P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 14:27:53 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9063: 640888f

Browse Source
This commit is contained in:
github-actions
2024-07-16 13:00:55 +00:00
parent 1ffdce6eeb
commit 230bbd3722
359 changed files with 16087 additions and 17528 deletions
Download Patch File Download Diff File Expand all files Collapse all files

176
reference/WHONET.html
View File

@ -1,161 +1,55 @@
<!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="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><title>Data Set with 500 Isolates - WHONET Example — WHONET • 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="Data Set with 500 Isolates - WHONET Example — WHONET"><meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><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]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body>
<!-- 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>Data Set with 500 Isolates - WHONET Example — WHONET • 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="Data Set with 500 Isolates - WHONET Example — WHONET"><meta name="description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes."><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>
<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">
<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>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<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
</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 &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; data.table
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; base R
</a>
</div>
</li>
<li class="active 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 &amp; dplyr/tidyverse</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; data.table</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; tidymodels</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; base R</a></li>
</ul></li>
<li class="active 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>Data Set with 500 Isolates - WHONET Example</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>WHONET.Rd</code></div>
</div>
@ -227,7 +121,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Carbapenemase &lt;lgl&gt;, `MRSA screening test` &lt;lgl&gt;, …</span></span>
</code></pre></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>
@ -241,9 +135,9 @@
</footer></div>
</body></html>