2018-12-23 21:26:21 +01:00
<!-- 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" >
2018-12-29 22:24:19 +01:00
< title > Function reference • AMR (for R)< / title >
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
<!-- 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" / >
2019-09-25 15:43:22 +02:00
2018-12-23 21:26:21 +01:00
<!-- jquery -->
2020-04-13 21:09:56 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
<!-- Bootstrap -->
2020-12-27 00:07:00 +01:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2019-09-25 15:43:22 +02:00
2020-12-21 22:46:29 +01:00
2020-12-24 23:29:10 +01:00
< 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 >
2020-12-21 22:46:29 +01:00
2020-04-13 21:09:56 +02:00
<!-- bootstrap - toc -->
< link rel = "stylesheet" href = "../bootstrap-toc.css" >
< script src = "../bootstrap-toc.js" > < / script >
2018-12-23 21:26:21 +01:00
<!-- Font Awesome icons -->
2020-04-13 21:09:56 +02:00
< 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" / >
2018-12-23 21:26:21 +01:00
<!-- clipboard.js -->
2020-04-13 21:09:56 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
2019-09-25 15:43:22 +02:00
<!-- headroom.js -->
2020-04-13 21:09:56 +02:00
< 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 >
2018-12-23 21:26:21 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
2018-12-29 22:24:19 +01:00
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2018-12-23 21:26:21 +01:00
2019-09-25 15:43:22 +02:00
< meta property = "og:title" content = "Function reference" / >
2020-09-14 14:08:07 +02:00
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.png" / >
2018-12-29 22:24:19 +01:00
2018-12-23 21:26:21 +01:00
2019-09-25 15:43:22 +02:00
2018-12-23 21:26:21 +01:00
<!-- 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]-->
2019-09-25 15:43:22 +02:00
2018-12-23 21:26:21 +01:00
< / head >
2020-04-13 21:09:56 +02:00
< body data-spy = "scroll" data-target = "#toc" >
2018-12-23 21:26:21 +01:00
< 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" >
2018-12-29 22:24:19 +01:00
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2021-05-23 23:11:16 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.6.0.9061< / span >
2018-12-23 21:26:21 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-home" > < / span >
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Home
2018-12-23 21:26:21 +01:00
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-question-circle" > < / span >
2019-01-02 23:24:07 +01:00
How to
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< span class = "caret" > < / span >
2018-12-29 22:24:19 +01:00
< / a >
2019-01-02 23:24:07 +01:00
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-directions" > < / span >
2019-01-02 23:24:07 +01:00
Conduct AMR analysis
< / a >
< / li >
< li >
2019-02-11 10:27:10 +01:00
< a href = "../articles/resistance_predict.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-dice" > < / span >
2019-01-02 23:24:07 +01:00
Predict antimicrobial resistance
< / a >
< / li >
2020-08-16 21:38:42 +02:00
< li >
< a href = "../articles/datasets.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-database" > < / span >
2020-08-16 21:38:42 +02:00
2020-09-03 12:31:48 +02:00
Data sets for download / own use
2020-08-16 21:38:42 +02:00
< / a >
< / li >
2020-03-07 21:48:21 +01:00
< li >
< a href = "../articles/PCA.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-compress" > < / span >
2020-03-07 21:48:21 +01:00
Conduct principal component analysis for AMR
< / a >
< / li >
2019-05-23 16:58:59 +02:00
< li >
< a href = "../articles/MDR.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-skull-crossbones" > < / span >
2019-05-23 16:58:59 +02:00
Determine multi-drug resistance (MDR)
< / a >
< / li >
2019-01-29 00:06:50 +01:00
< li >
< a href = "../articles/WHONET.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-globe-americas" > < / span >
2019-01-29 00:06:50 +01:00
Work with WHONET data
< / a >
< / li >
2019-02-14 15:18:17 +01:00
< li >
< a href = "../articles/SPSS.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-file-upload" > < / span >
2019-02-14 15:18:17 +01:00
Import data from SPSS/SAS/Stata
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< li >
< a href = "../articles/EUCAST.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-exchange-alt" > < / span >
2019-01-02 23:24:07 +01:00
Apply EUCAST rules
< / a >
< / li >
< li >
2019-02-11 10:27:10 +01:00
< a href = "../reference/mo_property.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-bug" > < / span >
2019-01-02 23:24:07 +01:00
Get properties of a microorganism
< / a >
< / li >
< li >
2019-05-10 16:44:59 +02:00
< a href = "../reference/ab_property.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-capsules" > < / span >
2019-01-02 23:24:07 +01:00
Get properties of an antibiotic
< / a >
< / li >
2019-01-11 20:37:23 +01:00
< li >
< a href = "../articles/benchmarks.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-shipping-fast" > < / span >
2019-01-11 20:37:23 +01:00
Other: benchmarks
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
2018-12-23 21:26:21 +01:00
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../reference/index.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-book-open" > < / span >
2018-12-29 22:24:19 +01:00
Manual
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2018-12-29 22:24:19 +01:00
< li >
< a href = "../authors.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-users" > < / span >
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Authors
2018-12-23 21:26:21 +01:00
< / a >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../news/index.html" >
2021-04-29 17:16:30 +02:00
< span class = "far fa-newspaper" > < / span >
2018-12-29 22:24:19 +01:00
Changelog
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
2020-07-08 14:48:06 +02:00
< a href = "https://github.com/msberends/AMR" >
2021-04-29 17:16:30 +02:00
< span class = "fab fa-github" > < / span >
2018-12-29 22:24:19 +01:00
Source Code
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2019-01-02 23:24:07 +01:00
< li >
2020-07-28 18:39:57 +02:00
< a href = "../survey.html" >
2021-04-29 17:16:30 +02:00
< span class = "fas fa-clipboard-list" > < / span >
2018-12-29 22:24:19 +01:00
2020-07-28 18:39:57 +02:00
Survey
2018-12-29 22:24:19 +01:00
< / a >
< / li >
2018-12-23 21:26:21 +01:00
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-09-25 15:43:22 +02:00
2018-12-23 21:26:21 +01:00
< / 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" >
2020-09-03 12:31:48 +02:00
< 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’ < / a > for more information about how to work with functions in this package.< / p > < / p >
2018-12-23 21:26:21 +01:00
< / th >
< / tr >
2020-04-13 21:09:56 +02:00
< / tbody > < tbody >
2018-12-23 21:26:21 +01:00
< tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "AMR.html" > AMR< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
2020-09-03 12:31:48 +02:00
< td > < p > The < code > AMR< / code > Package< / p > < / td >
2019-05-10 16:44:59 +02:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "example_isolates.html" > example_isolates< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Set with 2,000 Example Isolates< / p > < / td >
2019-05-10 16:44:59 +02:00
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "microorganisms.html" > microorganisms< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-03-05 01:31:46 +01:00
< td > < p > Data Set with 70,026 Microorganisms< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "microorganisms.codes.html" > microorganisms.codes< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-05-04 12:47:33 +02:00
< td > < p > Data Set with 5,605 Common Microorganism Codes< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "microorganisms.old.html" > microorganisms.old< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Set with Previously Accepted Taxonomic Names< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "antibiotics.html" > antibiotics< / a > < / code > < code > < a href = "antibiotics.html" > antivirals< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Sets with 558 Antimicrobials< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2020-06-25 19:20:50 +02:00
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "intrinsic_resistant.html" > intrinsic_resistant< / a > < / code > < / p >
2020-06-25 19:20:50 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Set with Bacterial Intrinsic Resistance< / p > < / td >
2020-06-25 19:20:50 +02:00
< / tr > < tr >
2019-05-10 16:44:59 +02:00
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "dosage.html" > dosage< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Set with Treatment Dosages as Defined by EUCAST< / p > < / td >
2019-05-10 16:44:59 +02:00
< / tr > < tr >
2019-01-06 20:23:49 +01:00
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "catalogue_of_life.html" > catalogue_of_life< / a > < / code > < / p >
2019-01-06 20:23:49 +01:00
< / td >
2021-01-12 22:08:04 +01:00
< td > < p > The Catalogue of Life< / p > < / td >
2020-09-03 12:31:48 +02:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "catalogue_of_life_version.html" > catalogue_of_life_version()< / a > < / code > < / p >
2020-09-03 12:31:48 +02:00
< / td >
2021-01-12 22:08:04 +01:00
< td > < p > Version info of included Catalogue of Life< / p > < / td >
2020-09-03 12:31:48 +02:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "WHOCC.html" > WHOCC< / a > < / code > < / p >
2020-09-03 12:31:48 +02:00
< / td >
2021-01-12 22:08:04 +01:00
< td > < p > WHOCC: WHO Collaborating Centre for Drug Statistics Methodology< / p > < / td >
2020-09-03 12:31:48 +02:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "lifecycle.html" > lifecycle< / a > < / code > < / p >
2020-09-03 12:31:48 +02:00
< / td >
2021-03-11 21:42:30 +01:00
< td > < p > Lifecycles of Functions in the < code > AMR< / code > Package< / p > < / td >
2020-09-03 12:31:48 +02:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "example_isolates_unclean.html" > example_isolates_unclean< / a > < / code > < / p >
2020-09-03 12:31:48 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Set with Unclean Data< / p > < / td >
2021-01-12 22:08:04 +01:00
< / tr > < tr >
< td >
< p > < code > < a href = "rsi_translation.html" > rsi_translation< / a > < / code > < / p >
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Set for R/SI Interpretation< / p > < / td >
2020-09-03 12:31:48 +02:00
< / tr > < tr >
< td >
< p > < code > < a href = "WHONET.html" > WHONET< / a > < / code > < / p >
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Data Set with 500 Isolates - WHONET Example< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2020-09-03 12:31:48 +02:00
< 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 >
2018-12-29 22:24:19 +01:00
< / th >
< / tr >
2020-04-13 21:09:56 +02:00
< / tbody > < tbody >
2018-12-29 22:24:19 +01:00
< tr >
2018-12-23 21:26:21 +01:00
< td >
2020-09-03 12:31:48 +02:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Transform Input to a Microorganism ID< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Get Properties of a Microorganism< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "mo_source.html" > set_mo_source()< / a > < / code > < code > < a href = "mo_source.html" > get_mo_source()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > User-Defined Reference Data Set for Microorganisms< / p > < / td >
2020-09-03 12:31:48 +02:00
< / 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 >
2018-12-23 21:26:21 +01:00
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "as.ab.html" > as.ab()< / a > < / code > < code > < a href = "as.ab.html" > is.ab()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Transform Input to an Antibiotic ID< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Get Properties of an Antibiotic< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "ab_from_text.html" > ab_from_text()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Retrieve Antimicrobial Drug Names and Doses from Clinical Text< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Get ATC Properties from WHOCC Website< / p > < / td >
2020-09-03 12:31:48 +02:00
< / 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 >
2020-10-08 11:16:03 +02:00
< 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 >
2020-09-03 12:31:48 +02:00
< / 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 >
2021-01-18 16:57:56 +01:00
< td > < p > Interpret MIC and Disk Values, or Clean Raw R/SI Data< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "as.mic.html" > as.mic()< / a > < / code > < code > < a href = "as.mic.html" > is.mic()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Transform Input to Minimum Inhibitory Concentrations (MIC)< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "as.disk.html" > as.disk()< / a > < / code > < code > < a href = "as.disk.html" > is.disk()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Transform Input to Disk Diffusion Diameters< / p > < / td >
2019-05-10 16:44:59 +02:00
< / tr > < tr >
< td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > < code > < a href = "eucast_rules.html" > eucast_dosage()< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Apply EUCAST Rules< / p > < / td >
2021-04-07 08:37:42 +02:00
< / tr > < tr >
< td >
< p > < code > < a href = "custom_eucast_rules.html" > custom_eucast_rules()< / a > < / code > < / p >
< / td >
2021-04-20 10:46:17 +02:00
< td > < p > Define Custom EUCAST Rules< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2020-09-03 12:31:48 +02:00
< h2 id = "section-analysing-data-antimicrobial-resistance" class = "hasAnchor" > < a href = "#section-analysing-data-antimicrobial-resistance" class = "anchor" > < / a > Analysing data: antimicrobial resistance< / h2 >
2021-05-20 00:07:27 +02:00
< 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/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 > < / p >
2018-12-29 22:24:19 +01:00
< / th >
< / tr >
2020-04-13 21:09:56 +02:00
< / tbody > < tbody >
2018-12-29 22:24:19 +01:00
< tr >
2018-12-23 21:26:21 +01:00
2020-03-07 21:48:21 +01:00
< 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 >
2021-01-18 16:57:56 +01:00
< td > < p > Calculate Microbial Resistance< / p > < / td >
2020-03-07 21:48:21 +01:00
< / 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 >
2021-01-18 16:57:56 +01:00
< td > < p > Count Available Isolates< / p > < / td >
2020-03-07 21:48:21 +01:00
< / tr > < tr >
2019-02-08 16:06:54 +01:00
< td >
2020-12-27 00:07:00 +01:00
< p > < code > < a href = "get_episode.html" > get_episode()< / a > < / code > < code > < a href = "get_episode.html" > is_new_episode()< / a > < / code > < / p >
2020-11-23 21:50:27 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Determine (New) Episodes for Patients< / p > < / td >
2020-11-23 21:50:27 +01:00
< / tr > < tr >
< td >
2021-04-29 17:16:30 +02:00
< p > < code > < a href = "first_isolate.html" > first_isolate()< / a > < / code > < code > < a href = "first_isolate.html" > filter_first_isolate()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Determine First (Weighted) Isolates< / p > < / td >
2020-03-07 21:48:21 +01:00
< / tr > < tr >
< td >
2021-04-27 10:27:13 +02:00
< p > < 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 > < / p >
2020-03-07 21:48:21 +01:00
< / td >
2021-04-27 10:27:13 +02:00
< td > < p > (Key) Antimicrobials for First Weighted Isolates< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2020-06-17 15:14:37 +02:00
< td >
2021-01-17 00:26:48 +01:00
< 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 >
2020-06-17 15:14:37 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Determine Multidrug-Resistant Organisms (MDRO)< / p > < / td >
2020-06-17 15:14:37 +02:00
< / tr > < tr >
2021-03-04 23:28:32 +01:00
< td >
< p > < code > < a href = "plot.html" > plot(< i > < mic> < / i > )< / a > < / code > < code > < a href = "plot.html" > ggplot(< i > < mic> < / i > )< / a > < / code > < code > < a href = "plot.html" > plot(< i > < disk> < / i > )< / a > < / code > < code > < a href = "plot.html" > ggplot(< i > < disk> < / i > )< / a > < / code > < code > < a href = "plot.html" > plot(< i > < rsi> < / i > )< / a > < / code > < code > < a href = "plot.html" > ggplot(< i > < rsi> < / i > )< / a > < / code > < / p >
< / td >
< td > < p > Plotting for Classes < code > rsi< / code > , < code > mic< / code > and < code > disk< / code > < / p > < / td >
< / tr > < tr >
2019-03-06 14:39:02 +01:00
< td >
2020-09-03 12:31:48 +02:00
< 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 >
2019-03-06 14:39:02 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > AMR Plots with < code > ggplot2< / code > < / p > < / td >
2019-03-06 14:39:02 +01:00
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2020-09-03 12:31:48 +02:00
< p > < 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 > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Determine Bug-Drug Combinations< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2021-05-18 00:53:04 +02:00
< 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" > 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" > 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 >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Antibiotic Class Selectors< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2021-05-13 19:31:47 +02:00
< 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 > < resistance_predict> < / i > )< / a > < / code > < code > < a href = "resistance_predict.html" > ggplot(< i > < resistance_predict> < / i > )< / a > < / code > < code > < a href = "resistance_predict.html" > ggplot_rsi_predict()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2020-09-03 12:31:48 +02:00
< td > < p > Predict antimicrobial resistance< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "guess_ab_col.html" > guess_ab_col()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Guess Antibiotic Column< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2020-09-03 12:31:48 +02:00
< 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 ‘ ’ < code > if (x %like% y) {...}< / code > .< / p > < / p >
2018-12-29 22:24:19 +01:00
< / th >
< / tr >
2020-04-13 21:09:56 +02:00
< / tbody > < tbody >
2018-12-29 22:24:19 +01:00
< tr >
2018-12-23 21:26:21 +01:00
2020-03-07 21:48:21 +01:00
< td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "age_groups.html" > age_groups()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Split Ages into Age Groups< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2020-08-15 12:54:47 +02:00
< td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "age.html" > age()< / a > < / code > < / p >
2020-08-15 12:54:47 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Age in Years of Individuals< / p > < / td >
2020-08-15 12:54:47 +02:00
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "availability.html" > availability()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Check Availability of Columns< / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr > < tr >
2020-02-21 21:13:38 +01:00
< td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "translate.html" > get_locale()< / a > < / code > < / p >
2020-02-21 21:13:38 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Translate Strings from AMR Package< / p > < / td >
2020-02-21 21:13:38 +01:00
< / tr > < tr >
2019-11-18 12:10:47 +01:00
< td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "ggplot_pca.html" > ggplot_pca()< / a > < / code > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > PCA Biplot with < code > ggplot2< / code > < / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr > < tr >
2021-05-03 13:06:43 +02:00
< td >
< p > < code > < a href = "italicise_taxonomy.html" > italicise_taxonomy()< / a > < / code > < code > < a href = "italicise_taxonomy.html" > italicize_taxonomy()< / a > < / code > < / p >
< / td >
< td > < p > Italicise Taxonomic Families, Genera, Species, Subspecies< / p > < / td >
< / tr > < tr >
2019-11-18 12:10:47 +01:00
< td >
2020-09-18 16:05:53 +02:00
< 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 >
2019-11-18 12:10:47 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Join microorganisms to a Data Set< / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr > < tr >
< td >
2021-04-23 09:59:36 +02:00
< p > < 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 > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2021-04-07 08:37:42 +02:00
< td > < p > Vectorised Pattern Matching with Keyboard Shortcut< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2020-09-19 12:57:51 +02:00
< td >
< p > < code > < a href = "mo_matching_score.html" > mo_matching_score()< / a > < / code > < / p >
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Calculate the Matching Score for Microorganisms< / p > < / td >
2020-09-19 12:57:51 +02:00
< / tr > < tr >
2019-01-29 20:20:09 +01:00
< td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "pca.html" > pca()< / a > < / code > < / p >
2019-01-29 20:20:09 +01:00
< / td >
2020-09-18 16:05:53 +02:00
< td > < p > Principal Component Analysis (for AMR)< / p > < / td >
2020-12-12 23:17:29 +01:00
< / 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 >
2021-01-18 16:57:56 +01:00
< td > < p > Random MIC Values/Disk Zones/RSI Generation< / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2020-09-03 12:31:48 +02:00
< h2 id = "section-other-statistical-tests" class = "hasAnchor" > < a href = "#section-other-statistical-tests" class = "anchor" > < / a > Other: statistical tests< / h2 >
2020-11-23 21:50:27 +01:00
< 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 >
2019-11-18 12:10:47 +01:00
< / th >
< / tr >
2020-04-13 21:09:56 +02:00
< / tbody > < tbody >
2019-11-18 12:10:47 +01:00
< tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "g.test.html" > g.test()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2020-09-03 12:31:48 +02:00
< td > < p > < em > G< / em > -test for Count Data< / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "kurtosis.html" > kurtosis()< / a > < / code > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Kurtosis of the Sample< / p > < / td >
2020-01-08 11:30:33 +01:00
< / tr > < tr >
< td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "skewness.html" > skewness()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Skewness of the Sample< / p > < / td >
2020-11-23 21:50:27 +01:00
< / 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 >
2018-12-23 21:26:21 +01:00
2019-06-09 08:57:54 +02:00
< td >
2021-05-19 22:55:42 +02:00
< p > < code > < a href = "AMR-deprecated.html" > p_symbol()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_first_weighted_isolate()< / a > < / code > < code > < a href = "AMR-deprecated.html" > key_antibiotics()< / a > < / code > < code > < a href = "AMR-deprecated.html" > key_antibiotics_equal()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_ab_class()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_aminoglycosides()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_betalactams()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_carbapenems()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_cephalosporins()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_1st_cephalosporins()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_2nd_cephalosporins()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_3rd_cephalosporins()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_4th_cephalosporins()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_5th_cephalosporins()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_fluoroquinolones()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_glycopeptides()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_macrolides()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_oxazolidinones()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_penicillins()< / a > < / code > < code > < a href = "AMR-deprecated.html" > filter_tetracyclines()< / a > < / code > < / p >
2019-06-09 08:57:54 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Deprecated Functions< / p > < / td >
2019-06-09 08:57:54 +02:00
< / tr >
2018-12-23 21:26:21 +01:00
< / tbody >
< / table >
< / div >
2020-04-13 21:09:56 +02:00
< 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 >
2018-12-23 21:26:21 +01:00
< / div >
< / div >
2019-09-25 15:43:22 +02:00
2018-12-23 21:26:21 +01:00
< footer >
< div class = "copyright" >
2020-02-17 14:38:01 +01:00
< 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 >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "pkgdown" >
2020-12-24 23:29:10 +01:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.6.1.< / p >
2018-12-23 21:26:21 +01:00
< / div >
2019-09-25 15:43:22 +02:00
2018-12-23 21:26:21 +01:00
< / footer >
< / div >
2019-09-25 15:43:22 +02:00
2018-12-23 21:26:21 +01:00
< / body >
< / html >
2019-09-25 15:43:22 +02:00
