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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>Function reference • 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="Function reference"><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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<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><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="">2.1.1.9022</small>
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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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Predict Antimicrobial Resistance
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</a>
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<a class="dropdown-item" href="../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="../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
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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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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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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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</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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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">
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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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<span class="fa fa-layer-group"></span>
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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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<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 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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</a>
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Manual
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Authors
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</a>
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</li>
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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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Changelog
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Source Code
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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>Function reference</h1>
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</div>
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<div class="section level2">
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<h2 id="introduction-to-the-package">Introduction to the package<a class="anchor" aria-label="anchor" href="#introduction-to-the-package"></a></h2>
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<div class="section-desc"><p>Please find the introduction to (and some general information about) our package here.</p></div>
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</div><div id="" class="section level2">
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<dl><dt>
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<code><a href="AMR.html">AMR-package</a></code> <code><a href="AMR.html">AMR</a></code>
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</dt>
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<dd>The <code>AMR</code> Package</dd>
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</dl></div><div class="section level2">
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<h2 id="preparing-data-microorganisms">Preparing data: microorganisms<a class="anchor" aria-label="anchor" href="#preparing-data-microorganisms"></a></h2>
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<div class="section-desc"><p>These functions are meant to get taxonomically valid properties of microorganisms from any input, but also properties derived from taxonomy, such as the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) , or <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganisms, and use `add_custom_microorganisms() to add your own custom microorganisms to this package.</p></div>
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</div><div id="" class="section level2">
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<dl><dt>
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<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_reset_session()</a></code> <code><a href="as.mo.html">mo_cleaning_regex()</a></code>
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</dt>
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<dd>Transform Arbitrary Input to Valid Microbial Taxonomy</dd>
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</dl><dl><dt>
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<code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_pathogenicity()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_oxygen_tolerance()</a></code> <code><a href="mo_property.html">mo_is_anaerobic()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_current()</a></code> <code><a href="mo_property.html">mo_group_members()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code>
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</dt>
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<dd>Get Properties of a Microorganism</dd>
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</dl><dl><dt>
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<code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code> <code><a href="add_custom_microorganisms.html">clear_custom_microorganisms()</a></code>
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</dt>
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<dd>Add Custom Microorganisms</dd>
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</dl><dl><dt>
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<code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code>
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</dt>
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<dd>User-Defined Reference Data Set for Microorganisms</dd>
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</dl></div><div class="section level2">
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<h2 id="preparing-data-antibiotics">Preparing data: antibiotics<a class="anchor" aria-label="anchor" href="#preparing-data-antibiotics"></a></h2>
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<div class="section-desc"><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p></div>
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</div><div id="" class="section level2">
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<dl><dt>
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<code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code>
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</dt>
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<dd>Transform Input to an Antibiotic ID</dd>
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</dl><dl><dt>
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<code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_ddd_units()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> <code><a href="ab_property.html">set_ab_names()</a></code>
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</dt>
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<dd>Get Properties of an Antibiotic</dd>
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</dl><dl><dt>
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<code><a href="ab_from_text.html">ab_from_text()</a></code>
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</dt>
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<dd>Retrieve Antimicrobial Drug Names and Doses from Clinical Text</dd>
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</dl><dl><dt>
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<code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> <code><a href="atc_online.html">atc_online_ddd_units()</a></code>
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</dt>
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<dd>Get ATC Properties from WHOCC Website</dd>
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</dl><dl><dt>
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<code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> <code><a href="add_custom_antimicrobials.html">clear_custom_antimicrobials()</a></code>
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</dt>
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<dd>Add Custom Antimicrobials</dd>
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</dl></div><div class="section level2">
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<h2 id="preparing-data">Preparing data<a class="anchor" aria-label="anchor" href="#preparing-data"></a></h2>
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<div class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></div>
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</div><div id="" class="section level2">
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<dl><dt>
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<code><a href="as.sir.html">as.sir()</a></code> <code><a href="as.sir.html">NA_sir_</a></code> <code><a href="as.sir.html">is.sir()</a></code> <code><a href="as.sir.html">is_sir_eligible()</a></code> <code><a href="as.sir.html">sir_interpretation_history()</a></code>
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</dt>
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<dd>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data</dd>
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</dl><dl><dt>
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<code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">limit_mic_range()</a></code> <code><a href="as.mic.html">droplevels(<i><mic></i>)</a></code>
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</dt>
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<dd>Transform Input to Minimum Inhibitory Concentrations (MIC)</dd>
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</dl><dl><dt>
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<code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">NA_disk_</a></code> <code><a href="as.disk.html">is.disk()</a></code>
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</dt>
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<dd>Transform Input to Disk Diffusion Diameters</dd>
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</dl><dl><dt>
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<code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_dosage()</a></code>
|
||
</dt>
|
||
<dd>Apply EUCAST Rules</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>
|
||
</dt>
|
||
<dd>Define Custom EUCAST Rules</dd>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="analysing-data">Analysing data<a class="anchor" aria-label="anchor" href="#analysing-data"></a></h2>
|
||
|
||
<div class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. With <code><a href="../reference/antibiogram.html">antibiogram()</a></code>, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination antibiogram(WISCA). This function also comes with support for R Markdown and Quarto. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></div>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="antibiogram.html">antibiogram()</a></code> <code><a href="antibiogram.html">plot(<i><antibiogram></i>)</a></code> <code><a href="antibiogram.html">autoplot(<i><antibiogram></i>)</a></code> <code><a href="antibiogram.html">knit_print(<i><antibiogram></i>)</a></code>
|
||
</dt>
|
||
<dd>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">sir_confidence_interval()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">sir_df()</a></code>
|
||
</dt>
|
||
<dd>Calculate Antimicrobial Resistance</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_sir()</a></code> <code><a href="count.html">count_df()</a></code>
|
||
</dt>
|
||
<dd>Count Available Isolates</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="get_episode.html">get_episode()</a></code> <code><a href="get_episode.html">is_new_episode()</a></code>
|
||
</dt>
|
||
<dd>Determine Clinical or Epidemic Episodes</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code>
|
||
</dt>
|
||
<dd>Determine First Isolates</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="key_antimicrobials.html">key_antimicrobials()</a></code> <code><a href="key_antimicrobials.html">all_antimicrobials()</a></code> <code><a href="key_antimicrobials.html">antimicrobials_equal()</a></code>
|
||
</dt>
|
||
<dd>(Key) Antimicrobials for First Weighted Isolates</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">custom_mdro_guideline()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code>
|
||
</dt>
|
||
<dd>Determine Multidrug-Resistant Organisms (MDRO)</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i><bug_drug_combinations></i>)</a></code>
|
||
</dt>
|
||
<dd>Determine Bug-Drug Combinations</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">ab_selector()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">aminopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">antifungals()</a></code> <code><a href="antibiotic_class_selectors.html">antimycobacterials()</a></code> <code><a href="antibiotic_class_selectors.html">betalactams()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">lincosamides()</a></code> <code><a href="antibiotic_class_selectors.html">lipoglycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">oxazolidinones()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">polymyxins()</a></code> <code><a href="antibiotic_class_selectors.html">streptogramins()</a></code> <code><a href="antibiotic_class_selectors.html">quinolones()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> <code><a href="antibiotic_class_selectors.html">trimethoprims()</a></code> <code><a href="antibiotic_class_selectors.html">ureidopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_per_os()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_iv()</a></code> <code><a href="antibiotic_class_selectors.html">not_intrinsic_resistant()</a></code>
|
||
</dt>
|
||
<dd>Antibiotic Selectors</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="mean_amr_distance.html">mean_amr_distance()</a></code> <code><a href="mean_amr_distance.html">amr_distance_from_row()</a></code>
|
||
</dt>
|
||
<dd>Calculate the Mean AMR Distance</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">sir_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_sir_predict()</a></code> <code><a href="resistance_predict.html">autoplot(<i><resistance_predict></i>)</a></code>
|
||
</dt>
|
||
<dd>Predict Antimicrobial Resistance</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="guess_ab_col.html">guess_ab_col()</a></code>
|
||
</dt>
|
||
<dd>Guess Antibiotic Column</dd>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="plotting-data">Plotting data<a class="anchor" aria-label="anchor" href="#plotting-data"></a></h2>
|
||
|
||
<div class="section-desc"><p>Use these functions for the plotting part. The <code>scale_*_mic()</code> functions extend the ggplot2 package to allow plotting of MIC values, even within a manually set range. If using <code><a href="../reference/plot.html">plot()</a></code> (base R) or <code>autoplot()</code> (ggplot2) on MIC values or disk diffusion values, the user can set the interpretation guideline to give the bars the right SIR colours. The <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> function is a short wrapper for users not much accustomed to ggplot2 yet. The <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function is a specific function to plot so-called biplots for PCA (principal component analysis).</p></div>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="plot.html">scale_x_mic()</a></code> <code><a href="plot.html">scale_y_mic()</a></code> <code><a href="plot.html">scale_colour_mic()</a></code> <code><a href="plot.html">scale_fill_mic()</a></code> <code><a href="plot.html">plot(<i><mic></i>)</a></code> <code><a href="plot.html">autoplot(<i><mic></i>)</a></code> <code><a href="plot.html">fortify(<i><mic></i>)</a></code> <code><a href="plot.html">plot(<i><disk></i>)</a></code> <code><a href="plot.html">autoplot(<i><disk></i>)</a></code> <code><a href="plot.html">fortify(<i><disk></i>)</a></code> <code><a href="plot.html">plot(<i><sir></i>)</a></code> <code><a href="plot.html">autoplot(<i><sir></i>)</a></code> <code><a href="plot.html">fortify(<i><sir></i>)</a></code>
|
||
</dt>
|
||
<dd>Plotting for Classes <code>sir</code>, <code>mic</code> and <code>disk</code></dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="ggplot_sir.html">ggplot_sir()</a></code> <code><a href="ggplot_sir.html">geom_sir()</a></code> <code><a href="ggplot_sir.html">facet_sir()</a></code> <code><a href="ggplot_sir.html">scale_y_percent()</a></code> <code><a href="ggplot_sir.html">scale_sir_colours()</a></code> <code><a href="ggplot_sir.html">theme_sir()</a></code> <code><a href="ggplot_sir.html">labels_sir_count()</a></code>
|
||
</dt>
|
||
<dd>AMR Plots with <code>ggplot2</code></dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="ggplot_pca.html">ggplot_pca()</a></code>
|
||
</dt>
|
||
<dd>PCA Biplot with <code>ggplot2</code></dd>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="other-amr-specific-options">Other: AMR-specific options<a class="anchor" aria-label="anchor" href="#other-amr-specific-options"></a></h2>
|
||
|
||
<div class="section-desc"><p>The AMR package is customisable, by providing settings that can be set per user or per team. For example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported language can be set for the whole team (system-language independent) for antibiotic names in a foreign language.</p></div>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="AMR-options.html">AMR-options</a></code>
|
||
</dt>
|
||
<dd>Options for the AMR package</dd>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="other-antiviral-drugs">Other: antiviral drugs<a class="anchor" aria-label="anchor" href="#other-antiviral-drugs"></a></h2>
|
||
|
||
<div class="section-desc"><p>This package also provides extensive support for antiviral agents, even though it is not the primary scope of this package. Working with data containing information about antiviral drugs was never easier. Use these functions to get valid properties of antiviral drugs from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/av_from_text.html">av_from_text()</a></code>.</p></div>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="as.av.html">as.av()</a></code> <code><a href="as.av.html">is.av()</a></code>
|
||
</dt>
|
||
<dd>Transform Input to an Antiviral Drug ID</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="av_property.html">av_name()</a></code> <code><a href="av_property.html">av_cid()</a></code> <code><a href="av_property.html">av_synonyms()</a></code> <code><a href="av_property.html">av_tradenames()</a></code> <code><a href="av_property.html">av_group()</a></code> <code><a href="av_property.html">av_atc()</a></code> <code><a href="av_property.html">av_loinc()</a></code> <code><a href="av_property.html">av_ddd()</a></code> <code><a href="av_property.html">av_ddd_units()</a></code> <code><a href="av_property.html">av_info()</a></code> <code><a href="av_property.html">av_url()</a></code> <code><a href="av_property.html">av_property()</a></code>
|
||
</dt>
|
||
<dd>Get Properties of an Antiviral Drug</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="av_from_text.html">av_from_text()</a></code>
|
||
</dt>
|
||
<dd>Retrieve Antiviral Drug Names and Doses from Clinical Text</dd>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="other-background-information-on-included-data">Other: background information on included data<a class="anchor" aria-label="anchor" href="#other-background-information-on-included-data"></a></h2>
|
||
|
||
<div class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></div>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="example_isolates.html">example_isolates</a></code>
|
||
</dt>
|
||
<dd>Data Set with 2 000 Example Isolates</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="microorganisms.html">microorganisms</a></code>
|
||
</dt>
|
||
<dd>Data Set with 52 171 Microorganisms</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
|
||
</dt>
|
||
<dd>Data Set with 4 957 Common Microorganism Codes</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="microorganisms.groups.html">microorganisms.groups</a></code>
|
||
</dt>
|
||
<dd>Data Set with 521 Microorganisms In Species Groups</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code>
|
||
</dt>
|
||
<dd>Data Sets with 603 Antimicrobial Drugs</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code>
|
||
</dt>
|
||
<dd>Data Set with Bacterial Intrinsic Resistance</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="dosage.html">dosage</a></code>
|
||
</dt>
|
||
<dd>Data Set with Treatment Dosages as Defined by EUCAST</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="WHOCC.html">WHOCC</a></code>
|
||
</dt>
|
||
<dd>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="example_isolates_unclean.html">example_isolates_unclean</a></code>
|
||
</dt>
|
||
<dd>Data Set with Unclean Data</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="clinical_breakpoints.html">clinical_breakpoints</a></code>
|
||
</dt>
|
||
<dd>Data Set with Clinical Breakpoints for SIR Interpretation</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="WHONET.html">WHONET</a></code>
|
||
</dt>
|
||
<dd>Data Set with 500 Isolates - WHONET Example</dd>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="other-miscellaneous-functions">Other: miscellaneous functions<a class="anchor" aria-label="anchor" href="#other-miscellaneous-functions"></a></h2>
|
||
|
||
<div class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></div>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="age_groups.html">age_groups()</a></code>
|
||
</dt>
|
||
<dd>Split Ages into Age Groups</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="age.html">age()</a></code>
|
||
</dt>
|
||
<dd>Age in Years of Individuals</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="availability.html">availability()</a></code>
|
||
</dt>
|
||
<dd>Check Availability of Columns</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="translate.html">get_AMR_locale()</a></code> <code><a href="translate.html">set_AMR_locale()</a></code> <code><a href="translate.html">reset_AMR_locale()</a></code> <code><a href="translate.html">translate_AMR()</a></code>
|
||
</dt>
|
||
<dd>Translate Strings from the AMR Package</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code> <code><a href="italicise_taxonomy.html">italicize_taxonomy()</a></code>
|
||
</dt>
|
||
<dd>Italicise Taxonomic Families, Genera, Species, Subspecies</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code>
|
||
</dt>
|
||
<dd>Join microorganisms to a Data Set</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%unlike%`</a></code> <code><a href="like.html">`%like_case%`</a></code> <code><a href="like.html">`%unlike_case%`</a></code>
|
||
</dt>
|
||
<dd>Vectorised Pattern Matching with Keyboard Shortcut</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="mo_matching_score.html">mo_matching_score()</a></code>
|
||
</dt>
|
||
<dd>Calculate the Matching Score for Microorganisms</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="pca.html">pca()</a></code>
|
||
</dt>
|
||
<dd>Principal Component Analysis (for AMR)</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="random.html">random_mic()</a></code> <code><a href="random.html">random_disk()</a></code> <code><a href="random.html">random_sir()</a></code>
|
||
</dt>
|
||
<dd>Random MIC Values/Disk Zones/SIR Generation</dd>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="other-statistical-tests">Other: statistical tests<a class="anchor" aria-label="anchor" href="#other-statistical-tests"></a></h2>
|
||
|
||
<div class="section-desc"><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p></div>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="g.test.html">g.test()</a></code>
|
||
</dt>
|
||
<dd><em>G</em>-test for Count Data</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="kurtosis.html">kurtosis()</a></code>
|
||
</dt>
|
||
<dd>Kurtosis of the Sample</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="skewness.html">skewness()</a></code>
|
||
</dt>
|
||
<dd>Skewness of the Sample</dd>
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