P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-30 11:57:51 +02:00
Code Releases Activity
Files
.github
R
data
data-raw
docs
articles
news
reference
figures
AMR-deprecated.html
AMR.html
Rplot001.png
WHOCC.html
WHONET.html
ab_from_text.html
ab_property.html
age.html
age_groups-1.png
age_groups.html
antibiotic_class_selectors.html
antibiotics.html
as.ab.html
as.disk.html
as.mic-1.png
as.mic.html
as.mo.html
as.rsi-1.png
as.rsi-2.png
as.rsi.html
atc_online.html
availability.html
bug_drug_combinations.html
catalogue_of_life.html
catalogue_of_life_version.html
count.html
dosage.html
eucast_rules.html
example_isolates.html
example_isolates_unclean.html
filter_ab_class.html
first_isolate.html
g.test.html
get_episode.html
ggplot_pca-1.png
ggplot_pca-2.png
ggplot_pca.html
ggplot_rsi-1.png
ggplot_rsi-2.png
ggplot_rsi-3.png
ggplot_rsi-4.png
ggplot_rsi-5.png
ggplot_rsi.html
guess_ab_col.html
index.html
intrinsic_resistant.html
is_new_episode.html
isolate_identifier.html
join.html
key_antibiotics.html
kurtosis.html
lifecycle.html
like.html
mdro.html
microorganisms.codes.html
microorganisms.html
microorganisms.old.html
mo_matching_score.html
mo_property.html
mo_source.html
p_symbol.html
pca-1.png
pca-2.png
pca.html
plot.html
proportion.html
random.html
resistance_predict-1.png
resistance_predict-2.png
resistance_predict-3.png
resistance_predict-4.png
resistance_predict.html
rsi_translation.html
skewness.html
translate.html
404.html
LICENSE-text.html
apple-touch-icon-120x120.png
apple-touch-icon-152x152.png
apple-touch-icon-180x180.png
apple-touch-icon-60x60.png
apple-touch-icon-76x76.png
apple-touch-icon.png
authors.html
bootstrap-toc.css
bootstrap-toc.js
code-color-scheme-dark.css
code-color-scheme-light.css
countries.png
countries_large.png
cover_r4ds.png
darkswitch.js
docsearch.css
docsearch.js
extra.css
extra.js
favicon-16x16.png
favicon-32x32.png
favicon.ico
import1.png
import2.png
index.html
lifecycle_archived.svg
lifecycle_dormant.svg
lifecycle_experimental.svg
lifecycle_maturing.svg
lifecycle_questioning.svg
lifecycle_retired.svg
lifecycle_stable.svg
lifecycle_tidyverse.svg
link.svg
logo.png
logo.svg
logo_certe.png
logo_eh1h.png
logo_interreg.png
logo_rug.png
logo_umcg.png
pkgdown.css
pkgdown.js
pkgdown.yml
preferably.css
sitemap.xml
survey.html
whonet.png
works_great_on.png
inst
man
pkgdown
tests
vignettes
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
git_merge.sh
git_premaster.sh
git_siteonly.sh
index.md
ddf88345f19ab462627befe42ab32736a63d9f3a
AMR/docs/reference/index.html

705 lines
32 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>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" />
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<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" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Function reference" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-index">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9028</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>Reference</h1>
</div>
<table class="ref-index">
<colgroup>
<col class="alias" />
<col class="title" />
</colgroup>
<tbody>
<tr>
<th colspan="2">
<h2 id="section-background-information-on-included-data" class="hasAnchor"><a href="#section-background-information-on-included-data" class="anchor"></a>Background information on included data</h2>
<p 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></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="AMR.html">AMR</a></code> </p>
</td>
<td><p>The <code>AMR</code> Package</p></td>
</tr><tr>
<td>
<p><code><a href="example_isolates.html">example_isolates</a></code> </p>
</td>
<td><p>Data Set with 2,000 Example Isolates</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data Set with 69,625 Microorganisms</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td>
<td><p>Data Set with 5,580 Common Microorganism Codes</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
</td>
<td><p>Data Set with Previously Accepted Taxonomic Names</p></td>
</tr><tr>
<td>
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
</td>
<td><p>Data Sets with 558 Antimicrobials</p></td>
</tr><tr>
<td>
<p><code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code> </p>
</td>
<td><p>Data Set with Bacterial Intrinsic Resistance</p></td>
</tr><tr>
<td>
<p><code><a href="dosage.html">dosage</a></code> </p>
</td>
<td><p>Data Set with Treatment Dosages as Defined by EUCAST</p></td>
</tr><tr>
<td>
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
</td>
<td><p>The Catalogue of Life</p></td>
</tr><tr>
<td>
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
</td>
<td><p>Version info of included Catalogue of Life</p></td>
</tr><tr>
<td>
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
</td>
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
</tr><tr>
<td>
<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
</td>
<td><p>Lifecycles of Functions in the <code>amr</code> Package</p></td>
</tr><tr>
<td>
<p><code><a href="example_isolates_unclean.html">example_isolates_unclean</a></code> </p>
</td>
<td><p>Data Set with Unclean Data</p></td>
</tr><tr>
<td>
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
</td>
<td><p>Data Set for R/SI Interpretation</p></td>
</tr><tr>
<td>
<p><code><a href="WHONET.html">WHONET</a></code> </p>
</td>
<td><p>Data Set with 500 Isolates - WHONET Example</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-preparing-data-microorganisms" class="hasAnchor"><a href="#section-preparing-data-microorganisms" class="anchor"></a>Preparing data: microorganisms</h2>
<p class="section-desc"><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></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><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_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
</td>
<td><p>Transform Input to a Microorganism ID</p></td>
</tr><tr>
<td>
<p><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_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_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_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Get Properties of a Microorganism</p></td>
</tr><tr>
<td>
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
</td>
<td><p>User-Defined Reference Data Set for Microorganisms</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-preparing-data-antibiotics" class="hasAnchor"><a href="#section-preparing-data-antibiotics" class="anchor"></a>Preparing data: antibiotics</h2>
<p 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></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
</td>
<td><p>Transform Input to an Antibiotic ID</p></td>
</tr><tr>
<td>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</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_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_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
</td>
<td><p>Get Properties of an Antibiotic</p></td>
</tr><tr>
<td>
<p><code><a href="ab_from_text.html">ab_from_text()</a></code> </p>
</td>
<td><p>Retrieve Antimicrobial Drug Names and Doses from Clinical Text</p></td>
</tr><tr>
<td>
<p><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> </p>
</td>
<td><p>Get ATC Properties from WHOCC Website</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-preparing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-preparing-data-antimicrobial-resistance" class="anchor"></a>Preparing data: antimicrobial resistance</h2>
<p 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.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/">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
</td>
<td><p>Interpret MIC and Disk Values, or Clean Raw R/SI Data</p></td>
</tr><tr>
<td>
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
</td>
<td><p>Transform Input to Minimum Inhibitory Concentrations (MIC)</p></td>
</tr><tr>
<td>
<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
</td>
<td><p>Transform Input to Disk Diffusion Diameters</p></td>
</tr><tr>
<td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_dosage()</a></code> </p>
</td>
<td><p>Apply EUCAST Rules</p></td>
</tr><tr>
<td>
<p><code><a href="isolate_identifier.html">isolate_identifier()</a></code> <code><a href="isolate_identifier.html">all.equal(<i>&lt;isolate_identifier&gt;</i>)</a></code> </p>
</td>
<td><p>Create Identifier of an Isolate</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-analysing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-analysing-data-antimicrobial-resistance" class="anchor"></a>Analysing data: antimicrobial resistance</h2>
<p 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. 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/filter_ab_class.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</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> </p>
</td>
<td><p>Calculate Microbial Resistance</p></td>
</tr><tr>
<td>
<p><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> </p>
</td>
<td><p>Count Available Isolates</p></td>
</tr><tr>
<td>
<p><code><a href="get_episode.html">get_episode()</a></code> <code><a href="get_episode.html">is_new_episode()</a></code> </p>
</td>
<td><p>Determine (New) Episodes for Patients</p></td>
</tr><tr>
<td>
<p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
</td>
<td><p>Determine First (Weighted) Isolates</p></td>
</tr><tr>
<td>
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
</td>
<td><p>Key Antibiotics for First (Weighted) Isolates</p></td>
</tr><tr>
<td>
<p><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> </p>
</td>
<td><p>Determine Multidrug-Resistant Organisms (MDRO)</p></td>
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
</tr><tr>
<td>
<p><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> </p>
</td>
<td><p>AMR Plots with <code>ggplot2</code></p></td>
</tr><tr>
<td>
<p><code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i>&lt;bug_drug_combinations&gt;</i>)</a></code> </p>
</td>
<td><p>Determine Bug-Drug Combinations</p></td>
</tr><tr>
<td>
<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</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">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">tetracyclines()</a></code> </p>
</td>
<td><p>Antibiotic Class Selectors</p></td>
</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_oxazolidinones()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter Isolates on Result in Antimicrobial Class</p></td>
</tr><tr>
<td>
<p><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>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
</td>
<td><p>Predict antimicrobial resistance</p></td>
</tr><tr>
<td>
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
</td>
<td><p>Guess Antibiotic Column</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-other-miscellaneous-functions" class="hasAnchor"><a href="#section-other-miscellaneous-functions" class="anchor"></a>Other: miscellaneous functions</h2>
<p 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></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
</td>
<td><p>Split Ages into Age Groups</p></td>
</tr><tr>
<td>
<p><code><a href="age.html">age()</a></code> </p>
</td>
<td><p>Age in Years of Individuals</p></td>
</tr><tr>
<td>
<p><code><a href="availability.html">availability()</a></code> </p>
</td>
<td><p>Check Availability of Columns</p></td>
</tr><tr>
<td>
<p><code><a href="translate.html">get_locale()</a></code> </p>
</td>
<td><p>Translate Strings from AMR Package</p></td>
</tr><tr>
<td>
<p><code><a href="ggplot_pca.html">ggplot_pca()</a></code> </p>
</td>
<td><p>PCA Biplot with <code>ggplot2</code></p></td>
</tr><tr>
<td>
<p><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> </p>
</td>
<td><p>Join microorganisms to a Data Set</p></td>
</tr><tr>
<td>
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
</td>
<td><p>Pattern Matching with Keyboard Shortcut</p></td>
</tr><tr>
<td>
<p><code><a href="mo_matching_score.html">mo_matching_score()</a></code> </p>
</td>
<td><p>Calculate the Matching Score for Microorganisms</p></td>
</tr><tr>
<td>
<p><code><a href="pca.html">pca()</a></code> </p>
</td>
<td><p>Principal Component Analysis (for AMR)</p></td>
</tr><tr>
<td>
<p><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> </p>
</td>
<td><p>Random MIC Values/Disk Zones/RSI Generation</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-other-statistical-tests" class="hasAnchor"><a href="#section-other-statistical-tests" class="anchor"></a>Other: statistical tests</h2>
<p class="section-desc"><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="g.test.html">g.test()</a></code> </p>
</td>
<td><p><em>G</em>-test for Count Data</p></td>
</tr><tr>
<td>
<p><code><a href="kurtosis.html">kurtosis()</a></code> </p>
</td>
<td><p>Kurtosis of the Sample</p></td>
</tr><tr>
<td>
<p><code><a href="skewness.html">skewness()</a></code> </p>
</td>
<td><p>Skewness of the Sample</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-other-deprecated-functions" class="hasAnchor"><a href="#section-other-deprecated-functions" class="anchor"></a>Other: deprecated functions</h2>
<p class="section-desc"><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></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> </p>
</td>
<td><p>Deprecated Functions</p></td>
</tr>
</tbody>
</table>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
</div>
</body>
</html>
View Git Blame Copy Permalink