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 -->
2020-04-13 21:09:56 +02:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2018-12-23 21:26:21 +01:00
2019-09-25 15:43:22 +02:00
2020-04-13 21:09:56 +02:00
< 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 >
<!-- 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" / >
2020-04-13 21:09:56 +02:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.svg" / >
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 >
2020-06-26 12:31:27 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.2.0.9017< / 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" >
2018-12-29 22:24:19 +01:00
< span class = "fa 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" >
< span class = "fa fa-question-circle" > < / span >
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" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< / li >
< li >
2019-02-11 10:27:10 +01:00
< a href = "../articles/resistance_predict.html" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
2020-03-07 21:48:21 +01:00
< li >
< a href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
Conduct principal component analysis for AMR
< / a >
< / li >
2019-05-23 16:58:59 +02:00
< li >
< a href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / a >
< / li >
2019-01-29 00:06:50 +01:00
< li >
< a href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< / li >
2019-02-14 15:18:17 +01:00
< li >
< a href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
2019-02-11 10:27:10 +01:00
< a href = "../reference/mo_property.html" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
2019-05-10 16:44:59 +02:00
< a href = "../reference/ab_property.html" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
2019-01-11 20:37:23 +01:00
< li >
< a href = "../articles/benchmarks.html" >
< span class = "fa fa-shipping-fast" > < / span >
Other: benchmarks
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
2018-12-23 21:26:21 +01:00
< / li >
< li >
2018-12-29 22:24:19 +01:00
< a href = "../reference/" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2018-12-29 22:24:19 +01:00
< li >
< a href = "../authors.html" >
< span class = "fa 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 >
2018-12-29 22:24:19 +01:00
< a href = "../news/" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
2018-12-29 22:24:19 +01:00
< a href = "https://gitlab.com/msberends/AMR" >
< span class = "fab fa fab fa-gitlab" > < / span >
Source Code
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2019-01-02 23:24:07 +01:00
< li >
2018-12-29 22:24:19 +01:00
< a href = "../LICENSE-text.html" >
< span class = "fa fa-book" > < / span >
Licence
< / 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" >
2018-12-29 22:24:19 +01:00
< h2 id = "section-cleaning-your-data" class = "hasAnchor" > < a href = "#section-cleaning-your-data" class = "anchor" > < / a > Cleaning your data< / h2 >
2019-01-02 23:24:07 +01:00
< p class = "section-desc" > < p > Functions for cleaning and optimising your data, to be able to add variables later on (like taxonomic properties) or to fix and extend antibiotic interpretations by applying < a href = "http://www.eucast.org/expert_rules_and_intrinsic_resistance/" > EUCAST rules< / a > .< / 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 >
2019-05-16 21:20:00 +02:00
< p > < code > < a href = "as.ab.html" > as.ab()< / a > < / code > < code > < a href = "as.ab.html" > is.ab()< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
< td > < p > Transform to antibiotic ID< / 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 > Class 'disk'< / p > < / td >
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2018-12-29 22:24:19 +01:00
< 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 >
2018-12-29 22:24:19 +01:00
< td > < p > Class 'mic'< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-01-31 23:27:38 +01:00
< 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 >
2018-12-29 22:24:19 +01:00
< td > < p > Transform to microorganism ID< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Class 'rsi'< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-06-01 20:40:49 +02:00
< p > < code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2020-01-26 20:20:00 +01:00
< td > < p > Apply EUCAST rules< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2020-06-25 19:20:50 +02:00
< td >
< p > < code > < a href = "ab_from_text.html" > ab_from_text()< / a > < / code > < / p >
< / td >
2020-06-26 12:31:27 +02:00
< td > < p > Retrieve antimicrobial drugs from clinical text< / p > < / td >
2020-06-25 19:20:50 +02:00
< / tr > < tr >
2019-05-10 16:44:59 +02:00
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "guess_ab_col.html" > guess_ab_col()< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > Guess antibiotic column< / p > < / td >
2019-05-10 16:44:59 +02:00
< / tr > < tr >
2019-01-06 20:23:49 +01:00
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "mo_source.html" > set_mo_source()< / a > < / code > < code > < a href = "mo_source.html" > get_mo_source()< / a > < / code > < / p >
2019-01-06 20:23:49 +01:00
< / td >
2020-05-25 01:01:14 +02:00
< td > < p > User-defined reference data set for microorganisms< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2019-11-18 12:10:47 +01:00
< h2 id = "section-enhancing-your-data" class = "hasAnchor" > < a href = "#section-enhancing-your-data" class = "anchor" > < / a > Enhancing your data< / h2 >
< p class = "section-desc" > < p > Functions to add new data to your existing data, such as the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.< / 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 >
2020-05-22 20:15:19 +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 >
2019-11-18 12:10:47 +01:00
< td > < p > Property of an antibiotic< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "age_groups.html" > age_groups()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > Split ages into age groups< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "age.html" > age()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > Age in years of individuals< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< 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 >
2019-11-18 12:10:47 +01:00
< td > < p > Get ATC properties from WHOCC website< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > Determine first (weighted) isolates< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2020-05-16 13:05:47 +02:00
< td > < p > Join microorganisms to a data set< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "key_antibiotics.html" > key_antibiotics()< / a > < / code > < code > < a href = "key_antibiotics.html" > key_antibiotics_equal()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > Key antibiotics for first < em > weighted< / em > isolates< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "mdro.html" > mdro()< / 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 >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > Determine multidrug-resistant organisms (MDRO)< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-06-22 11:18:40 +02:00
< 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_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 >
2019-11-18 12:10:47 +01:00
< td > < p > Property of a microorganism< / p > < / td >
2019-05-10 16:44:59 +02:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "p_symbol.html" > p_symbol()< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
2019-11-28 22:32:17 +01:00
< td > < p > Symbol of a p-value< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2018-12-30 10:27:28 +01:00
< h2 id = "section-analysing-your-data" class = "hasAnchor" > < a href = "#section-analysing-your-data" class = "anchor" > < / a > Analysing your data< / h2 >
2019-07-29 13:33:48 +02:00
< p class = "section-desc" > < p > Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, or make plots.< / 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 >
< 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 >
2019-02-08 16:06:54 +01:00
< td >
< p > < code > < a href = "availability.html" > availability()< / a > < / code > < / p >
< / td >
< td > < p > Check availability of columns< / p > < / td >
< / tr > < tr >
2019-08-26 16:02:03 +02:00
< td >
2019-08-27 22:41:09 +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 >
2019-08-26 16:02:03 +02:00
< / td >
< td > < p > Determine bug-drug combinations< / p > < / td >
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2020-03-07 21:48:21 +01:00
< 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_rsi_predict()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2020-03-07 21:48:21 +01:00
< td > < p > Predict antimicrobial resistance< / p > < / td >
< / tr > < tr >
< td >
2020-03-08 11:18:59 +01:00
< p > < code > < a href = "pca.html" > pca()< / a > < / code > < / p >
2020-03-07 21:48:21 +01:00
< / td >
< td > < p > Principal Component Analysis (for AMR)< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2020-06-17 15:14:37 +02:00
< 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" > penicillins()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > tetracyclines()< / a > < / code > < / p >
< / td >
< td > < p > Antibiotic class selectors< / p > < / td >
< / tr > < tr >
2019-03-06 14:39:02 +01:00
< td >
2020-06-03 11:48:00 +02:00
< 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_penicillins()< / a > < / code > < code > < a href = "filter_ab_class.html" > filter_tetracyclines()< / a > < / code > < / p >
2019-03-06 14:39:02 +01:00
< / td >
2020-05-16 13:05:47 +02:00
< td > < p > Filter isolates on result in antimicrobial class< / p > < / td >
2019-03-06 14:39:02 +01:00
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "g.test.html" > g.test()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > < em > G< / em > -test for Count Data< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< 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 >
2018-12-23 21:26:21 +01:00
< / td >
2019-01-27 19:30:40 +01:00
< td > < p > AMR plots with < code > ggplot2< / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2020-03-07 21:48:21 +01:00
< p > < code > < a href = "ggplot_pca.html" > ggplot_pca()< / a > < / code > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2020-03-07 21:48:21 +01:00
< td > < p > PCA biplot with < code > ggplot2< / code > < / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2020-03-07 21:48:21 +01:00
< p > < code > < a href = "kurtosis.html" > kurtosis()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2020-03-07 21:48:21 +01:00
< td > < p > Kurtosis of the sample< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "skewness.html" > skewness()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Skewness of the sample< / p > < / td >
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
< h2 id = "section-included-data-sets" class = "hasAnchor" > < a href = "#section-included-data-sets" class = "anchor" > < / a > Included data sets< / h2 >
2019-11-18 12:10:47 +01:00
< p class = "section-desc" > < p > Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.< / 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 = "microorganisms.html" > microorganisms< / a > < / code > < / p >
< / td >
2020-05-28 10:51:56 +02:00
< td > < p > Data set with 67,108 microorganisms< / p > < / td >
2020-03-07 21:48:21 +01:00
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2019-11-23 12:39:57 +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 >
2020-06-09 16:18:03 +02:00
< td > < p > Data sets with 558 antimicrobials< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-08-27 16:45:42 +02:00
< p > < code > < a href = "example_isolates.html" > example_isolates< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > Data set with 2,000 example isolates< / p > < / td >
< / tr > < tr >
2020-02-21 21:13:38 +01:00
< 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 >
2019-11-18 12:10:47 +01:00
< td >
2020-03-07 21:48:21 +01:00
< p > < code > < a href = "rsi_translation.html" > rsi_translation< / a > < / code > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2020-03-07 21:48:21 +01:00
< td > < p > Data set for R/SI interpretation< / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr > < tr >
< td >
2020-03-07 21:48:21 +01:00
< p > < code > < a href = "microorganisms.codes.html" > microorganisms.codes< / a > < / code > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2020-05-27 16:37:49 +02:00
< td > < p > Translation table with 5,582 common microorganism codes< / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr > < tr >
< td >
2020-03-07 21:48:21 +01:00
< p > < code > < a href = "microorganisms.old.html" > microorganisms.old< / a > < / code > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2020-03-07 21:48:21 +01:00
< td > < p > Data set with previously accepted taxonomic names< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2019-01-29 20:20:09 +01:00
< td >
< p > < code > < a href = "WHONET.html" > WHONET< / a > < / code > < / p >
< / td >
< td > < p > Data set with 500 isolates - WHONET example< / p > < / td >
2019-11-18 12:10:47 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
< h2 id = "section-background-information" class = "hasAnchor" > < a href = "#section-background-information" class = "anchor" > < / a > Background information< / 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 >
< / th >
< / tr >
2020-04-13 21:09:56 +02:00
< / tbody > < tbody >
2019-11-18 12:10:47 +01:00
< tr >
< td >
< p > < code > < a href = "AMR.html" > AMR< / a > < / code > < / p >
< / td >
< td > < p > The < code > AMR< / code > Package< / p > < / td >
2019-01-29 20:20:09 +01:00
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "catalogue_of_life.html" > catalogue_of_life< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< td > < p > The Catalogue of Life< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-11-18 12:10:47 +01:00
< p > < code > < a href = "catalogue_of_life_version.html" > catalogue_of_life_version()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-11-18 12:10:47 +01:00
< 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 >
2020-01-08 11:30:33 +01:00
< / 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 >
2018-12-29 22:24:19 +01:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2019-03-15 13:57:25 +01:00
< h2 id = "section-other-functions" class = "hasAnchor" > < a href = "#section-other-functions" class = "anchor" > < / a > Other functions< / h2 >
2019-01-11 20:37:23 +01:00
< 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
< td >
2019-05-10 16:44:59 +02:00
< p > < code > < a href = "translate.html" > get_locale()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-05-10 16:44:59 +02:00
< td > < p > Translate strings from AMR package< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2019-06-09 08:57:54 +02:00
< td >
2019-11-23 12:39:57 +01:00
< 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 >
2019-06-09 08:57:54 +02:00
< / td >
2019-11-23 12:39:57 +01:00
< td > < p > Pattern Matching< / p > < / td >
2019-06-09 08:57:54 +02:00
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2019-11-23 12:39:57 +01:00
< h2 id = "section-deprecated-functions" class = "hasAnchor" > < a href = "#section-deprecated-functions" class = "anchor" > < / a > Deprecated functions< / h2 >
2019-11-18 12:10:47 +01:00
< 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 >
2019-03-15 13:57:25 +01:00
< / th >
< / tr >
2020-04-13 21:09:56 +02:00
< / tbody > < tbody >
2019-03-15 13:57:25 +01:00
< tr >
2018-12-23 21:26:21 +01:00
2019-01-26 23:22:56 +01:00
< td >
2020-05-16 13:05:47 +02:00
< p > < code > < a href = "AMR-deprecated.html" > portion_R()< / a > < / code > < code > < a href = "AMR-deprecated.html" > portion_IR()< / a > < / code > < code > < a href = "AMR-deprecated.html" > portion_I()< / a > < / code > < code > < a href = "AMR-deprecated.html" > portion_SI()< / a > < / code > < code > < a href = "AMR-deprecated.html" > portion_S()< / a > < / code > < code > < a href = "AMR-deprecated.html" > portion_df()< / a > < / code > < / p >
2019-01-26 23:22:56 +01:00
< / td >
< td > < p > Deprecated functions< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< / 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" >
2020-04-29 14:33:44 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.< / 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
