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@@ -16,30 +16,26 @@
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<link href="https://msberends.github.io/AMR/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
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<script src="https://msberends.github.io/AMR/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://msberends.github.io/AMR/deps/Lato-0.4.9/font.css" rel="stylesheet">
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<link href="https://msberends.github.io/AMR/deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
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<!-- 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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<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://msberends.github.io/AMR/pkgdown.js"></script><link href="https://msberends.github.io/AMR/extra.css" rel="stylesheet">
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<link href="https://msberends.github.io/AMR/deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
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<script src="https://msberends.github.io/AMR/deps/headroom-0.11.0/headroom.min.js"></script><script src="https://msberends.github.io/AMR/deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="https://msberends.github.io/AMR/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="https://msberends.github.io/AMR/deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="https://msberends.github.io/AMR/deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="https://msberends.github.io/AMR/deps/search-1.0.0/fuse.min.js"></script><script src="https://msberends.github.io/AMR/deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="https://msberends.github.io/AMR/pkgdown.js"></script><link href="https://msberends.github.io/AMR/extra.css" rel="stylesheet">
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
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<meta name="twitter:card" content="summary_large_image">
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<meta name="twitter:creator" content="@msberends">
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<meta name="twitter:site" content="@msberends">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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<![endif]-->
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</head>
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<body>
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<a href="https://msberends.github.io/AMR/#main" class="visually-hidden-focusable">Skip to contents</a>
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<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<span class="navbar-toggler-icon"></span>
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</button>
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@@ -47,147 +43,47 @@
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<div id="navbar" class="collapse navbar-collapse ms-3">
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<ul class="navbar-nav me-auto">
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<li class="nav-item dropdown">
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<a href="https://msberends.github.io/AMR/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
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<span class="fa fa-question-circle"></span>
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How to
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</a>
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<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
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<a class="dropdown-item" href="https://msberends.github.io/AMR/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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<a class="dropdown-item" href="https://msberends.github.io/AMR/reference/antibiogram.html">
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<span class="fa fa-file-prescription"></span>
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Generate Antibiogram (Trad./Syndromic/WISCA)
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</a>
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<a class="dropdown-item" href="https://msberends.github.io/AMR/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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<a class="dropdown-item" href="https://msberends.github.io/AMR/articles/datasets.html">
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<span class="fa fa-database"></span>
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Download Data Sets for Own Use
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</a>
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<a class="dropdown-item" href="https://msberends.github.io/AMR/reference/AMR-options.html">
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<span class="fa fa-gear"></span>
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Set User- Or Team-specific Package Settings
|
||||
</a>
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<a class="dropdown-item" href="https://msberends.github.io/AMR/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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<a class="dropdown-item" href="https://msberends.github.io/AMR/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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<a class="dropdown-item" href="https://msberends.github.io/AMR/articles/WHONET.html">
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<span class="fa fa-globe-americas"></span>
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Work with WHONET Data
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</a>
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<a class="dropdown-item" href="https://msberends.github.io/AMR/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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<a class="dropdown-item" href="https://msberends.github.io/AMR/reference/mo_property.html">
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<span class="fa fa-bug"></span>
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Get Taxonomy of a Microorganism
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</a>
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<a class="dropdown-item" href="https://msberends.github.io/AMR/reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get Properties of an Antibiotic Drug
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</a>
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||||
<a class="dropdown-item" href="https://msberends.github.io/AMR/reference/av_property.html">
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<span class="fa fa-capsules"></span>
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Get Properties of an Antiviral Drug
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</a>
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</div>
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||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
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<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
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<li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
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<li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
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</ul>
|
||||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="https://msberends.github.io/AMR/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
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<span class="fa fa-layer-group"></span>
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||||
With other pkgs
|
||||
</a>
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||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
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||||
<a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html">
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||||
<span class="fa fa-layer-group"></span>
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||||
AMR & dplyr/tidyverse
|
||||
</a>
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||||
<a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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AMR & data.table
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</a>
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<a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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AMR & tidymodels
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||||
</a>
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<a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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AMR & base R
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||||
</a>
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||||
</div>
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||||
</li>
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<li class="nav-item">
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||||
<a class="nav-link" href="https://msberends.github.io/AMR/reference/index.html">
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||||
<span class="fa fa-book-open"></span>
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||||
Manual
|
||||
</a>
|
||||
</li>
|
||||
<li class="nav-item">
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||||
<a class="nav-link" href="https://msberends.github.io/AMR/authors.html">
|
||||
<span class="fa fa-users"></span>
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||||
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Authors
|
||||
</a>
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||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
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||||
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
|
||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
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||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
||||
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="nav-item"><a class="nav-link" href="https://msberends.github.io/AMR/reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
|
||||
<li class="nav-item"><a class="nav-link" href="https://msberends.github.io/AMR/authors.html"><span class="fa fa-users"></span> Authors</a></li>
|
||||
</ul>
|
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<form class="form-inline my-2 my-lg-0" role="search">
|
||||
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
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</form>
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<ul class="navbar-nav">
|
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<li class="nav-item">
|
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<a class="nav-link" href="https://msberends.github.io/AMR/news/index.html">
|
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<span class="far fa far fa-newspaper"></span>
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|
||||
Changelog
|
||||
</a>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="external-link nav-link" href="https://github.com/msberends/AMR">
|
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<span class="fab fa fab fa-github"></span>
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|
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Source Code
|
||||
</a>
|
||||
</li>
|
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<ul class="navbar-nav">
|
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<li class="nav-item"><a class="nav-link" href="https://msberends.github.io/AMR/news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
|
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<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
||||
</ul>
|
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</div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-title-body">
|
||||
<div class="row">
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
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<img src="https://msberends.github.io/AMR/logo.svg" class="logo" alt=""><h1>Page not found (404)</h1>
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|
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</div>
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|
||||
Content not found. Please use links in the navbar.
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@@ -207,9 +103,9 @@ Content not found. Please use links in the navbar.
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</footer>
|
||||
</div>
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</body>
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</html>
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<svg
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version="1.1"
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id="svg1"
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width="564.80664"
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height="266.66666"
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viewBox="0 0 564.80664 266.66666"
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xml:space="preserve"
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xmlns:xlink="http://www.w3.org/1999/xlink"
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xmlns="http://www.w3.org/2000/svg"
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xmlns:svg="http://www.w3.org/2000/svg"><defs
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id="defs1"><color-profile
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name="Coated-FOGRA39-ISO-12647-2:2004"
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:19.1091px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#2d3f50;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="0 10.62466 20.179209 25.835503 30.421688 44.906384 49.492569 58.340084 64.703415 73.875778 83.430328 88.016518 97.207993 101.79417 106.38036 117.00502 125.85253 134.33698 138.92316 147.40759 153.06389 162.25537 171.80992 180.65742 189.50494 194.09113 199.74742 210.37209 224.51282 235.13748 240.79376 245.37996 256.34857 265.54004 271.19635 280.38782 284.26697 294.89163 304.44617 313.63766 318.22385 326.70828 335.19272 339.7789 348.26334 352.84952 357.43573 366.99026 371.57645"
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y="0"
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id="tspan1053">Antimicrobial Resistance (AMR) Data Analysis in R</tspan></text><text
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transform="matrix(1.3333333,0,0,1.599968,169.0488,74.044933)"><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="0 6.1751237 10.50021 14.9753 19.300386 21.925438 26.250525 28.717241 33.042328 37.050739"
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y="0"
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id="tspan1054">Generates </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="39.367455 43.375866 47.542618 50.009335 52.009373 56.176125 58.176163 62.176243 66.342995 69.11805 73.126465 79.443253"
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id="tspan1055">antibiograms</tspan><tspan
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x="83.143326 85.460045 89.626793 91.943504 94.410225 97.035271 101.36036 106.14379 107.68549 110.15221 111.6939 116.32732 120.80241 125.1275 126.6692 128.98592 131.30263 135.62772 140.26114 147.20294 151.98637 153.52808 158.00316 162.32825 167.11168 169.42839 171.7451 175.75351 179.61192 184.08702 188.87044 191.34467 195.97809 202.91989 204.46159 208.78668 211.10339 213.4201 217.74519 222.22028 227.00371 229.32042 233.64551 237.50392 241.82901 246.30409 248.6208 256.17929 258.02933 263.27942 269.14621"
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y="0"
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id="tspan1056"> – traditional, combined, syndromic, and even WISCA</tspan><tspan
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x="0 5.2501049 7.7251544 12.358581 16.216991 17.758688 22.542118 26.867205 30.875618 33.192329 35.659046 40.134136 44.459221"
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y="15.0003"
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id="tspan1057">Provides the </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="46.775936 49.242653 53.409401 55.409443 57.409481 59.409523 65.726311 67.726357 71.584763 74.359818 78.359901 82.526649 84.526688 88.526772 90.52681 94.526894 98.693642 100.69368 104.55209 108.5605 110.56055 112.56059 115.0273 119.03571 122.88579 126.88587 131.05263 135.0527 141.36949"
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y="15.0003"
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id="tspan1058">full microbiological taxonomy</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="145.06956 147.38628 151.71136 156.18646 160.96988 163.28661 168.07002 172.39511 174.86183 179.18692 181.50363 186.13705 190.61215"
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y="15.0003"
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id="tspan1059"> and data on </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="192.92886 196.93727 198.93732 200.93735 202.93739 206.9458 211.11255 213.57927 215.57932 221.8961 223.89615 227.75456 230.52962 234.52969 238.69644 240.69649 244.7049 246.70494 248.70497 252.87172 255.64677 259.81354 263.98029"
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y="15.0003"
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id="tspan1060">all antimicrobial drugs</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="0 5.2501049 10.033534 14.816963 16.35866 17.900358 22.225445 26.233858 28.550571 32.875656 34.417355 35.959053 38.275764 40.749981 45.075069 49.400154 53.725243 58.200329"
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y="30.000601"
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id="tspan1061">Applies all recent</tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="60.667046 62.667088 67.142174 71.000587 75.325676 77.475716 79.475754 83.484169 87.650917 91.817673 93.817711 97.826126 102.30955 106.78464 111.41806 115.74315 119.74323 121.74327 125.43501 127.43505 129.43509 133.60184 135.60188 139.4603 143.4687 145.46875 147.46878 151.63553 154.41058 158.269 162.2774 166.44417 170.61092 174.61099 176.61104 180.77779 183.24449"
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y="30.000601"
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id="tspan1062"> CLSI and EUCAST clinical breakpoints</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="186.94456 189.26129 191.41966 196.05309 198.67815 200.99486 207.83665 209.68669 215.55348 219.56189 221.8786 226.20369 230.67879 235.4622 237.77892 242.56235 244.10405 248.11246 252.27921 254.59593 258.45435 263.08777 267.56287 271.88794"
|
||||
y="30.000601"
|
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id="tspan1063"> for MICs and disk zones</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="0 5.8667841 10.50021 13.125262 15.600312 19.925398 24.250484 26.717201 30.725615 33.042328 35.200703 39.834129 42.459183 44.775894 49.559326 54.034412 58.817844 60.359539 61.901237 66.226326 70.551414 73.018127 77.343216 79.659927 81.201622 85.210037 89.84346 91.385162 95.710251 98.176964 102.50205 106.51046 108.82718"
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y="45.0009"
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id="tspan1064">Corrects for duplicate isolates, </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="111.14389 115.0023 119.01071 121.01075 124.86916 129.03592 131.03595 135.04437 137.51108 141.36949 145.06956 147.06961 151.07802 155.24477 159.41151 161.41156 165.57831 168.35336 172.21178 176.37852 178.37857 182.23698 184.70369 188.40376 190.09464 194.72806 200.89485"
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y="45.0009"
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id="tspan1065">calculates and predicts AMR</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="205.52827 207.84499 212.62842 216.95351 219.57855 221.89526 226.22035 230.69545 233.16217 234.70386 239.48729 241.02899 245.66241 248.12914 249.67082 253.99591 256.31262 260.63773 262.17941 266.50449 270.51291"
|
||||
y="45.0009"
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||||
id="tspan1066"> per antibiotic class</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="0 1.850037 6.3251266 8.7918425 13.116929 17.750355 20.375408 24.700495 27.16721 31.492296 35.50071 37.817425 43.992546 45.534245 48.000961 52.476051"
|
||||
y="60.001202"
|
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id="tspan1067">Integrates with </tspan><tspan
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||||
style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="54.792763 61.126221 65.759651 70.393074 75.176506 79.184914"
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y="60.001202"
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id="tspan1068">WHONET</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="83.184998 85.501709 87.81842 92.501846 97.135277 103.00206 105.31877"
|
||||
y="60.001202"
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id="tspan1069">, ATC, </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="107.63548 111.6439 116.27733 120.91075 125.23584 128.31923 133.10266 136.96107"
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y="60.001202"
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id="tspan1070">EARS-Net</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="139.4278 141.74451 144.06122 149.31133 153.78641 158.56984 164.43661 168.91171 173.2368 180.1786 182.49532"
|
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y="60.001202"
|
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id="tspan1071">, PubChem, </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="184.81203 188.67044 193.30386 195.4539 200.23734 204.71243"
|
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y="60.001202"
|
||||
id="tspan1072">LOINC </tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
|
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x="206.71246 211.03755 215.51265 220.29607"
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||||
y="60.001202"
|
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id="tspan1073">and </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="222.61279 226.93787 231.7213 236.35472 242.52151 246.52994 251.31335 253.3134 257.78848"
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y="60.001202"
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id="tspan1074">SNOMED CT</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="0 7.4084816 12.041907 14.66696 18.83371 22.842123 25.158836 29.792263 34.267353 36.584064 44.343388 45.885086 50.360172 55.143604 59.777027 65.952156 69.960564 72.277275 74.593994 81.535797 85.860886 90.185974 96.361092 101.6112 103.92791 108.253 112.72809 117.51152 119.82823 124.30332 125.84502 130.3201 134.7952 138.8036 141.12032 147.29544 148.83714 151.30386 155.77895"
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||||
y="75.001503"
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id="tspan1075">Works on Windows, macOS and Linux with </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="158.09566 162.10408 164.10411 166.10416 168.1042 171.80428 175.66267 178.43773 182.1378 184.13785 188.13792 192.30467 196.00476 198.00479 202.00487 204.47159 206.47163"
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||||
y="75.001503"
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id="tspan1076">all versions of R</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="211.10506 213.42177 217.43018 218.97188 223.44698 227.77205 232.09714 234.41385 239.97231 243.05569 247.68912 250.00583 254.63927 256.95596 261.28107 265.75613"
|
||||
y="75.001503"
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id="tspan1077"> since R-3.0 and</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="0 1.5416975 5.5501108 7.8668242 12.191911 16.825336 23.767141 28.550571 30.092268 34.417355 36.884071 41.209156 42.750854 46.609264"
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y="85.001701"
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id="tspan1078">is completely </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="48.92598 53.092728 56.951138 61.117889 64.976303 69.143051 73.309799 77.168213 81.334961 85.025864 88.725945 91.809334 94.276054 97.051109 100.90952"
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y="85.001701"
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id="tspan1079">dependency-free</tspan><tspan
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style="font-variant:normal;font-weight:300;font-stretch:normal;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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x="104.76793 107.08464 109.40135 113.87644 115.41814 120.05157 124.52666 126.06835 129.92676 132.24348 136.25189 140.72697 142.26868 144.7354 149.06049 153.8439 155.3856 159.71069 162.0274 164.18579 168.81921 171.44426 173.76097 178.5444 180.08611 184.41119 188.73627 193.06136 197.06978 199.38649 205.56161 207.1033 209.57002 214.04512"
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y="85.001701"
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id="tspan1080">, highly suitable for places with </tspan><tspan
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style="font-variant:normal;font-weight:700;font-stretch:condensed;font-size:8.3335px;font-family:'Helvetica Neue';writing-mode:lr-tb;fill:#1d1d1b;fill-opacity:1;fill-rule:nonzero;stroke:none"
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y="85.001701"
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y="0"
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id="tspan1082">https://msberends.github.io/AMRhttps://doi.org/10.18637/jss.v104.i03</tspan></text><g
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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<a class="dropdown-item" 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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|
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<a class="dropdown-item" href="reference/antibiogram.html">
|
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<span class="fa fa-file-prescription"></span>
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Generate Antibiogram (Trad./Syndromic/WISCA)
|
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</a>
|
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<a class="dropdown-item" 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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Set User- Or Team-specific Package Settings
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Conduct Principal Component Analysis for AMR
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<a class="dropdown-item" 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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Get Taxonomy of a Microorganism
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Get Properties of an Antibiotic Drug
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<a class="dropdown-item" href="reference/av_property.html">
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<span class="fa fa-capsules"></span>
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Get Properties of an Antiviral Drug
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
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|
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<li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
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<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
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|
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|
||||
<li><a class="dropdown-item" href="reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
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<a class="dropdown-item" href="articles/other_pkg.html">
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AMR & dplyr/tidyverse
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<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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Source Code
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|
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs"><li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
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<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
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|
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<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
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</ul></li>
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<li class="nav-item"><a class="nav-link" href="reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
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</ul></div>
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|
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|
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</div>
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</nav><div class="container template-title-body">
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<div class="row">
|
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<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="logo.svg" class="logo" alt=""><h1>License</h1>
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
<pre>GNU GENERAL PUBLIC LICENSE
|
||||
@@ -421,9 +315,9 @@ END OF TERMS AND CONDITIONS
|
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</footer></div>
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</body></html>
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+107
-234
@@ -5,7 +5,6 @@
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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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<title>How to conduct AMR data analysis • AMR (for R)</title>
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<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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@@ -17,31 +16,22 @@
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<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
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<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
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<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
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<!-- 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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
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Conduct Principal Component Analysis for AMR
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Get Taxonomy of a Microorganism
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
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<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
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With other pkgs
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AMR & dplyr/tidyverse
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Changelog
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Source Code
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||||
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</div>
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</nav><div class="container template-article">
|
||||
|
||||
@@ -195,7 +85,7 @@
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>AMR.Rmd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -205,7 +95,7 @@
|
||||
website update since they are based on randomly created values and the
|
||||
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
|
||||
Markdown</a>. However, the methodology remains unchanged. This page was
|
||||
generated on 23 June 2024.</p>
|
||||
generated on 16 July 2024.</p>
|
||||
<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h2>
|
||||
@@ -261,21 +151,21 @@ make the structure of your data generally look like this:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2024-06-23</td>
|
||||
<td align="center">2024-07-16</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2024-06-23</td>
|
||||
<td align="center">2024-07-16</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2024-06-23</td>
|
||||
<td align="center">2024-07-16</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@@ -318,9 +208,8 @@ have extracted from their laboratory systems:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 E. coli R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 E. coli S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 S. aureus S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># we will use 'our_data' as the data set name for this tutorial</span></span>
|
||||
<span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">example_isolates_unclean</span></span></code></pre></div>
|
||||
<p>For AMR data analysis, we would like the microorganism column to
|
||||
@@ -333,24 +222,21 @@ cleaned as SIR values as well.</p>
|
||||
<p>With <code><a href="../reference/as.mo.html">as.mo()</a></code>, users can transform arbitrary
|
||||
microorganism names or codes to current taxonomy. The <code>AMR</code>
|
||||
package contains up-to-date taxonomic data. To be specific, currently
|
||||
included data were retrieved on 11 Dec 2022.</p>
|
||||
included data were retrieved on 24 Jun 2024.</p>
|
||||
<p>The codes of the AMR packages that come from <code><a href="../reference/as.mo.html">as.mo()</a></code> are
|
||||
short, but still human readable. More importantly, <code><a href="../reference/as.mo.html">as.mo()</a></code>
|
||||
supports all kinds of input:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Class 'mo'</span></span>
|
||||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span>
|
||||
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Class 'mo'</span></span>
|
||||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLEPNE"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span>
|
||||
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLEPNE"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Class 'mo'</span></span>
|
||||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLPN"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span>
|
||||
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLPN"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Class 'mo'</span></span>
|
||||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span></code></pre></div>
|
||||
<p>The first character in above codes denote their taxonomic kingdom,
|
||||
@@ -360,58 +246,53 @@ retrieve taxonomic properties, such as the name, genus, species, family,
|
||||
order, and even Gram-stain. They all start with <code>mo_</code> and
|
||||
they use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally, so that still any arbitrary
|
||||
user input can be used:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] "Enterobacteriaceae"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] "Klebsiella"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] "pneumoniae"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> [1] "Enterobacteriaceae"</span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] "Klebsiella"</span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] "pneumoniae"</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] "Gram-negative"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> [1] "Gram-negative"</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_ref</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] "Trevisan, 1887"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> [1] "Trevisan, 1887"</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [[1]]</span></span>
|
||||
<span><span class="co">#> [1] "1098101000112102" "446870005" "1098201000112108" "409801009" </span></span>
|
||||
<span><span class="co">#> [5] "56415008" "714315002" "713926009"</span></span></code></pre></div>
|
||||
<p>Now we can thus clean our data:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ Microorganism translation was uncertain for four microorganisms. Run</span></span>
|
||||
<span><span class="co">#> mo_uncertainties() to review these uncertainties, or use</span></span>
|
||||
<span><span class="co">#> add_custom_microorganisms() to add custom entries.</span></span></code></pre></div>
|
||||
<p>Apparently, there was some uncertainty about the translation to
|
||||
taxonomic codes. Let’s check this:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Matching scores are based on the resemblance between the input and the full</span></span>
|
||||
<span><span class="co">#> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
|
||||
<span><span class="co">#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
|
||||
<span><span class="co">#> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
|
||||
<span><span class="co">#> Also matched: Escherichia coli coli (0.643), Escherichia coli</span></span>
|
||||
<span><span class="co">#> expressing (0.611), Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
|
||||
<span><span class="co">#> (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span></span>
|
||||
<span><span class="co">#> (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span></span>
|
||||
<span><span class="co">#> (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae</span></span>
|
||||
<span><span class="co">#> cloacae (0.571), Enterobacter cloacae complex (0.571), and Ehrlichia</span></span>
|
||||
<span><span class="co">#> canis (0.567)</span></span>
|
||||
<span><span class="co">#> (0.583), Enterococcus casseliflavus (0.577), and Enterobacter cloacae</span></span>
|
||||
<span><span class="co">#> cloacae (0.571)</span></span>
|
||||
<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
|
||||
<span><span class="co">#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
|
||||
<span><span class="co">#> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
|
||||
<span><span class="co">#> pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span></span>
|
||||
<span><span class="co">#> (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span></span>
|
||||
<span><span class="co">#> Kingella potus (0.400), Kosakonia pseudosacchari (0.361), Kaistella</span></span>
|
||||
<span><span class="co">#> palustris (0.333), Kocuria palustris (0.333), and Kocuria pelophila</span></span>
|
||||
<span><span class="co">#> (0.333)</span></span>
|
||||
<span><span class="co">#> Kingella potus (0.400), Kluyveromyces pseudotropicale (0.386),</span></span>
|
||||
<span><span class="co">#> Kluyveromyces pseudotropicalis (0.363), Kosakonia pseudosacchari</span></span>
|
||||
<span><span class="co">#> (0.361), and Kluyveromyces pseudotropicalis pseudotropicalis (0.361)</span></span>
|
||||
<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
|
||||
<span><span class="co">#> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
|
||||
<span><span class="co">#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
|
||||
@@ -448,7 +329,7 @@ diffusion values, read more about that on the <code><a href="../reference/as.sir
|
||||
page.</p>
|
||||
<p>For now, we will just clean the SIR columns in our data using
|
||||
dplyr:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># method 1, be explicit about the columns:</span></span>
|
||||
<span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">:</span><span class="va">GEN</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
|
||||
@@ -516,7 +397,7 @@ analysis, but the default phenotype-based method is in any case the
|
||||
method to properly correct for most duplicate isolates. Read more about
|
||||
the methods on the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> page.</p>
|
||||
<p>The outcome of the function can easily be added to our data:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ Determining first isolates using an episode length of 365 days</span></span>
|
||||
@@ -530,16 +411,16 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
|
||||
<p>So only 90% is suitable for resistance analysis! We can now filter on
|
||||
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
|
||||
<code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>For future use, the above two syntaxes can be shortened:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>So we end up with 2 712 isolates for analysis. Now our data looks
|
||||
like:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,712 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
@@ -564,7 +445,7 @@ like:</p>
|
||||
<p>The base R <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function gives a good first
|
||||
impression, as it comes with support for the new <code>mo</code> and
|
||||
<code>sir</code> classes that we now have in our data set:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> patient_id hospital date </span></span>
|
||||
<span><span class="co">#> Length:2712 Length:2712 Min. :2011-01-01 </span></span>
|
||||
@@ -586,9 +467,8 @@ impression, as it comes with support for the new <code>mo</code> and
|
||||
<span><span class="co">#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> %I : 6.6% (n=178) %I : 3.1% (n=85) </span></span>
|
||||
<span><span class="co">#> %R :42.0% (n=1138) %R :37.3% (n=1011) </span></span>
|
||||
<span><span class="co">#> %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Rows: 2,712</span></span>
|
||||
<span><span class="co">#> Columns: 9</span></span>
|
||||
@@ -600,9 +480,8 @@ impression, as it comes with support for the new <code>mo</code> and
|
||||
<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I, I, I, S, S, S, S, S, S, S, S, S, I, S, S, S, S, R, S, S,…</span></span>
|
||||
<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ first <span style="color: #949494; font-style: italic;"><lgl></span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> $ first <span style="color: #949494; font-style: italic;"><lgl></span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># number of unique values per column:</span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP </span></span>
|
||||
@@ -615,7 +494,7 @@ impression, as it comes with support for the new <code>mo</code> and
|
||||
<p>To just get an idea how the species are distributed, create a
|
||||
frequency table with <code><a href="../reference/count.html">count()</a></code> based on the name of the
|
||||
microorganisms:</p>
|
||||
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||||
@@ -624,9 +503,8 @@ microorganisms:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>518</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 730</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 426</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||||
@@ -643,7 +521,7 @@ microorganisms:</p>
|
||||
<p>Using so-called antibiotic class selectors, you can select or filter
|
||||
columns based on the antibiotic class that your antibiotic results are
|
||||
in:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
|
||||
@@ -660,9 +538,8 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2015-04-27 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2011-06-21 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2014-09-05 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
|
||||
@@ -680,9 +557,8 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,712 × 5</span></span></span>
|
||||
@@ -698,9 +574,8 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># filtering using AB selectors is also possible:</span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
@@ -718,9 +593,8 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 1,001 more rows</span></span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 1,001 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
|
||||
@@ -738,9 +612,8 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 473 more rows</span></span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 473 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># even works in base R (since R 3.0):</span></span>
|
||||
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
|
||||
<span><span class="co">#> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
|
||||
@@ -793,7 +666,7 @@ failure</li>
|
||||
function to create any of the above antibiogram types. For starters,
|
||||
this is what the included <code>example_isolates</code> data set looks
|
||||
like:</p>
|
||||
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">example_isolates</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
|
||||
<span><span class="co">#> date patient age gender ward mo PEN OXA FLC AMX </span></span>
|
||||
@@ -822,7 +695,7 @@ like:</p>
|
||||
should be used. The <code>antibiotics</code> argument in the
|
||||
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> function supports any (combination) of the
|
||||
previously mentioned antibiotic class selectors:</p>
|
||||
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
|
||||
@@ -949,7 +822,7 @@ Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian,
|
||||
Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish,
|
||||
Swedish, Turkish, or Ukrainian. In this next example, we force the
|
||||
language to be Spanish using the <code>language</code> argument:</p>
|
||||
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||||
@@ -995,7 +868,7 @@ language to be Spanish using the <code>language</code> argument:</p>
|
||||
</h4>
|
||||
<p>To create a combined antibiogram, use antibiotic codes or names with
|
||||
a plus <code>+</code> character like this:</p>
|
||||
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
@@ -1077,7 +950,7 @@ a plus <code>+</code> character like this:</p>
|
||||
<p>To create a syndromic antibiogram, the <code>syndromic_group</code>
|
||||
argument must be used. This can be any column in the data, or e.g. an
|
||||
<code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> with calculations based on certain columns:</p>
|
||||
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
|
||||
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span>
|
||||
@@ -1271,7 +1144,7 @@ Antibiogram) in which cases are predefined based on clinical or
|
||||
demographic characteristics (e.g., endocarditis in 75+ females). This
|
||||
next example is a simplification without clinical characteristics, but
|
||||
just gives an idea of how a WISCA can be created:</p>
|
||||
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">wisca</span> <span class="op"><-</span> <span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC+CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span>
|
||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
|
||||
@@ -1339,7 +1212,7 @@ just gives an idea of how a WISCA can be created:</p>
|
||||
<p>Antibiograms can be plotted using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> from the
|
||||
<code>ggplot2</code> packages, since this <code>AMR</code> package
|
||||
provides an extension to that function:</p>
|
||||
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">wisca</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><img src="AMR_files/figure-html/unnamed-chunk-10-1.png" width="720"></p>
|
||||
<p>To calculate antimicrobial resistance in a more sensible way, also by
|
||||
@@ -1368,12 +1241,12 @@ proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a>
|
||||
I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to
|
||||
<code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their
|
||||
own:</p>
|
||||
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] 0.4288348</span></span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
|
||||
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span><span class="op">)</span></span>
|
||||
@@ -1387,7 +1260,7 @@ own:</p>
|
||||
<p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
|
||||
</div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
</nav></aside>
|
||||
</div>
|
||||
|
||||
@@ -1404,9 +1277,9 @@ own:</p>
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
+48
-160
@@ -5,7 +5,6 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
||||
<meta name="description" content="AMR">
|
||||
<title>How to apply EUCAST rules • 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">
|
||||
@@ -17,31 +16,22 @@
|
||||
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
|
||||
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
|
||||
<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
|
||||
<!-- 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">
|
||||
<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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@@ -195,7 +85,7 @@
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>How to apply EUCAST rules</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>EUCAST.Rmd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -248,9 +138,8 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
|
||||
<span><span class="va">oops</span></span>
|
||||
<span><span class="co">#> mo ampicillin</span></span>
|
||||
<span><span class="co">#> 1 Klebsiella S</span></span>
|
||||
<span><span class="co">#> 2 Escherichia S</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> 2 Escherichia S</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> mo ampicillin</span></span>
|
||||
<span><span class="co">#> 1 Klebsiella R</span></span>
|
||||
@@ -259,14 +148,13 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
|
||||
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline,
|
||||
but allows to check for one or more specific microorganisms or
|
||||
antibiotics:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
|
||||
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
|
||||
<span> <span class="st">"ampicillin"</span></span>
|
||||
<span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] TRUE FALSE</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> [1] TRUE FALSE</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
|
||||
<span> <span class="st">"Klebsiella"</span>,</span>
|
||||
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span></span>
|
||||
@@ -277,7 +165,7 @@ used for filling in known resistance and susceptibility based on results
|
||||
of other antimicrobials drugs. This process is called <em>interpretive
|
||||
reading</em>, is basically a form of imputation, and is part of the
|
||||
<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||||
<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
|
||||
<span> <span class="st">"Staphylococcus aureus"</span>,</span>
|
||||
@@ -295,7 +183,7 @@ reading</em>, is basically a form of imputation, and is part of the
|
||||
<span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span>
|
||||
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span>
|
||||
<span><span class="op">)</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
@@ -361,7 +249,7 @@ reading</em>, is basically a form of imputation, and is part of the
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
@@ -428,7 +316,7 @@ reading</em>, is basically a form of imputation, and is part of the
|
||||
</tbody>
|
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</table>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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</nav></aside>
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@@ -445,9 +333,9 @@ reading</em>, is basically a form of imputation, and is part of the
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</footer>
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@@ -195,7 +85,7 @@
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<img src="../logo.svg" class="logo" alt=""><h1>How to determine multi-drug resistance (MDR)</h1>
|
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|
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|
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
|
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<div class="d-none name"><code>MDR.Rmd</code></div>
|
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</div>
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|
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@@ -495,7 +385,7 @@ Unique: 5</p>
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<title>How to conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
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Conduct AMR Analysis
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Predict Antimicrobial Resistance
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Set User- Or Team-specific Package Settings
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<span class="fa fa-compress"></span>
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Conduct Principal Component Analysis for AMR
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Determine Multi-Drug Resistance (MDR)
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<span class="fa fa-bug"></span>
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Get Taxonomy of a Microorganism
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|
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|
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<span class="fa fa-capsules"></span>
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Get Properties of an Antibiotic Drug
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</a>
|
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<a class="dropdown-item" href="../reference/av_property.html">
|
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<span class="fa fa-capsules"></span>
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Get Properties of an Antiviral Drug
|
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
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<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
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<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
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<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
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<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
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<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
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<span class="fa fa-layer-group"></span>
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With other pkgs
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<a class="dropdown-item" href="../articles/other_pkg.html">
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AMR & dplyr/tidyverse
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<span class="fa fa-layer-group"></span>
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AMR & data.table
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<span class="fa fa-layer-group"></span>
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AMR & tidymodels
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<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
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AMR & base R
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|
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Manual
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Authors
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
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</ul>
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</li>
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<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
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<span class="far fa far fa-newspaper"></span>
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Changelog
|
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|
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<a class="external-link nav-link" href="https://github.com/msberends/AMR">
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Source Code
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<ul class="navbar-nav">
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<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
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<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
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||||
|
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</div>
|
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</nav><div class="container template-article">
|
||||
|
||||
@@ -195,7 +85,7 @@
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct principal component analysis (PCA) for AMR</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>PCA.Rmd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -337,7 +227,7 @@ automatically adds the right labels and even groups:</p>
|
||||
<span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
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</nav></aside>
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</div>
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@@ -354,9 +244,9 @@ automatically adds the right labels and even groups:</p>
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</footer>
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</body>
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</html>
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+40
-150
@@ -5,7 +5,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<title>How to work with WHONET data • AMR (for R)</title>
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<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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@@ -17,31 +16,22 @@
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<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
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<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
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||||
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||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -49,141 +39,41 @@
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<div id="navbar" class="collapse navbar-collapse ms-3">
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<li class="active nav-item dropdown">
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<a class="dropdown-item" href="../articles/AMR.html">
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Conduct AMR Analysis
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<span class="fa fa-file-prescription"></span>
|
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Generate Antibiogram (Trad./Syndromic/WISCA)
|
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</a>
|
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|
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<span class="fa fa-dice"></span>
|
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|
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Predict Antimicrobial Resistance
|
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</a>
|
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|
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<span class="fa fa-database"></span>
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Download Data Sets for Own Use
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</a>
|
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|
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<span class="fa fa-gear"></span>
|
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Set User- Or Team-specific Package Settings
|
||||
</a>
|
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<a class="dropdown-item" href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
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|
||||
Conduct Principal Component Analysis for AMR
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/MDR.html">
|
||||
<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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<a class="dropdown-item" href="../articles/WHONET.html">
|
||||
<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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<a class="dropdown-item" href="../articles/EUCAST.html">
|
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<span class="fa fa-exchange-alt"></span>
|
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|
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Apply Eucast Rules
|
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</a>
|
||||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
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|
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Get Taxonomy of a Microorganism
|
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</a>
|
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<a class="dropdown-item" href="../reference/ab_property.html">
|
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<span class="fa fa-capsules"></span>
|
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|
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Get Properties of an Antibiotic Drug
|
||||
</a>
|
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<a class="dropdown-item" href="../reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
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|
||||
Get Properties of an Antiviral Drug
|
||||
</a>
|
||||
</div>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
|
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
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<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
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<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
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<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
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<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
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<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
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<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
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<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul>
|
||||
</li>
|
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<li class="nav-item dropdown">
|
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
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|
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AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
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|
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AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
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<li class="nav-item">
|
||||
<a class="nav-link" href="../reference/index.html">
|
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<span class="fa fa-book-open"></span>
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|
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Manual
|
||||
</a>
|
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</li>
|
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<li class="nav-item">
|
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<a class="nav-link" href="../authors.html">
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<span class="fa fa-users"></span>
|
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|
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Authors
|
||||
</a>
|
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
|
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<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
|
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</ul>
|
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<form class="form-inline my-2 my-lg-0" role="search">
|
||||
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
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</form>
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<ul class="navbar-nav">
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<li class="nav-item">
|
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<a class="nav-link" href="../news/index.html">
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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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</li>
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<li class="nav-item">
|
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<a class="external-link nav-link" href="https://github.com/msberends/AMR">
|
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<span class="fab fa fab fa-github"></span>
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Source Code
|
||||
</a>
|
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</li>
|
||||
<ul class="navbar-nav">
|
||||
<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
|
||||
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
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</ul>
|
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</div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-article">
|
||||
|
||||
@@ -195,7 +85,7 @@
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>How to work with WHONET data</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>WHONET.Rmd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -427,7 +317,7 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
|
||||
<span> <span class="fu"><a href="../reference/ggplot_sir.html">ggplot_sir</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">"ab"</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
</nav></aside>
|
||||
</div>
|
||||
|
||||
@@ -444,9 +334,9 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
|
||||
</footer>
|
||||
</div>
|
||||
|
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|
||||
|
||||
|
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|
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|
||||
</body>
|
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</html>
|
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+128
-213
@@ -5,7 +5,6 @@
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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, shrink-to-fit=no">
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<meta name="description" content="AMR">
|
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<title>Data sets for download / own use • AMR (for R)</title>
|
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<!-- 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">
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@@ -17,31 +16,22 @@
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<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
|
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<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
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<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
|
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<!-- 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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<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
||||
<link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
|
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<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
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<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script><meta property="og:title" content="Data sets for download / own use">
|
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<meta property="og:description" content="AMR">
|
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
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<meta name="twitter:card" content="summary_large_image">
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<meta name="twitter:creator" content="@msberends">
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<meta name="twitter:site" content="@msberends">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
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<![endif]-->
|
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</head>
|
||||
<body>
|
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<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||
|
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|
||||
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
|
||||
|
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|
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<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
|
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|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<span class="navbar-toggler-icon"></span>
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</button>
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@@ -49,141 +39,41 @@
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<div id="navbar" class="collapse navbar-collapse ms-3">
|
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<ul class="navbar-nav me-auto">
|
||||
<li class="active nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
|
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<span class="fa fa-question-circle"></span>
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|
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How to
|
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</a>
|
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<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
|
||||
<a class="dropdown-item" href="../articles/AMR.html">
|
||||
<span class="fa fa-directions"></span>
|
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|
||||
Conduct AMR Analysis
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/antibiogram.html">
|
||||
<span class="fa fa-file-prescription"></span>
|
||||
|
||||
Generate Antibiogram (Trad./Syndromic/WISCA)
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict Antimicrobial Resistance
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/datasets.html">
|
||||
<span class="fa fa-database"></span>
|
||||
|
||||
Download Data Sets for Own Use
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/AMR-options.html">
|
||||
<span class="fa fa-gear"></span>
|
||||
|
||||
Set User- Or Team-specific Package Settings
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct Principal Component Analysis for AMR
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
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|
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Determine Multi-Drug Resistance (MDR)
|
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</a>
|
||||
<a class="dropdown-item" href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
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|
||||
Work with WHONET Data
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
||||
|
||||
Apply Eucast Rules
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
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|
||||
Get Taxonomy of a Microorganism
|
||||
</a>
|
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<a class="dropdown-item" href="../reference/ab_property.html">
|
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<span class="fa fa-capsules"></span>
|
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|
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Get Properties of an Antibiotic Drug
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</a>
|
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<a class="dropdown-item" href="../reference/av_property.html">
|
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<span class="fa fa-capsules"></span>
|
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|
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Get Properties of an Antiviral Drug
|
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</a>
|
||||
</div>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
|
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
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<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
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<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
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<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul>
|
||||
</li>
|
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<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
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<span class="fa fa-layer-group"></span>
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With other pkgs
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</a>
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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AMR & dplyr/tidyverse
|
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</a>
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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AMR & data.table
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</a>
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
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|
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AMR & tidymodels
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</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
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|
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AMR & base R
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</a>
|
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</div>
|
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</li>
|
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<li class="nav-item">
|
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<a class="nav-link" href="../reference/index.html">
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Manual
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<li class="nav-item">
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<a class="nav-link" href="../authors.html">
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Authors
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</a>
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
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||||
</ul>
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||||
</li>
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<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
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</ul>
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<form class="form-inline my-2 my-lg-0" role="search">
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<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
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</form>
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<ul class="navbar-nav">
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<li class="nav-item">
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<a class="nav-link" href="../news/index.html">
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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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</li>
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<li class="nav-item">
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<a class="external-link nav-link" href="https://github.com/msberends/AMR">
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<span class="fab fa fab fa-github"></span>
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Source Code
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||||
</a>
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||||
</li>
|
||||
<ul class="navbar-nav">
|
||||
<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
|
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<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
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</ul>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-article">
|
||||
|
||||
@@ -194,9 +84,9 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">23 June 2024</h4>
|
||||
<h4 data-toc-skip class="date">16 July 2024</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -215,43 +105,44 @@ of the data sets look like.</p>
|
||||
<h2 id="microorganisms-full-microbial-taxonomy">
|
||||
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
|
||||
</h2>
|
||||
<p>A data set with 52 171 rows and 23 columns, containing the following
|
||||
<p>A data set with 70 547 rows and 26 columns, containing the following
|
||||
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
|
||||
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
|
||||
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
|
||||
<em>ref</em>, <em>oxygen_tolerance</em>, <em>source</em>, <em>lpsn</em>,
|
||||
<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>,
|
||||
<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>mycobank</em>,
|
||||
<em>mycobank_parent</em>, <em>mycobank_renamed_to</em>, <em>gbif</em>,
|
||||
<em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em>, and
|
||||
<em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after
|
||||
you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 July 2023 08:49:06 UTC. Find more info
|
||||
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original
|
||||
R Data Structure (RDS) file</a> (1.2 MB)<br>
|
||||
R Data Structure (RDS) file</a> (1.6 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
|
||||
text file</a> (11.7 MB)<br>
|
||||
text file</a> (15.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (5.2 MB)<br>
|
||||
Excel workbook</a> (7.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
|
||||
Feather file</a> (5.5 MB)<br>
|
||||
Feather file</a> (19 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache
|
||||
Parquet file</a> (2.6 MB)<br>
|
||||
Parquet file</a> (0 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xpt" class="external-link">SAS
|
||||
transport (XPT) file</a> (48.6 MB)<br>
|
||||
transport (XPT) file</a> (69.5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
|
||||
SPSS Statistics data file</a> (17.8 MB)<br>
|
||||
SPSS Statistics data file</a> (24.5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
|
||||
DTA file</a> (48.6 MB)</li>
|
||||
DTA file</a> (69.5 MB)</li>
|
||||
</ul>
|
||||
<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
|
||||
the first 50 SNOMED codes per record, as their file size would otherwise
|
||||
@@ -263,16 +154,16 @@ all SNOMED codes as comma separated values.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
|
||||
</h3>
|
||||
<p>This data set contains the full microbial taxonomy of five kingdoms
|
||||
<p>This data set contains the full microbial taxonomy of six kingdoms
|
||||
from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
|
||||
and the Global Biodiversity Information Facility (GBIF):</p>
|
||||
<ul>
|
||||
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names
|
||||
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
|
||||
International Journal of Systematic and Evolutionary Microbiology, 70,
|
||||
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on December 11th, 2022.</li>
|
||||
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on June 24th, 2024.</li>
|
||||
<li>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset .
|
||||
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on January 8th, 2024.</li>
|
||||
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on June 24th, 2024.</li>
|
||||
<li>Public Health Information Network Vocabulary Access and Distribution
|
||||
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
|
||||
Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
|
||||
@@ -295,52 +186,55 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Animalia</td>
|
||||
<td align="center">1 379</td>
|
||||
<td align="center">1 713</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Archaea</td>
|
||||
<td align="center">1 314</td>
|
||||
<td align="center">1 418</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Bacteria</td>
|
||||
<td align="center">36 501</td>
|
||||
<td align="center">39 238</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Fungi</td>
|
||||
<td align="center">7 905</td>
|
||||
<td align="center">Chromista</td>
|
||||
<td align="center">164</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Protozoa</td>
|
||||
<td align="center">5 071</td>
|
||||
<td align="center">Fungi</td>
|
||||
<td align="center">19 878</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
|
||||
<table class="table">
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="3%">
|
||||
<col width="7%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="4%">
|
||||
<col width="5%">
|
||||
<col width="4%">
|
||||
<col width="5%">
|
||||
<col width="3%">
|
||||
<col width="4%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="6%">
|
||||
<col width="7%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="4%">
|
||||
<col width="4%">
|
||||
<col width="4%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="5%">
|
||||
<col width="6%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="4%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="11%">
|
||||
<col width="2%">
|
||||
<col width="10%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">mo</th>
|
||||
@@ -361,6 +255,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<th align="center">lpsn</th>
|
||||
<th align="center">lpsn_parent</th>
|
||||
<th align="center">lpsn_renamed_to</th>
|
||||
<th align="center">mycobank</th>
|
||||
<th align="center">mycobank_parent</th>
|
||||
<th align="center">mycobank_renamed_to</th>
|
||||
<th align="center">gbif</th>
|
||||
<th align="center">gbif_parent</th>
|
||||
<th align="center">gbif_renamed_to</th>
|
||||
@@ -387,7 +284,10 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center">515602</td>
|
||||
<td align="center">482</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">3221780</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">11158430</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1.0</td>
|
||||
@@ -407,7 +307,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center"></td>
|
||||
<td align="center">species</td>
|
||||
<td align="center">Leclerc, 1962</td>
|
||||
<td align="center">aerobe</td>
|
||||
<td align="center">likely facultative anaerobe</td>
|
||||
<td align="center">LPSN</td>
|
||||
<td align="center">776052</td>
|
||||
<td align="center">515602</td>
|
||||
@@ -415,6 +315,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1.0</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
@@ -432,13 +335,16 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center"></td>
|
||||
<td align="center">species</td>
|
||||
<td align="center">Huys et al., 2003</td>
|
||||
<td align="center">aerobe</td>
|
||||
<td align="center">facultative anaerobe</td>
|
||||
<td align="center">LPSN</td>
|
||||
<td align="center">776053</td>
|
||||
<td align="center">515602</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">5427575</td>
|
||||
<td align="center">3221780</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1.0</td>
|
||||
<td align="center">419388003</td>
|
||||
@@ -465,6 +371,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1.5</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
@@ -487,15 +396,18 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center">776057</td>
|
||||
<td align="center">515602</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">11286021</td>
|
||||
<td align="center">3221780</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1.0</td>
|
||||
<td align="center">1095001000112106, 715307006, 737528008, …</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">B_ESCHR_DYSN</td>
|
||||
<td align="center">Escherichia dysenteriae</td>
|
||||
<td align="center">B_ESCHR_COLI_COLI</td>
|
||||
<td align="center">Escherichia coli coli</td>
|
||||
<td align="center">accepted</td>
|
||||
<td align="center">Bacteria</td>
|
||||
<td align="center">Pseudomonadota</td>
|
||||
@@ -503,19 +415,22 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center">Enterobacteriaceae</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">dysenteriae</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">subspecies</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">species</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">likely facultative anaerobe</td>
|
||||
<td align="center">GBIF</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">10862979</td>
|
||||
<td align="center">3221780</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1.5</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">12233256</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1.0</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@@ -912,7 +827,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
|
||||
<em>breakpoint_R</em>, <em>uti</em>, and <em>is_SDD</em>.</p>
|
||||
<p>This data set is in R available as <code>clinical_breakpoints</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 19 June 2024 13:08:23 UTC. Find more info
|
||||
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
@@ -923,7 +838,7 @@ R Data Structure (RDS) file</a> (70 kB)<br>
|
||||
text file</a> (3.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (1.7 MB)<br>
|
||||
Excel workbook</a> (2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
|
||||
Feather file</a> (4.9 MB)<br>
|
||||
@@ -1125,37 +1040,37 @@ use.</p>
|
||||
<code>intrinsic_resistant</code>: Intrinsic Bacterial
|
||||
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
|
||||
</h2>
|
||||
<p>A data set with 134 634 rows and 2 columns, containing the following
|
||||
<p>A data set with 340 804 rows and 2 columns, containing the following
|
||||
column names:<br><em>mo</em> and <em>ab</em>.</p>
|
||||
<p>This data set is in R available as <code>intrinsic_resistant</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 16 December 2022 15:10:43 UTC. Find more info
|
||||
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original
|
||||
R Data Structure (RDS) file</a> (78 kB)<br>
|
||||
R Data Structure (RDS) file</a> (0.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated
|
||||
text file</a> (5.1 MB)<br>
|
||||
text file</a> (12.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (1.3 MB)<br>
|
||||
Excel workbook</a> (3.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache
|
||||
Feather file</a> (1.2 MB)<br>
|
||||
Feather file</a> (13.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache
|
||||
Parquet file</a> (0.2 MB)<br>
|
||||
Parquet file</a> (0 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xpt" class="external-link">SAS
|
||||
transport (XPT) file</a> (9.5 MB)<br>
|
||||
transport (XPT) file</a> (28.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM
|
||||
SPSS Statistics data file</a> (7.4 MB)<br>
|
||||
SPSS Statistics data file</a> (18.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
|
||||
DTA file</a> (9.5 MB)</li>
|
||||
DTA file</a> (28.3 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
|
||||
@@ -2188,7 +2103,7 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
|
||||
column names:<br><em>code</em> and <em>mo</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms.codes</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 16 June 2024 09:28:56 UTC. Find more info
|
||||
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
@@ -2199,7 +2114,7 @@ R Data Structure (RDS) file</a> (22 kB)<br>
|
||||
text file</a> (0.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (91 kB)<br>
|
||||
Excel workbook</a> (82 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.feather" class="external-link">Apache
|
||||
Feather file</a> (0.1 MB)<br>
|
||||
@@ -2259,7 +2174,7 @@ laboratory systems and <a href="https://whonet.org" class="external-link">WHONET
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
</nav></aside>
|
||||
</div>
|
||||
|
||||
@@ -2276,9 +2191,9 @@ laboratory systems and <a href="https://whonet.org" class="external-link">WHONET
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
+33
-139
@@ -1,155 +1,49 @@
|
||||
<!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, shrink-to-fit=no"><title>Articles • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<!-- 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, shrink-to-fit=no"><title>Articles • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"></head><body>
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Conduct AMR Analysis
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Generate Antibiogram (Trad./Syndromic/WISCA)
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict Antimicrobial Resistance
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/datasets.html">
|
||||
<span class="fa fa-database"></span>
|
||||
|
||||
Download Data Sets for Own Use
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/AMR-options.html">
|
||||
<span class="fa fa-gear"></span>
|
||||
|
||||
Set User- Or Team-specific Package Settings
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct Principal Component Analysis for AMR
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine Multi-Drug Resistance (MDR)
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET Data
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
||||
|
||||
Apply Eucast Rules
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get Taxonomy of a Microorganism
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antibiotic Drug
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antiviral Drug
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul></li>
|
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<li class="nav-item dropdown">
|
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
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<span class="fa fa-layer-group"></span>
|
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|
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With other pkgs
|
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</a>
|
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
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|
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AMR & dplyr/tidyverse
|
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</a>
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
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|
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AMR & data.table
|
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</a>
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
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|
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AMR & tidymodels
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</a>
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
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|
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AMR & base R
|
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</a>
|
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</div>
|
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</li>
|
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<li class="nav-item">
|
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<a class="nav-link" href="../reference/index.html">
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<span class="fa fa-book-open"></span>
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<a class="nav-link" href="../authors.html">
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Authors
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|
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</ul><form class="form-inline my-2 my-lg-0" role="search">
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<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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<a class="nav-link" href="../news/index.html">
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<span class="far fa far fa-newspaper"></span>
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Source Code
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
|
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs"><li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
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</ul></li>
|
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<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
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</ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
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<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
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</ul></div>
|
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|
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|
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|
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</div>
|
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</nav><div class="container template-article-index">
|
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<div class="row">
|
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@@ -193,9 +87,9 @@
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</footer></div>
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</body></html>
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+39
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@@ -5,7 +5,6 @@
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<title>Using AMR with other packages: AMR & dplyr/tidyverse • AMR (for R)</title>
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<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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@@ -17,31 +16,22 @@
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<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
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<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
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<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
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<!-- 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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<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
||||
<link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
|
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<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
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<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
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<script src="../extra.js"></script><meta property="og:title" content="Using AMR with other packages: AMR & dplyr/tidyverse">
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<meta name="twitter:creator" content="@msberends">
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<meta name="twitter:site" content="@msberends">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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<![endif]-->
|
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</head>
|
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<body>
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<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -49,141 +39,41 @@
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<div id="navbar" class="collapse navbar-collapse ms-3">
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<ul class="navbar-nav me-auto">
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<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
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<span class="fa fa-question-circle"></span>
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How to
|
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</a>
|
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<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
|
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<a class="dropdown-item" href="../articles/AMR.html">
|
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<span class="fa fa-directions"></span>
|
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|
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Conduct AMR Analysis
|
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</a>
|
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<a class="dropdown-item" href="../reference/antibiogram.html">
|
||||
<span class="fa fa-file-prescription"></span>
|
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|
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Generate Antibiogram (Trad./Syndromic/WISCA)
|
||||
</a>
|
||||
<a class="dropdown-item" 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>
|
||||
<a class="dropdown-item" href="../articles/datasets.html">
|
||||
<span class="fa fa-database"></span>
|
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|
||||
Download Data Sets for Own Use
|
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</a>
|
||||
<a class="dropdown-item" href="../reference/AMR-options.html">
|
||||
<span class="fa fa-gear"></span>
|
||||
|
||||
Set User- Or Team-specific Package Settings
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct Principal Component Analysis for AMR
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine Multi-Drug Resistance (MDR)
|
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</a>
|
||||
<a class="dropdown-item" href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET Data
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
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|
||||
Apply Eucast Rules
|
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</a>
|
||||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get Taxonomy of a Microorganism
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antibiotic Drug
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antiviral Drug
|
||||
</a>
|
||||
</div>
|
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
|
||||
<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul>
|
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</li>
|
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<li class="active nav-item dropdown">
|
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
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<span class="fa fa-layer-group"></span>
|
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|
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With other pkgs
|
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</a>
|
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
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AMR & dplyr/tidyverse
|
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</a>
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<a class="dropdown-item" href="../articles/other_pkg.html">
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AMR & data.table
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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AMR & tidymodels
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</a>
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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AMR & base R
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<li class="nav-item">
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
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<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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</div>
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</nav><div class="container template-article">
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@@ -195,7 +85,7 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Using AMR with other packages: AMR & dplyr/tidyverse</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/other_pkg.Rmd" class="external-link"><code>vignettes/other_pkg.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/other_pkg.Rmd" class="external-link"><code>vignettes/other_pkg.Rmd</code></a></small>
|
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<div class="d-none name"><code>other_pkg.Rmd</code></div>
|
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</div>
|
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@@ -220,9 +110,9 @@ used to working in <code>dplyr</code> or other tidyverse packages.</p>
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</footer>
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@@ -17,31 +16,22 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
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@@ -49,141 +39,41 @@
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<ul class="navbar-nav me-auto">
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<span class="fa fa-question-circle"></span>
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How to
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</a>
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<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
|
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<a class="dropdown-item" 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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<a class="dropdown-item" href="../reference/antibiogram.html">
|
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<span class="fa fa-file-prescription"></span>
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Generate Antibiogram (Trad./Syndromic/WISCA)
|
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</a>
|
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<a class="dropdown-item" href="../articles/resistance_predict.html">
|
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<span class="fa fa-dice"></span>
|
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|
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Predict Antimicrobial Resistance
|
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</a>
|
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<a class="dropdown-item" href="../articles/datasets.html">
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Download Data Sets for Own Use
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Set User- Or Team-specific Package Settings
|
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</a>
|
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<a class="dropdown-item" 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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<a class="dropdown-item" href="../articles/MDR.html">
|
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<span class="fa fa-skull-crossbones"></span>
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|
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Determine Multi-Drug Resistance (MDR)
|
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</a>
|
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<a class="dropdown-item" href="../articles/WHONET.html">
|
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<span class="fa fa-globe-americas"></span>
|
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Work with WHONET Data
|
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|
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<a class="dropdown-item" href="../articles/EUCAST.html">
|
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<span class="fa fa-exchange-alt"></span>
|
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|
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Apply Eucast Rules
|
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</a>
|
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<a class="dropdown-item" href="../reference/mo_property.html">
|
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<span class="fa fa-bug"></span>
|
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Get Taxonomy of a Microorganism
|
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</a>
|
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<a class="dropdown-item" href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
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|
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Get Properties of an Antibiotic Drug
|
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</a>
|
||||
<a class="dropdown-item" href="../reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
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|
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Get Properties of an Antiviral Drug
|
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</a>
|
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</div>
|
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
|
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
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<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
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<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
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<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
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</ul>
|
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</li>
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<li class="nav-item dropdown">
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With other pkgs
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
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<a class="dropdown-item" href="../articles/other_pkg.html">
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AMR & dplyr/tidyverse
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</a>
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AMR & tidymodels
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<a class="dropdown-item" href="../articles/other_pkg.html">
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
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<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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|
||||
</nav><div class="container template-article">
|
||||
|
||||
@@ -195,7 +85,7 @@
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>How to predict antimicrobial resistance</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>resistance_predict.Rmd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -362,16 +252,15 @@ model might be more appropriate:</p>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> Family: binomial </span></span>
|
||||
<span><span class="co">#> Link function: logit</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co">#> Link function: logit</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span></span>
|
||||
<span><span class="co">#> Estimate Std. Error z value Pr(>|z|)</span></span>
|
||||
<span><span class="co">#> (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span></span>
|
||||
<span><span class="co">#> year 0.09883005 0.02295317 4.305725 1.664395e-05</span></span></code></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
</nav></aside>
|
||||
</div>
|
||||
|
||||
@@ -388,9 +277,9 @@ model might be more appropriate:</p>
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
+40
-150
@@ -5,7 +5,6 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
||||
<meta name="description" content="AMR">
|
||||
<title>Welcome to the `AMR` package • 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">
|
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@@ -17,31 +16,22 @@
|
||||
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
|
||||
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
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||||
<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
|
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|
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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">
|
||||
<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
||||
<link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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||||
<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
|
||||
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script><meta property="og:title" content="Welcome to the `AMR` package">
|
||||
<meta property="og:description" content="AMR">
|
||||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
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<meta name="twitter:card" content="summary_large_image">
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<meta name="twitter:creator" content="@msberends">
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<meta name="twitter:site" content="@msberends">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
<![endif]-->
|
||||
</head>
|
||||
<body>
|
||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||
|
||||
|
||||
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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||||
|
||||
|
||||
<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
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<span class="navbar-toggler-icon"></span>
|
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</button>
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@@ -49,141 +39,41 @@
|
||||
<div id="navbar" class="collapse navbar-collapse ms-3">
|
||||
<ul class="navbar-nav me-auto">
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
|
||||
<a class="dropdown-item" href="../articles/AMR.html">
|
||||
<span class="fa fa-directions"></span>
|
||||
|
||||
Conduct AMR Analysis
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/antibiogram.html">
|
||||
<span class="fa fa-file-prescription"></span>
|
||||
|
||||
Generate Antibiogram (Trad./Syndromic/WISCA)
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict Antimicrobial Resistance
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/datasets.html">
|
||||
<span class="fa fa-database"></span>
|
||||
|
||||
Download Data Sets for Own Use
|
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</a>
|
||||
<a class="dropdown-item" href="../reference/AMR-options.html">
|
||||
<span class="fa fa-gear"></span>
|
||||
|
||||
Set User- Or Team-specific Package Settings
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct Principal Component Analysis for AMR
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine Multi-Drug Resistance (MDR)
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
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Work with WHONET Data
|
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</a>
|
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<a class="dropdown-item" href="../articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
||||
|
||||
Apply Eucast Rules
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get Taxonomy of a Microorganism
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antibiotic Drug
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antiviral Drug
|
||||
</a>
|
||||
</div>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
|
||||
<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="../reference/index.html">
|
||||
<span class="fa fa-book-open"></span>
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||||
Manual
|
||||
</a>
|
||||
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|
||||
<a class="nav-link" href="../authors.html">
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Authors
|
||||
</a>
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
|
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<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
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<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
|
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<form class="form-inline my-2 my-lg-0" role="search">
|
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<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
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Changelog
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|
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Source Code
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<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
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<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
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</div>
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|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-article">
|
||||
|
||||
@@ -195,7 +85,7 @@
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Welcome to the `AMR` package</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>welcome_to_AMR.Rmd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -222,7 +112,7 @@ this a successful and durable project!</p>
|
||||
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
||||
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
|
||||
10.33612/diss.192486375</a>).</p>
|
||||
<p>After installing this package, R knows ~52 000 distinct microbial
|
||||
<p>After installing this package, R knows ~71 000 distinct microbial
|
||||
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
|
||||
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
|
||||
CT), and knows all about valid SIR and MIC values. The integral
|
||||
@@ -313,9 +203,9 @@ included with the package. </small></p>
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
+49
-154
@@ -1,155 +1,49 @@
|
||||
<!DOCTYPE html>
|
||||
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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<a class="dropdown-item" href="articles/AMR.html">
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Conduct AMR Analysis
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<span class="fa fa-file-prescription"></span>
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<span class="fa fa-dice"></span>
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Conduct Principal Component Analysis for AMR
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<span class="fa fa-skull-crossbones"></span>
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Get Taxonomy of a Microorganism
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</a>
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<a class="dropdown-item" href="reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get Properties of an Antibiotic Drug
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</a>
|
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<a class="dropdown-item" href="reference/av_property.html">
|
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<span class="fa fa-capsules"></span>
|
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Get Properties of an Antiviral Drug
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</a>
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</div>
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</li>
|
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<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
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<li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
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<li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
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<li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
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<li><a class="dropdown-item" href="articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul></li>
|
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<li class="nav-item dropdown">
|
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
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<span class="fa fa-layer-group"></span>
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|
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With other pkgs
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</a>
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
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<a class="dropdown-item" href="articles/other_pkg.html">
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<span class="fa fa-layer-group"></span>
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|
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AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
||||
|
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AMR & data.table
|
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</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
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<span class="fa fa-layer-group"></span>
|
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|
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AMR & tidymodels
|
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</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="reference/index.html">
|
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<span class="fa fa-book-open"></span>
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Manual
|
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</a>
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</li>
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<li class="active nav-item">
|
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<a class="nav-link" href="authors.html">
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<span class="fa fa-users"></span>
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|
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Authors
|
||||
</a>
|
||||
</li>
|
||||
</ul><form class="form-inline my-2 my-lg-0" role="search">
|
||||
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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|
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<a class="nav-link" href="news/index.html">
|
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<span class="far fa far fa-newspaper"></span>
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|
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Changelog
|
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</a>
|
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<li class="nav-item">
|
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<a class="external-link nav-link" href="https://github.com/msberends/AMR">
|
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<span class="fab fa fab fa-github"></span>
|
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|
||||
Source Code
|
||||
</a>
|
||||
</li>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs"><li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
||||
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
|
||||
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
||||
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
||||
</ul></li>
|
||||
<li class="nav-item"><a class="nav-link" href="reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
|
||||
<li class="active nav-item"><a class="nav-link" href="authors.html"><span class="fa fa-users"></span> Authors</a></li>
|
||||
</ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
|
||||
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
||||
</ul></div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-citation-authors">
|
||||
<div class="row">
|
||||
@@ -157,9 +51,9 @@
|
||||
<img src="logo.svg" class="logo" alt=""><h1>Authors and Citation</h1>
|
||||
</div>
|
||||
|
||||
<div class="section level2 citation">
|
||||
<div class="section level2">
|
||||
<h2>Authors</h2>
|
||||
|
||||
|
||||
<ul class="list-unstyled"><li>
|
||||
<p><strong>Matthijs S. Berends</strong>. Author, maintainer. <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
@@ -169,7 +63,7 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Erwin E. A. Hassing</strong>. Author, contributor.
|
||||
<p><strong>Erwin E. A. Hassing</strong>. Author, contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -181,7 +75,7 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Judith M. Fonville</strong>. Contributor.
|
||||
<p><strong>Judith M. Fonville</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -193,7 +87,7 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Eric H. L. C. M. Hazenberg</strong>. Contributor.
|
||||
<p><strong>Eric H. L. C. M. Hazenberg</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -209,15 +103,15 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Bart C. Meijer</strong>. Contributor.
|
||||
<p><strong>Bart C. Meijer</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Dmytro Mykhailenko</strong>. Contributor.
|
||||
<p><strong>Dmytro Mykhailenko</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Anton Mymrikov</strong>. Contributor.
|
||||
<p><strong>Anton Mymrikov</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -229,11 +123,11 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Matthew Saab</strong>. Contributor.
|
||||
<p><strong>Matthew Saab</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Jonas Salm</strong>. Contributor.
|
||||
<p><strong>Jonas Salm</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -241,7 +135,7 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Rogier P. Schade</strong>. Contributor.
|
||||
<p><strong>Rogier P. Schade</strong>. Contributor.
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -262,14 +156,14 @@
|
||||
</li>
|
||||
</ul></div>
|
||||
|
||||
<div class="section level2 citation">
|
||||
<div class="section level2">
|
||||
<h2 id="citation">Citation</h2>
|
||||
<p><small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
|
||||
<p><small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
|
||||
|
||||
<p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022).
|
||||
“AMR: An R Package for Working with Antimicrobial Resistance Data.”
|
||||
<em>Journal of Statistical Software</em>, <b>104</b>(3), 1–31.
|
||||
<a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>.
|
||||
<a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>.
|
||||
</p>
|
||||
<pre>@Article{,
|
||||
title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},
|
||||
@@ -282,7 +176,8 @@
|
||||
doi = {10.18637/jss.v104.i03},
|
||||
}</pre>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
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|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
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|
Before Width: | Height: | Size: 97 KiB |
@@ -7,9 +7,9 @@
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# PLEASE CITE THIS SOFTWARE AS: #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
|
||||
# Journal of Statistical Software, 104(3), 1-31. #
|
||||
# https://doi.org/10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen and the University Medical #
|
||||
|
||||
@@ -7,9 +7,9 @@
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# PLEASE CITE THIS SOFTWARE AS: #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
|
||||
# Journal of Statistical Software, 104(3), 1-31. #
|
||||
# https://doi.org/10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen and the University Medical #
|
||||
|
||||
+39
-143
@@ -5,7 +5,6 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
||||
<meta name="description" content="Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.">
|
||||
<title>Antimicrobial Resistance Data Analysis • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
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||||
<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
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<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/Lato-0.4.9/font.css" rel="stylesheet">
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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">
|
||||
<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
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<link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
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<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
|
||||
<script src="extra.js"></script><meta property="og:title" content="Antimicrobial Resistance Data Analysis">
|
||||
<meta name="description" content="Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.">
|
||||
<meta property="og:description" content="Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.">
|
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<![endif]-->
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</head>
|
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<body>
|
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<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||
|
||||
|
||||
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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|
||||
<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<span class="navbar-toggler-icon"></span>
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</button>
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@@ -49,141 +45,41 @@
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<div id="navbar" class="collapse navbar-collapse ms-3">
|
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<ul class="navbar-nav me-auto">
|
||||
<li class="nav-item dropdown">
|
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
|
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<span class="fa fa-question-circle"></span>
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How to
|
||||
</a>
|
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<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
|
||||
<a class="dropdown-item" href="articles/AMR.html">
|
||||
<span class="fa fa-directions"></span>
|
||||
|
||||
Conduct AMR Analysis
|
||||
</a>
|
||||
<a class="dropdown-item" href="reference/antibiogram.html">
|
||||
<span class="fa fa-file-prescription"></span>
|
||||
|
||||
Generate Antibiogram (Trad./Syndromic/WISCA)
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict Antimicrobial Resistance
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/datasets.html">
|
||||
<span class="fa fa-database"></span>
|
||||
|
||||
Download Data Sets for Own Use
|
||||
</a>
|
||||
<a class="dropdown-item" href="reference/AMR-options.html">
|
||||
<span class="fa fa-gear"></span>
|
||||
|
||||
Set User- Or Team-specific Package Settings
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct Principal Component Analysis for AMR
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine Multi-Drug Resistance (MDR)
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET Data
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
||||
|
||||
Apply Eucast Rules
|
||||
</a>
|
||||
<a class="dropdown-item" href="reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get Taxonomy of a Microorganism
|
||||
</a>
|
||||
<a class="dropdown-item" href="reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antibiotic Drug
|
||||
</a>
|
||||
<a class="dropdown-item" href="reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antiviral Drug
|
||||
</a>
|
||||
</div>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
|
||||
<li><a class="dropdown-item" href="articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
||||
<li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
||||
<li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
||||
<li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||||
<li><a class="dropdown-item" href="articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="reference/index.html">
|
||||
<span class="fa fa-book-open"></span>
|
||||
|
||||
Manual
|
||||
</a>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="authors.html">
|
||||
<span class="fa fa-users"></span>
|
||||
|
||||
Authors
|
||||
</a>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
|
||||
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
||||
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
|
||||
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
||||
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="nav-item"><a class="nav-link" href="reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
|
||||
<li class="nav-item"><a class="nav-link" href="authors.html"><span class="fa fa-users"></span> Authors</a></li>
|
||||
</ul>
|
||||
<form class="form-inline my-2 my-lg-0" role="search">
|
||||
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
|
||||
</form>
|
||||
|
||||
<ul class="navbar-nav">
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="news/index.html">
|
||||
<span class="far fa far fa-newspaper"></span>
|
||||
|
||||
Changelog
|
||||
</a>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="external-link nav-link" href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa fab fa-github"></span>
|
||||
|
||||
Source Code
|
||||
</a>
|
||||
</li>
|
||||
<ul class="navbar-nav">
|
||||
<li class="nav-item"><a class="nav-link" href="news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
|
||||
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-home">
|
||||
<div class="row">
|
||||
@@ -872,9 +768,9 @@
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
@@ -0,0 +1,14 @@
|
||||
// https://github.com/jgm/pandoc/blob/29fa97ab96b8e2d62d48326e1b949a71dc41f47a/src/Text/Pandoc/Writers/HTML.hs#L332-L345
|
||||
document.addEventListener("DOMContentLoaded", function () {
|
||||
var mathElements = document.getElementsByClassName("math");
|
||||
var macros = [];
|
||||
for (var i = 0; i < mathElements.length; i++) {
|
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var texText = mathElements[i].firstChild;
|
||||
if (mathElements[i].tagName == "SPAN") {
|
||||
katex.render(texText.data, mathElements[i], {
|
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displayMode: mathElements[i].classList.contains("display"),
|
||||
throwOnError: false,
|
||||
macros: macros,
|
||||
fleqn: false
|
||||
});
|
||||
}}});
|
||||
@@ -1,6 +0,0 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<svg version="1.0" xmlns="http://www.w3.org/2000/svg" width="900" height="600">
|
||||
<rect width="900" height="600" fill="#d7141a"/>
|
||||
<rect width="900" height="300" fill="#fff"/>
|
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<path d="M 450,300 0,0 V 600 z" fill="#11457e"/>
|
||||
</svg>
|
||||
|
Before Width: | Height: | Size: 275 B |
@@ -1 +0,0 @@
|
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<?xml version="1.0" encoding="UTF-8"?><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 37 28"><path fill="#c60c30" d="M0,0H37V28H0Z"/><path fill="#fff" d="M0,12H12V0H16V12H37V16H16V28H12V16H0Z"/></svg>
|
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|
Before Width: | Height: | Size: 205 B |
@@ -1,9 +0,0 @@
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
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<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
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"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
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||||
<svg xmlns="http://www.w3.org/2000/svg" width="1000" height="600" viewBox="0 0 5 3">
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<desc>Flag of Germany</desc>
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<rect id="black_stripe" width="5" height="3" y="0" x="0" fill="#000"/>
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<rect id="red_stripe" width="5" height="2" y="1" x="0" fill="#D00"/>
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<rect id="gold_stripe" width="5" height="1" y="2" x="0" fill="#FFCE00"/>
|
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</svg>
|
||||
|
Before Width: | Height: | Size: 502 B |
@@ -1,5 +0,0 @@
|
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<?xml version="1.0" encoding="UTF-8"?>
|
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<svg xmlns="http://www.w3.org/2000/svg" width="600" height="400" viewBox="0 0 27 18">
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<rect fill="#0D5EAF" width="27" height="18"/>
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<path fill="none" stroke-width="2" stroke="#FFF" d="M5,0V11 M0,5H10 M10,3H27 M10,7H27 M0,11H27 M0,15H27"/>
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</svg>
|
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|
Before Width: | Height: | Size: 284 B |
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|
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<?xml version="1.0"?>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 60 30" width="1200" height="600">
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<clipPath id="s">
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<path d="M0,0 v30 h60 v-30 z"/>
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</clipPath>
|
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<clipPath id="t">
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<path d="M30,15 h30 v15 z v15 h-30 z h-30 v-15 z v-15 h30 z"/>
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</clipPath>
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<g clip-path="url(#s)">
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<path d="M0,0 v30 h60 v-30 z" fill="#012169"/>
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<path d="M0,0 L60,30 M60,0 L0,30" stroke="#fff" stroke-width="6"/>
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<path d="M0,0 L60,30 M60,0 L0,30" clip-path="url(#t)" stroke="#C8102E" stroke-width="4"/>
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<path d="M30,0 v30 M0,15 h60" stroke="#fff" stroke-width="10"/>
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<path d="M30,0 v30 M0,15 h60" stroke="#C8102E" stroke-width="6"/>
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</g>
|
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</svg>
|
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|
Before Width: | Height: | Size: 641 B |
-406
@@ -1,406 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" height="500" width="750">
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<rect width="750" height="500" fill="#c60b1e"/>
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<rect width="750" height="250" y="125" fill="#ffc400"/>
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<g id="coa" stroke="#000" stroke-width="0.39">
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<g id="supporters">
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<g id="crown_left" stroke-width="0.26">
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* Licensed under the Creative Commons Attribution 3.0 Unported License.
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const themeSwitcher = document.querySelector('#dropdown-lightswitch')
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if (!themeSwitcher) {
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return
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}
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themeSwitcher.setAttribute('aria-label', activeLabel)
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themeSwitcher.querySelector('span').classList.value = activeIcon;
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themeSwitcher.focus()
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const storedTheme = getStoredTheme()
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if (storedTheme !== 'light' && storedTheme !== 'dark') {
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setTheme(getPreferredTheme())
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window.addEventListener('DOMContentLoaded', () => {
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showActiveTheme(getPreferredTheme())
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document
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toggle.addEventListener('click', () => {
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setTheme(theme)
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setStoredTheme(theme)
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showActiveTheme(theme, true)
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setTheme(getPreferredTheme());
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bsSetupThemeToggle();
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||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9061" id="amr-2119061">AMR 2.1.1.9061<a class="anchor" aria-label="anchor" href="#amr-2119061"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9063" id="amr-2119063">AMR 2.1.1.9063<a class="anchor" aria-label="anchor" href="#amr-2119063"></a></h2>
|
||||
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
|
||||
<div class="section level5">
|
||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9061">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9061"></a></h5>
|
||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9063">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9063"></a></h5>
|
||||
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="breaking-2-1-1-9061">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9061"></a></h3>
|
||||
<h3 id="breaking-2-1-1-9063">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9063"></a></h3>
|
||||
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="new-2-1-1-9061">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9061"></a></h3>
|
||||
<h3 id="new-2-1-1-9063">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9063"></a></h3>
|
||||
<ul><li>One Health implementation
|
||||
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
||||
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
|
||||
@@ -186,15 +80,24 @@
|
||||
<code><a href="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “NI” for non-interpretable and “SDD” for susceptible dose-dependent. Currently, the <code>clinical_breakpoints</code> data set contains 24 breakpoints that can return the value “SDD” instead of “I”.</li>
|
||||
</ul></li>
|
||||
<li>MIC plotting and transforming
|
||||
<ul><li>The function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
|
||||
<li>Function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
|
||||
<ul><li>New function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
|
||||
<li>New function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
|
||||
</ul></li>
|
||||
<li>Microbiological taxonomy (<code>microorganisms</code> data set) updated to June 2024, with some exciting new features:
|
||||
<ul><li>Added MycoBank as the primary taxonomic source for fungi
|
||||
<ul><li>The <code>microorganisms</code> data set now contains additional columns <code>mycobank</code>, <code>mycobank_parent</code>, and <code>mycobank_renamed_to</code>
|
||||
</li>
|
||||
<li>New function <code><a href="../reference/mo_property.html">mo_mycobank()</a></code> to get the MycoBank record number, analogous to existing functions <code><a href="../reference/mo_property.html">mo_lpsn()</a></code> and <code><a href="../reference/mo_property.html">mo_gbif()</a></code>
|
||||
</li>
|
||||
</ul></li>
|
||||
<li>We’ve welcomed over 2,000 records from 2023, over 900 from 2024, and many thousands of new fungi</li>
|
||||
</ul></li>
|
||||
<li>Other
|
||||
<ul><li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
|
||||
<ul><li>New function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
|
||||
</ul></li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="changed-2-1-1-9061">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9061"></a></h3>
|
||||
<h3 id="changed-2-1-1-9063">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9063"></a></h3>
|
||||
<ul><li>SIR interpretation
|
||||
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
||||
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
|
||||
@@ -231,9 +134,10 @@
|
||||
<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy</li>
|
||||
<li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy. Specifically, more weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species.</li>
|
||||
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
|
||||
<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="other-2-1-1-9061">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9061"></a></h3>
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||||
<h3 id="other-2-1-1-9063">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9063"></a></h3>
|
||||
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
|
||||
</ul></div>
|
||||
</div>
|
||||
@@ -455,7 +359,7 @@
|
||||
</ul><hr><p>This changelog only contains changes from AMR v2.0 (January 2023) and later. For prior versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our archive</a>.</p>
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</div>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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</nav></aside></div>
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</footer></div>
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</body></html>
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@@ -152,5 +152,3 @@ async function searchFuse(query, callback) {
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});
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});
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})(window.jQuery || window.$)
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+2
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pandoc: 3.1.11
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pkgdown: 2.0.9
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pkgdown: 2.1.0
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pkgdown_sha: ~
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articles:
|
||||
AMR: AMR.html
|
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@@ -11,8 +11,7 @@ articles:
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||||
resistance_predict: resistance_predict.html
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||||
welcome_to_AMR: welcome_to_AMR.html
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WHONET: WHONET.html
|
||||
last_built: 2024-06-23T14:21Z
|
||||
last_built: 2024-07-16T12:57Z
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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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||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
|
||||
<a class="dropdown-item" href="../articles/AMR.html">
|
||||
<span class="fa fa-directions"></span>
|
||||
|
||||
Conduct AMR Analysis
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/antibiogram.html">
|
||||
<span class="fa fa-file-prescription"></span>
|
||||
|
||||
Generate Antibiogram (Trad./Syndromic/WISCA)
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict Antimicrobial Resistance
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/datasets.html">
|
||||
<span class="fa fa-database"></span>
|
||||
|
||||
Download Data Sets for Own Use
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/AMR-options.html">
|
||||
<span class="fa fa-gear"></span>
|
||||
|
||||
Set User- Or Team-specific Package Settings
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct Principal Component Analysis for AMR
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
|
||||
Determine Multi-Drug Resistance (MDR)
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET Data
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
||||
|
||||
Apply Eucast Rules
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get Taxonomy of a Microorganism
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antibiotic Drug
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get Properties of an Antiviral Drug
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||||
</ul></li>
|
||||
<li class="nav-item dropdown">
|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
With other pkgs
|
||||
</a>
|
||||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & dplyr/tidyverse
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & data.table
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & tidymodels
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||||
<span class="fa fa-layer-group"></span>
|
||||
|
||||
AMR & base R
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="../reference/index.html">
|
||||
<span class="fa fa-book-open"></span>
|
||||
|
||||
Manual
|
||||
</a>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="../authors.html">
|
||||
<span class="fa fa-users"></span>
|
||||
|
||||
Authors
|
||||
</a>
|
||||
</li>
|
||||
</ul><form class="form-inline my-2 my-lg-0" role="search">
|
||||
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
|
||||
|
||||
<ul class="navbar-nav"><li class="nav-item">
|
||||
<a class="nav-link" href="../news/index.html">
|
||||
<span class="far fa far fa-newspaper"></span>
|
||||
|
||||
Changelog
|
||||
</a>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="external-link nav-link" href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa fab fa-github"></span>
|
||||
|
||||
Source Code
|
||||
</a>
|
||||
</li>
|
||||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
|
||||
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs"><li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
||||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
||||
</ul></li>
|
||||
<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
|
||||
<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
|
||||
</ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
|
||||
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
||||
</ul></div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-reference-topic">
|
||||
<div class="row">
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Options for the AMR package</h1>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/aa_options.R" class="external-link"><code>R/aa_options.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/aa_options.R" class="external-link"><code>R/aa_options.R</code></a></small>
|
||||
<div class="d-none name"><code>AMR-options.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -166,7 +60,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="options">Options<a class="anchor" aria-label="anchor" href="#options"></a></h2>
|
||||
|
||||
|
||||
|
||||
<ul><li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li>
|
||||
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
|
||||
@@ -183,7 +77,7 @@
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="saving-settings-between-sessions">Saving Settings Between Sessions<a class="anchor" aria-label="anchor" href="#saving-settings-between-sessions"></a></h2>
|
||||
|
||||
|
||||
|
||||
<p>Settings in <span style="R">R</span> are not saved globally and are thus lost when <span style="R">R</span> is exited. You can save your options to your own <code>.Rprofile</code> file, which is a user-specific file. You can edit it using:</p>
|
||||
<p></p><div class="sourceCode r"><pre><code><span> <span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span></code></pre><p></p></div>
|
||||
@@ -203,7 +97,7 @@
|
||||
|
||||
</div>
|
||||
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
</nav></aside></div>
|
||||
|
||||
|
||||
@@ -217,9 +111,9 @@
|
||||
|
||||
</footer></div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body></html>
|
||||
|
||||
@@ -0,0 +1,8 @@
|
||||
<html>
|
||||
<head>
|
||||
<meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/AMR.html" />
|
||||
<meta name="robots" content="noindex">
|
||||
<link rel="canonical" href="https://msberends.github.io/AMR/reference/AMR.html">
|
||||
</head>
|
||||
</html>
|
||||
|
||||
+41
-147
@@ -1,175 +1,69 @@
|
||||
<!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, shrink-to-fit=no"><meta name="description" content="Welcome to the AMR package.
|
||||
<!-- 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, shrink-to-fit=no"><title>The AMR Package — AMR • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta name="description" content="Welcome to the AMR package.
|
||||
The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
|
||||
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
|
||||
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
|
||||
and doi:10.33612/diss.192486375
|
||||
).
|
||||
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><title>The AMR Package — AMR • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package.
|
||||
After installing this package, R knows ~71 000 microorganisms (updated June 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
|
||||
The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
|
||||
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
|
||||
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
|
||||
and doi:10.33612/diss.192486375
|
||||
).
|
||||
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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|
||||
<![endif]--></head><body>
|
||||
After installing this package, R knows ~71 000 microorganisms (updated June 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"></head><body>
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Get Properties of an Antibiotic Drug
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
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<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
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<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs"><li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
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<main id="main" class="col-md-9"><div class="page-header">
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||||
<img src="../logo.svg" class="logo" alt=""><h1>The <code>AMR</code> Package</h1>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/aa_amr-package.R" class="external-link"><code>R/aa_amr-package.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/aa_amr-package.R" class="external-link"><code>R/aa_amr-package.R</code></a></small>
|
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<div class="d-none name"><code>AMR.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -180,7 +74,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
||||
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
|
||||
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
|
||||
).</p>
|
||||
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated January 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (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 public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||||
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~71 000 microorganisms</strong></a> (updated June 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (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 public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||||
<p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
||||
</div>
|
||||
|
||||
@@ -206,7 +100,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
@@ -246,7 +140,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
||||
<li><p>Anita Williams (<a href="https://orcid.org/0000-0002-5295-8451" class="external-link">ORCID</a>) [contributor]</p></li>
|
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</ul></div>
|
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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@@ -260,9 +154,9 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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<img src="../logo.svg" class="logo" alt=""><h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/whocc.R" class="external-link"><code>R/whocc.R</code></a></small>
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<div class="d-none name"><code>WHOCC.Rd</code></div>
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@@ -166,7 +60,7 @@
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<div class="section level2">
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<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
|
||||
|
||||
|
||||
|
||||
<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) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://atcddd.fhi.no" class="external-link">https://atcddd.fhi.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
@@ -189,7 +83,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex" </span>
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</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 500 Isolates - WHONET Example</h1>
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@@ -227,7 +121,7 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Carbapenemase <lgl>, `MRSA screening test` <lgl>, …</span></span>
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