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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-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/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.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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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<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="">1.8.2.9035</small>
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How to
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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="../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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Data sets for download / own use
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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 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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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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<span class="fa fa-bug"></span>
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Get properties of a microorganism
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Get properties of an antibiotic
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Source Code
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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="preparing-data-microorganisms">Preparing data: microorganisms<a class="anchor" aria-label="anchor" href="#preparing-data-microorganisms"></a></h2>
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<p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganism codes.</p>
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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 Input to a Microorganism Code</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_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_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_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="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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<p class="section-desc"></p><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>
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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 to This Package</dd>
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</dl></div><div class="section level2">
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<h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance<a class="anchor" aria-label="anchor" href="#preparing-data-antimicrobial-resistance"></a></h2>
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<p class="section-desc"></p><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.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI 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>
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</div><div id="" class="section level2">
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<dl><dt>
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<code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_rsi_</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> <code><a href="as.rsi.html">rsi_interpretation_history()</a></code>
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</dt>
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<dd>Interpret MIC and Disk Values, or Clean Raw R/SI 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">NA_mic_</a></code> <code><a href="as.mic.html">is.mic()</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>
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</dt>
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<dd>Apply EUCAST Rules</dd>
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</dl><dl><dt>
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<code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>
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</dt>
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<dd>Define Custom EUCAST Rules</dd>
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</dl></div><div class="section level2">
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<h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance<a class="anchor" aria-label="anchor" href="#analysing-data-antimicrobial-resistance"></a></h2>
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<p class="section-desc"></p><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. 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>
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</div><div id="" class="section level2">
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<dl><dt>
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<code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">rsi_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">rsi_df()</a></code>
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</dt>
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<dd>Calculate Microbial Resistance</dd>
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</dl><dl><dt>
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<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_rsi()</a></code> <code><a href="count.html">count_df()</a></code>
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</dt>
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<dd>Count Available Isolates</dd>
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</dl><dl><dt>
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<code><a href="get_episode.html">get_episode()</a></code> <code><a href="get_episode.html">is_new_episode()</a></code>
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</dt>
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<dd>Determine (New) Episodes for Patients</dd>
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</dl><dl><dt>
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<code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code>
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</dt>
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<dd>Determine First Isolates</dd>
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</dl><dl><dt>
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<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="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><rsi></i>)</a></code> <code><a href="plot.html">autoplot(<i><rsi></i>)</a></code> <code><a href="plot.html">fortify(<i><rsi></i>)</a></code>
|
||
</dt>
|
||
<dd>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code>
|
||
</dt>
|
||
<dd>AMR Plots with <code>ggplot2</code></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>Mean AMR Distance</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_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="background-information-on-included-data">Background information on included data<a class="anchor" aria-label="anchor" href="#background-information-on-included-data"></a></h2>
|
||
|
||
<p class="section-desc"></p><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 id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="AMR.html">AMR</a></code> <code><a href="AMR.html">AMR-package</a></code>
|
||
</dt>
|
||
<dd>The <code>AMR</code> Package</dd>
|
||
</dl><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 48,883 Microorganisms</dd>
|
||
</dl><dl><dt>
|
||
|
||
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
|
||
</dt>
|
||
<dd>Data Set with 5,932 Common Microorganism Codes</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 566 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="rsi_translation.html">rsi_translation</a></code>
|
||
</dt>
|
||
<dd>Data Set for R/SI 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>
|
||
|
||
<p class="section-desc"></p><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 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="ggplot_pca.html">ggplot_pca()</a></code>
|
||
</dt>
|
||
<dd>PCA Biplot with <code>ggplot2</code></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_rsi()</a></code>
|
||
</dt>
|
||
<dd>Random MIC Values/Disk Zones/RSI 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>
|
||
|
||
<p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p>
|
||
|
||
|
||
</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>
|
||
</dl></div><div class="section level2">
|
||
<h2 id="other-deprecated-functions">Other: deprecated functions<a class="anchor" aria-label="anchor" href="#other-deprecated-functions"></a></h2>
|
||
|
||
<p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p>
|
||
|
||
|
||
</div><div id="" class="section level2">
|
||
|
||
|
||
|
||
|
||
<dl><dt>
|
||
|
||
<code><a href="AMR-deprecated.html">AMR-deprecated</a></code>
|
||
</dt>
|
||
<dd>Deprecated Functions</dd>
|
||
</dl></div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
|
||
</div>
|
||
|
||
</footer></div>
|
||
|
||
|
||
|
||
|
||
|
||
</body></html>
|
||
|