>Character (vector) with class <code>ab</code>. Unknown values will return <code>NA</code>.</p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>All entries in the <a href='antibiotics.html'>antibiotics</a> data set have three different identifiers: a human readable EARS-Net code (column <code>ab</code>, used by ECDC and WHONET), an ATC code (column <code>atc</code>, used by WHO), and a CID code (column <code>cid</code>, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.</p>
|
||||
<p>All these properties will be searched for the user input. The <code>as.ab()</code> can correct for different forms of misspelling:</p><ul>
|
||||
<li><p>Wrong spelling of drug names (like "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.</p></li>
|
||||
<li><p>Too few or too many vowels or consonants</p></li>
|
||||
<li><p>Switching two characters (like "mreopenem", often the case in clinical data, when doctors typed too fast)</p></li>
|
||||
<li><p>Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.</p></li>
|
||||
</ul>
|
||||
|
||||
<p>Use the <code><a href='ab_property.html'>ab_property()</a></code> functions to get properties based on the returned antibiotic ID, see Examples.</p>
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
|
||||
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
|
||||
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'>
|
||||
<ul>
|
||||
<li><p><a href='antibiotics.html'>antibiotics</a> for the dataframe that is being used to determine ATCs</p></li>
|
||||
<li><p><code><a href='ab_from_text.html'>ab_from_text()</a></code> for a function to retrieve antimicrobial drugs from clinical text (from health care records)</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"eryt"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>" eryt 123"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"ERYT"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"ERY"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"eritromicine"</span>) <span class='co'># spelled wrong, yet works</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Romycin"</span>) <span class='co'># trade name</span>
|
||||
|
||||
<span class='co'># spelling from different languages and dyslexia are no problem</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"ceftriaxon"</span>)
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephtriaxone"</span>) <span class='co'># small spelling error</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephthriaxone"</span>) <span class='co'># or a bit more severe</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"seephthriaaksone"</span>) <span class='co'># and even this works</span>
|
||||
|
||||
<span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
|
||||
<span class='co'># they use as.ab() internally:</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>
|
||||
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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 class="page-header">
|
||||
<h1>Class 'disk'</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
|
||||
<div class="hidden name"><code>as.disk.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>This transforms a vector to a new class <code>disk</code>, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.disk</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>is.disk</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>vector</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>na.rm</th>
|
||||
<td><p>a logical indicating whether missing values should be removed</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> with additional new class <code>disk</code></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Interpret disk values as RSI values with <code><a href='as.rsi.html'>as.rsi()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
||||
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
|
||||
<span class='co'># transform existing disk zones to the `disk` class</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
|
||||
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fl'>20</span>,
|
||||
<span class='kw'>CIP</span> <span class='kw'>=</span> <span class='fl'>14</span>,
|
||||
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fl'>18</span>,
|
||||
<span class='kw'>TOB</span> <span class='kw'>=</span> <span class='fl'>16</span>)
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.disk</span>)
|
||||
<span class='no'>df</span>
|
||||
|
||||
<span class='co'># interpret disk values, see ?as.rsi</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.disk</span>(<span class='fl'>18</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='no'>df</span>)
|
||||
}</pre>
|
||||
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<h1>Class 'mic'</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
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<div class="hidden name"><code>as.mic.Rd</code></div>
|
||||
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|
||||
|
||||
<div class="ref-description">
|
||||
<p>This transforms a vector to a new class <code>mic</code>, which is an ordered <code><a href='https://rdrr.io/r/base/factor.html'>factor</a></code> with valid MIC values as levels. Invalid MIC values will be translated as <code>NA</code> with a warning.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.mic</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>is.mic</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>vector</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>na.rm</th>
|
||||
<td><p>a logical indicating whether missing values should be removed</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>Ordered <code><a href='https://rdrr.io/r/base/factor.html'>factor</a></code> with new class <code>mic</code></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>To interpret MIC values as RSI values, use <code><a href='as.rsi.html'>as.rsi()</a></code> on MIC values. It supports guidelines from EUCAST and CLSI.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
||||
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='no'>mic_data</span> <span class='kw'><-</span> <span class='fu'>as.mic</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>">=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"<=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span>))
|
||||
<span class='fu'>is.mic</span>(<span class='no'>mic_data</span>)
|
||||
|
||||
<span class='co'># this can also coerce combined MIC/RSI values:</span>
|
||||
<span class='fu'>as.mic</span>(<span class='st'>"<=0.002; S"</span>) <span class='co'># will return <=0.002</span>
|
||||
|
||||
<span class='co'># interpret MIC values</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.mic</span>(<span class='fl'>2</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.mic</span>(<span class='fl'>4</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>mic_data</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>mic_data</span>)</pre>
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<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like "Staphylococcus aureus"), an abbreviated name (like "S. aureus"), an abbreviation known in the field (like "MRSA"), or just a genus. Please see Examples." />
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||||
<h1>Transform to microorganism ID</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
|
||||
<div class="hidden name"><code>as.mo.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>Use this function to determine a valid microorganism ID (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (like <code>"S. aureus"</code>), an abbreviation known in the field (like <code>"MRSA"</code>), or just a genus. Please see <em>Examples</em>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.mo</span>(
|
||||
<span class='no'>x</span>,
|
||||
<span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
|
||||
<span class='no'>...</span>
|
||||
)
|
||||
|
||||
<span class='fu'>is.mo</span>(<span class='no'>x</span>)
|
||||
|
||||
<span class='fu'>mo_failures</span>()
|
||||
|
||||
<span class='fu'>mo_uncertainties</span>()
|
||||
|
||||
<span class='fu'>mo_renamed</span>()</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>a character vector or a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with one or two columns</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>Becker</th>
|
||||
<td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into coagulase-negative <em>Staphylococci</em> ("CoNS") and coagulase-positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2). Note that this does not include species that were newly named after these publications, like <em>S. caeli</em>.</p>
|
||||
<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>Lancefield</th>
|
||||
<td><p>a logical to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (3). These <em>Streptococci</em> will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
|
||||
<p>This excludes <em>Enterococci</em> at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all <em>Enterococci</em> as group D.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>allow_uncertain</th>
|
||||
<td><p>a number between <code>0</code> (or <code>"none"</code>) and <code>3</code> (or <code>"all"</code>), or <code>TRUE</code> (= <code>2</code>) or <code>FALSE</code> (= <code>0</code>) to indicate whether the input should be checked for less probable results, please see <em>Details</em></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>reference_df</th>
|
||||
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> to be used for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source()</a></code> and <code><a href='mo_source.html'>get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>other parameters passed on to functions</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vector with class <code>mo</code></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
|
||||
<h3>General info</h3>
|
||||
|
||||
|
||||
<p>A microorganism ID from this package (class: <code>mo</code>) typically looks like these examples:</p><pre> Code Full name
|
||||
--------------- --------------------------------------
|
||||
B_KLBSL Klebsiella
|
||||
B_KLBSL_PNMN Klebsiella pneumoniae
|
||||
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
|
||||
| | | |
|
||||
| | | |
|
||||
| | | ---&gt; subspecies, a 4-5 letter acronym
|
||||
| | ----&gt; species, a 4-5 letter acronym
|
||||
| ----&gt; genus, a 5-7 letter acronym
|
||||
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
|
||||
C (Chromista), F (Fungi), P (Protozoa)
|
||||
</pre>
|
||||
|
||||
<p>Values that cannot be coered will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
|
||||
<p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see Examples.</p>
|
||||
<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href='microorganisms.html'>microorganisms</a>).</p>
|
||||
<p>The <code>as.mo()</code> function uses several coercion rules for fast and logical results. It assesses the input matching criteria in the following order:</p><ol>
|
||||
<li><p>Human pathogenic prevalence: the function starts with more prevalent microorganisms, followed by less prevalent ones;</p></li>
|
||||
<li><p>Taxonomic kingdom: the function starts with determining Bacteria, then Fungi, then Protozoa, then others;</p></li>
|
||||
<li><p>Breakdown of input values to identify possible matches.</p></li>
|
||||
</ol>
|
||||
|
||||
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
|
||||
|
||||
<h3>Coping with uncertain results</h3>
|
||||
|
||||
|
||||
<p>In addition, the <code>as.mo()</code> function can differentiate four levels of uncertainty to guess valid results:</p><ul>
|
||||
<li><p>Uncertainty level 0: no additional rules are applied;</p></li>
|
||||
<li><p>Uncertainty level 1: allow previously accepted (but now invalid) taxonomic names and minor spelling errors;</p></li>
|
||||
<li><p>Uncertainty level 2: allow all of level 1, strip values between brackets, inverse the words of the input, strip off text elements from the end keeping at least two elements;</p></li>
|
||||
<li><p>Uncertainty level 3: allow all of level 1 and 2, strip off text elements from the end, allow any part of a taxonomic name.</p></li>
|
||||
</ul>
|
||||
|
||||
<p>This leads to e.g.:</p><ul>
|
||||
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRPB</code>) needs review.</p></li>
|
||||
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AURS</code>) needs review.</p></li>
|
||||
<li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GNRR</code>) needs review.</p></li>
|
||||
</ul>
|
||||
|
||||
<p>The level of uncertainty can be set using the argument <code>allow_uncertain</code>. The default is <code>allow_uncertain = TRUE</code>, which is equal to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> is equal to uncertainty level 0 and will skip all rules. You can also use e.g. <code>as.mo(..., allow_uncertain = 1)</code> to only allow up to level 1 uncertainty.</p>
|
||||
<p>There are three helper functions that can be run after then <code>as.mo()</code> function:</p><ul>
|
||||
<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \((n - 0.5 * L) / n\), where <em>n</em> is the number of characters of the returned full name of the microorganism, and <em>L</em> is the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between that full name and the user input.</p></li>
|
||||
<li><p>Use <code>mo_failures()</code> to get a <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> with all values that could not be coerced to a valid value.</p></li>
|
||||
<li><p>Use <code>mo_renamed()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that could be coerced based on an old, previously accepted taxonomic name.</p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
<h3>Microbial prevalence of pathogens in humans</h3>
|
||||
|
||||
|
||||
<p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href='microorganisms.html'>microorganisms</a> and <a href='microorganisms.old.html'>microorganisms.old</a> data sets. The grouping into prevalence groups is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence.</p>
|
||||
<p>Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacteriales.</p>
|
||||
<p>Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Aspergillus</em>, <em>Bacteroides</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Chryseobacterium</em>, <em>Cryptococcus</em>, <em>Elisabethkingia</em>, <em>Flavobacterium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Leptotrichia</em>, <em>Mycoplasma</em>, <em>Prevotella</em>, <em>Rhodotorula</em>, <em>Treponema</em>, <em>Trichophyton</em> or <em>Ureaplasma</em>.</p>
|
||||
<p>Group 3 (least prevalent microorganisms) consists of all other microorganisms.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
|
||||
|
||||
<ol>
|
||||
<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li>
|
||||
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li>
|
||||
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li>
|
||||
<li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
|
||||
</ol>
|
||||
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
||||
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
|
||||
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a> for the <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that is being used to determine ID's.</p>
|
||||
<p>The <code><a href='mo_property.html'>mo_property()</a></code> functions (like <code><a href='mo_property.html'>mo_genus()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>) to get properties based on the returned code.</p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='co'># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"sau"</span>) <span class='co'># WHONET code</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"stau"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"STAU"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"staaur"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. aureus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S aureus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Zthafilokkoockus oureuz"</span>) <span class='co'># handles incorrect spelling</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
|
||||
<span class='fu'>as.mo</span>(<span class='fl'>115329001</span>) <span class='co'># SNOMED CT code</span>
|
||||
|
||||
<span class='co'># Dyslexia is no problem - these all work:</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticum"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasmium urealytica"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplazma urealitycium"</span>)
|
||||
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
|
||||
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPDR</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CONS</span>
|
||||
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYGN</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRPA</span>
|
||||
|
||||
<span class='co'># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Gram negative"</span>
|
||||
|
||||
<span class='co'># }</span>
|
||||
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
|
||||
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'><-</span> <span class='fu'>as.mo</span>(<span class='no'>df</span>$<span class='no'>microorganism_name</span>)
|
||||
|
||||
<span class='co'># the select function of the Tidyverse is also supported:</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>as.mo</span>()
|
||||
|
||||
<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
|
||||
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>as.mo</span>()
|
||||
<span class='co'># although this works easier and does the same:</span>
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
|
||||
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