2022-08-21 16:59:35 +02:00
<!DOCTYPE html>
2023-05-08 13:11:46 +02:00
<!-- Generated by pkgdown: do not edit by hand --> < html lang = "en" > < head > < meta http-equiv = "Content-Type" content = "text/html; charset=UTF-8" > < meta charset = "utf-8" > < meta http-equiv = "X-UA-Compatible" content = "IE=edge" > < meta name = "viewport" content = "width=device-width, initial-scale=1, shrink-to-fit=no" > < meta name = "description" content = "Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." > < title > Get Properties of an Antibiotic — ab_property • AMR (for R)< / title > <!-- favicons --> < link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" > < link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "180x180" href = "../apple-touch-icon.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "120x120" href = "../apple-touch-icon-120x120.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "76x76" href = "../apple-touch-icon-76x76.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "60x60" href = "../apple-touch-icon-60x60.png" > < script src = "../deps/jquery-3.6.0/jquery-3.6.0.min.js" > < / script > < meta name = "viewport" content = "width=device-width, initial-scale=1, shrink-to-fit=no" > < link href = "../deps/bootstrap-5.2.2/bootstrap.min.css" rel = "stylesheet" > < script src = "../deps/bootstrap-5.2.2/bootstrap.bundle.min.js" > < / script > < link href = "../deps/Fira_Code-0.4.6/font.css" rel = "stylesheet" > <!-- Font Awesome icons --> < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity = "sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin = "anonymous" > < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity = "sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin = "anonymous" > <!-- bootstrap - toc --> < script src = "https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity = "sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin = "anonymous" > < / script > <!-- headroom.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity = "sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script > <!-- clipboard.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script > <!-- search --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity = "sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity = "sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity = "sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin = "anonymous" > < / script > <!-- pkgdown --> < script src = "../pkgdown.js" > < / script > < link href = "../extra.css" rel = "stylesheet" > < script src = "../extra.js" > < / script > < meta property = "og:title" content = "Get Properties of an Antibiotic — ab_property" > < meta property = "og:description" content = "Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." > < meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" > < meta name = "twitter:card" content = "summary_large_image" > < meta name = "twitter:creator" content = "@msberends" > < meta name = "twitter:site" content = "@msberends" > <!-- mathjax --> < script src = "https://cdn
2022-08-21 16:59:35 +02:00
< 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 >
< a href = "#main" class = "visually-hidden-focusable" > Skip to contents< / a >
< nav class = "navbar fixed-top navbar-dark navbar-expand-lg bg-primary" > < div class = "container" >
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
2023-05-24 16:03:18 +02:00
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.0.0.9019< / small >
2022-08-21 16:59:35 +02:00
< button class = "navbar-toggler" type = "button" data-bs-toggle = "collapse" data-bs-target = "#navbar" aria-controls = "navbar" aria-expanded = "false" aria-label = "Toggle navigation" >
< span class = "navbar-toggler-icon" > < / span >
< / button >
< div id = "navbar" class = "collapse navbar-collapse ms-3" >
2023-05-24 16:03:18 +02:00
< ul class = "navbar-nav me-auto" > < li class = "active nav-item dropdown" >
2022-08-21 16:59:35 +02:00
< a href = "#" class = "nav-link dropdown-toggle" data-bs-toggle = "dropdown" role = "button" aria-expanded = "false" aria-haspopup = "true" id = "dropdown--how-to" >
< span class = "fa fa-question-circle" > < / span >
How to
< / a >
< div class = "dropdown-menu" aria-labelledby = "dropdown--how-to" >
< a class = "dropdown-item" href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
2023-01-23 20:14:37 +01:00
Conduct AMR Analysis
2022-08-21 16:59:35 +02:00
< / a >
2023-02-08 17:01:47 +01:00
< a class = "dropdown-item" href = "../reference/antibiogram.html" >
< span class = "fa fa-file-prescription" > < / span >
Generate Antibiogram (Trad./Syndromic/WISCA)
< / a >
2022-08-21 16:59:35 +02:00
< a class = "dropdown-item" href = "../articles/resistance_predict.html" >
< span class = "fa fa-dice" > < / span >
2023-01-23 20:14:37 +01:00
Predict Antimicrobial Resistance
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/datasets.html" >
< span class = "fa fa-database" > < / span >
2023-02-26 21:34:01 +01:00
Download Data Sets for Own Use
< / a >
< a class = "dropdown-item" href = "../reference/AMR-options.html" >
< span class = "fa fa-gear" > < / span >
Set User- Or Team-specific Package Settings
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
2023-01-23 20:14:37 +01:00
Conduct Principal Component Analysis for AMR
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
2023-01-23 20:14:37 +01:00
Determine Multi-Drug Resistance (MDR)
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
2023-01-23 20:14:37 +01:00
Work with WHONET Data
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
2023-01-23 20:14:37 +01:00
Apply Eucast Rules
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../reference/mo_property.html" >
< span class = "fa fa-bug" > < / span >
2023-01-23 20:14:37 +01:00
Get Taxonomy of a Microorganism
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../reference/ab_property.html" >
< span class = "fa fa-capsules" > < / span >
2023-01-23 20:14:37 +01:00
Get Properties of an Antibiotic Drug
2022-08-21 16:59:35 +02:00
< / a >
2022-11-13 08:54:32 +01:00
< a class = "dropdown-item" href = "../reference/av_property.html" >
< span class = "fa fa-capsules" > < / span >
2023-01-23 20:14:37 +01:00
Get Properties of an Antiviral Drug
2022-11-13 08:54:32 +01:00
< / a >
2022-08-21 16:59:35 +02:00
< / div >
< / li >
2023-05-24 16:03:18 +02:00
< li class = "nav-item dropdown" >
< a href = "#" class = "nav-link dropdown-toggle" data-bs-toggle = "dropdown" role = "button" aria-expanded = "false" aria-haspopup = "true" id = "dropdown--with-other-pkgs" >
< span class = "fa fa-circles-overlap" > < / span >
With other pkgs
< / a >
< div class = "dropdown-menu" aria-labelledby = "dropdown--with-other-pkgs" >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap" > < / span >
AMR & dplyr/tidyverse
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap" > < / span >
AMR & data.table
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap" > < / span >
AMR & tidymodels
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap" > < / span >
AMR & base R
< / a >
< / div >
< / li >
2022-08-21 16:59:35 +02:00
< li class = "nav-item" >
< a class = "nav-link" href = "../reference/index.html" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
< / li >
< li class = "nav-item" >
< a class = "nav-link" href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
2023-05-24 16:03:18 +02:00
< / ul > < form class = "form-inline my-2 my-lg-0" role = "search" >
< input type = "search" class = "form-control me-sm-2" aria-label = "Toggle navigation" name = "search-input" data-search-index = "../search.json" id = "search-input" placeholder = "Search for" autocomplete = "off" > < / form >
< ul class = "navbar-nav" > < li class = "nav-item" >
2022-08-21 16:59:35 +02:00
< a class = "nav-link" href = "../news/index.html" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
2023-05-24 16:03:18 +02:00
< li class = "nav-item" >
2022-08-21 16:59:35 +02:00
< a class = "external-link nav-link" href = "https://github.com/msberends/AMR" >
< span class = "fab fa fab fa-github" > < / span >
Source Code
< / a >
< / li >
< / ul > < / div >
< / div >
< / nav > < div class = "container template-reference-topic" >
< div class = "row" >
< main id = "main" class = "col-md-9" > < div class = "page-header" >
< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Get Properties of an Antibiotic< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/ab_property.R" class = "external-link" > < code > R/ab_property.R< / code > < / a > < / small >
< div class = "d-none name" > < code > ab_property.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
< p > Use these functions to return a specific property of an antibiotic from the < a href = "antibiotics.html" > antibiotics< / a > data set. All input values will be evaluated internally with < code > < a href = "as.ab.html" > as.ab()< / a > < / code > .< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , tolower < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_cid< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_synonyms< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_tradenames< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_group< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , only_first < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_atc_group1< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_atc_group2< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_loinc< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_ddd< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , administration < span class = "op" > =< / span > < span class = "st" > "oral"< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_ddd_units< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , administration < span class = "op" > =< / span > < span class = "st" > "oral"< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_info< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_url< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , open < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_property< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , property < span class = "op" > =< / span > < span class = "st" > "name"< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < / span >
< span > < span class = "va" > data< / span > ,< / span >
< span > < span class = "va" > ...< / span > ,< / span >
< span > property < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > snake_case < span class = "op" > =< / span > < span class = "cn" > NULL< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > x< / dt >
2022-11-13 13:52:01 +01:00
< dd > < p > any (vector of) text that can be coerced to a valid antibiotic drug code with < code > < a href = "as.ab.html" > as.ab()< / a > < / code > < / p > < / dd >
2022-08-21 16:59:35 +02:00
< dt > language< / dt >
2023-02-22 14:47:35 +01:00
< dd > < p > language of the returned text - the default is the current system language (see < code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > ) and can also be set with the < a href = "AMR-options.html" > package option< / a > < code > < a href = "AMR-options.html" > AMR_locale< / a > < / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / dd >
2022-08-21 16:59:35 +02:00
< dt > tolower< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether the first < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > of every output should be transformed to a lower case < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > . This will lead to e.g. "polymyxin B" and not "polymyxin b".< / p > < / dd >
< dt > ...< / dt >
2023-01-05 14:53:59 +01:00
< dd > < p > in case of < code > set_ab_names()< / code > and < code > data< / code > is a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > : columns to select (supports tidy selection such as < code > column1:column4< / code > ), otherwise other arguments passed on to < code > < a href = "as.ab.html" > as.ab()< / a > < / code > < / p > < / dd >
2022-08-21 16:59:35 +02:00
< dt > only_first< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)< / p > < / dd >
< dt > administration< / dt >
< dd > < p > way of administration, either < code > "oral"< / code > or < code > "iv"< / code > < / p > < / dd >
< dt > open< / dt >
< dd > < p > browse the URL using < code > < a href = "https://rdrr.io/r/utils/browseURL.html" class = "external-link" > utils::browseURL()< / a > < / code > < / p > < / dd >
< dt > property< / dt >
< dd > < p > one of the column names of one of the < a href = "antibiotics.html" > antibiotics< / a > data set: < code > vector_or(colnames(antibiotics), sort = FALSE)< / code > .< / p > < / dd >
< dt > data< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > of which the columns need to be renamed, or a < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > vector of column names< / p > < / dd >
< dt > snake_case< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether the names should be in so-called < a href = "https://en.wikipedia.org/wiki/Snake_case" class = "external-link" > snake case< / a > : in lower case and all spaces/slashes replaced with an underscore (< code > _< / code > )< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "value" > Value< a class = "anchor" aria-label = "anchor" href = "#value" > < / a > < / h2 >
< ul > < li > < p > An < a href = "https://rdrr.io/r/base/integer.html" class = "external-link" > integer< / a > in case of < code > ab_cid()< / code > < / p > < / li >
< li > < p > A named < a href = "https://rdrr.io/r/base/list.html" class = "external-link" > list< / a > in case of < code > ab_info()< / code > and multiple < code > ab_atc()< / code > /< code > ab_synonyms()< / code > /< code > ab_tradenames()< / code > < / p > < / li >
< li > < p > A < a href = "https://rdrr.io/r/base/double.html" class = "external-link" > double< / a > in case of < code > ab_ddd()< / code > < / p > < / li >
< li > < p > A < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > in case of < code > set_ab_names()< / code > < / p > < / li >
< li > < p > A < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > in all other cases< / p > < / li >
< / ul > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
< p > All output < a href = "translate.html" > will be translated< / a > where possible.< / p >
< p > The function < code > ab_url()< / code > will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.< / p >
< p > The function < code > set_ab_names()< / code > is a special column renaming function for < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If < code > property = "atc"< / code > is set, preference is given to ATC codes from the J-group.< / p >
< / div >
< div class = "section level2" >
< h2 id = "source" > Source< a class = "anchor" aria-label = "anchor" href = "#source" > < / a > < / h2 >
< p > World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: < a href = "https://www.whocc.no/atc_ddd_index/" class = "external-link" > https://www.whocc.no/atc_ddd_index/< / a > < / p >
< p > European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: < a href = "https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class = "external-link" > https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm< / a > < / p >
< / div >
< div class = "section level2" >
< h2 id = "reference-data-publicly-available" > Reference Data Publicly Available< a class = "anchor" aria-label = "anchor" href = "#reference-data-publicly-available" > < / a > < / h2 >
2023-01-21 23:53:21 +01:00
< p > All data sets in this < code > AMR< / code > package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit < a href = "https://msberends.github.io/AMR/articles/datasets.html" > our website for the download links< / a > . The actual files are of course available on < a href = "https://github.com/msberends/AMR/tree/main/data-raw" class = "external-link" > our GitHub repository< / a > .< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "section level2" >
< h2 id = "see-also" > See also< a class = "anchor" aria-label = "anchor" href = "#see-also" > < / a > < / h2 >
< div class = "dont-index" > < p > < a href = "antibiotics.html" > antibiotics< / a > < / p > < / div >
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # all properties:< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Amoxicillin"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CA04"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_cid< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 33613< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_synonyms< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "actimoxi" "amoclen" "amolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [4] "amopen" "amopenixin" "amoxibiotic" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "amoxicaps" "amoxicilina" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "amoxiden" "amoxil" "amoxivet" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [16] "amoxy" "amoxycillin" "amoxyke" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "anemolin" "aspenil" "atoksilin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "biomox" "bristamox" "cemoxin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "clamoxyl" "damoxy" "delacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [28] "demoksil" "dispermox" "efpenix" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "flemoxin" "hiconcil" "histocillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [34] "hydroxyampicillin" "ibiamox" "imacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "lamoxy" "largopen" "metafarma capsules" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [40] "metifarma capsules" "moksilin" "moxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "moxatag" "ospamox" "pamoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [46] "piramox" "promoxil" "remoxil" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] "robamox" "sawamox pm" "tolodina" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [52] "topramoxin" "unicillin" "utimox" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [55] "vetramox" < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_tradenames< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "actimoxi" "amoclen" "amolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [4] "amopen" "amopenixin" "amoxibiotic" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "amoxicaps" "amoxicilina" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "amoxiden" "amoxil" "amoxivet" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [16] "amoxy" "amoxycillin" "amoxyke" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "anemolin" "aspenil" "atoksilin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "biomox" "bristamox" "cemoxin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "clamoxyl" "damoxy" "delacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [28] "demoksil" "dispermox" "efpenix" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "flemoxin" "hiconcil" "histocillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [34] "hydroxyampicillin" "ibiamox" "imacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "lamoxy" "largopen" "metafarma capsules" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [40] "metifarma capsules" "moksilin" "moxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "moxatag" "ospamox" "pamoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [46] "piramox" "promoxil" "remoxil" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] "robamox" "sawamox pm" "tolodina" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [52] "topramoxin" "unicillin" "utimox" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [55] "vetramox" < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_group< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactams/penicillins"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc_group1< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactam antibacterials, penicillins"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc_group2< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Penicillins with extended spectrum"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_url< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Amoxicillin < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > "https://www.whocc.no/atc_ddd_index/?code=J01CA04& showdescription=no" < / span >
< span class = "r-in" > < span > < / span > < / span >
2023-05-24 16:03:18 +02:00
< span class = "r-in" > < span > < span class = "co" > # smart lowercase transformation< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > x < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "PLB"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Amoxicillin/clavulanic acid" "Polymyxin B" < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > x < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "PLB"< / span > < span class = "op" > )< / span > , tolower < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "amoxicillin/clavulanic acid" "polymyxin B" < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # defined daily doses (DDD)< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "oral"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 1.5< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd_units< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "oral"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "iv"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 3< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd_units< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "iv"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
< span class = "r-in" > < span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "fu" > ab_info< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < span class = "co" > # all properties as a list< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ab< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "AMX"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $cid< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 33613< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $name< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Amoxicillin"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $group< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactams/penicillins"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CA04"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactam antibacterials, penicillins"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Penicillins with extended spectrum"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $tradenames< / span >
2022-10-30 14:40:31 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "actimoxi" "amoclen" "amolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [4] "amopen" "amopenixin" "amoxibiotic" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "amoxicaps" "amoxicilina" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "amoxiden" "amoxil" "amoxivet" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [16] "amoxy" "amoxycillin" "amoxyke" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "anemolin" "aspenil" "atoksilin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "biomox" "bristamox" "cemoxin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "clamoxyl" "damoxy" "delacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [28] "demoksil" "dispermox" "efpenix" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "flemoxin" "hiconcil" "histocillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [34] "hydroxyampicillin" "ibiamox" "imacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "lamoxy" "largopen" "metafarma capsules" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [40] "metifarma capsules" "moksilin" "moxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "moxatag" "ospamox" "pamoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [46] "piramox" "promoxil" "remoxil" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] "robamox" "sawamox pm" "tolodina" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [52] "topramoxin" "unicillin" "utimox" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [55] "vetramox" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $loinc< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "16365-9" "25274-2" "3344-9" "80133-2"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 1.5< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 3< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "AMP"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CA01" "S01AA19"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_group< / span > < span class = "op" > (< / span > < span class = "st" > "J01CA01"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactams/penicillins"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_loinc< / span > < span class = "op" > (< / span > < span class = "st" > "ampicillin"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "st" > "21066-6"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Ampicillin"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "fl" > 6249< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Ampicillin"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "st" > "J01CA01"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Ampicillin"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # spelling from different languages and dyslexia are no problem< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "ceftriaxon"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "cephtriaxone"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "cephthriaxone"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "seephthriaaksone"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # use set_ab_names() for renaming columns< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" "age" "gender" "ward" "mo" "PEN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [8] "OXA" "FLC" "AMX" "AMC" "AMP" "TZP" "CZO" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [15] "FEP" "CXM" "FOX" "CTX" "CAZ" "CRO" "GEN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "TOB" "AMK" "KAN" "TMP" "SXT" "NIT" "FOS" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "LNZ" "CIP" "MFX" "VAN" "TEC" "TCY" "TGC" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [36] "DOX" "ERY" "CLI" "AZM" "IPM" "MEM" "MTR" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "CHL" "COL" "MUP" "RIF" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [3] "age" "gender" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [5] "ward" "mo" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "benzylpenicillin" "oxacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [9] "flucloxacillin" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [11] "amoxicillin_clavulanic_acid" "ampicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "piperacillin_tazobactam" "cefazolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [15] "cefepime" "cefuroxime" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [17] "cefoxitin" "cefotaxime" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "ceftazidime" "ceftriaxone" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [21] "gentamicin" "tobramycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [23] "amikacin" "kanamycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "trimethoprim" "trimethoprim_sulfamethoxazole"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [27] "nitrofurantoin" "fosfomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "linezolid" "ciprofloxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "moxifloxacin" "vancomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [33] "teicoplanin" "tetracycline" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [35] "tigecycline" "doxycycline" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "erythromycin" "clindamycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [39] "azithromycin" "imipenem" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [41] "meropenem" "metronidazole" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "chloramphenicol" "colistin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [45] "mupirocin" "rifampicin" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > , < span class = "va" > NIT< / span > < span class = "op" > :< / span > < span class = "va" > VAN< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" "age" "gender" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [5] "ward" "mo" "PEN" "OXA" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [9] "FLC" "AMX" "AMC" "AMP" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "TZP" "CZO" "FEP" "CXM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [17] "FOX" "CTX" "CAZ" "CRO" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [21] "GEN" "TOB" "AMK" "KAN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [33] "TEC" "TCY" "TGC" "DOX" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "ERY" "CLI" "AZM" "IPM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [41] "MEM" "MTR" "CHL" "COL" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [45] "MUP" "RIF" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # this does the same:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/rename.html" class = "external-link" > rename_with< / a > < / span > < span class = "op" > (< / span > < span class = "va" > set_ab_names< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # set_ab_names() works with any AB property:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > property < span class = "op" > =< / span > < span class = "st" > "atc"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.sir< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "va" > NIT< / span > < span class = "op" > :< / span > < span class = "va" > VAN< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" "age" "gender" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [5] "ward" "mo" "PEN" "OXA" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [9] "FLC" "AMX" "AMC" "AMP" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "TZP" "CZO" "FEP" "CXM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [17] "FOX" "CTX" "CAZ" "CRO" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [21] "GEN" "TOB" "AMK" "KAN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [33] "TEC" "TCY" "TGC" "DOX" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "ERY" "CLI" "AZM" "IPM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [41] "MEM" "MTR" "CHL" "COL" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [45] "MUP" "RIF" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
< / code > < / pre > < / div >
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
< / nav > < / aside > < / div >
< footer > < div class = "pkgdown-footer-left" >
2022-12-11 11:50:34 +01:00
< p > < / p > < p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "pkgdown-footer-right" >
2022-12-11 11:50:34 +01:00
< p > < / p > < p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
2022-08-21 16:59:35 +02:00
< / div >
< / footer > < / div >
< / body > < / html >
