2022-10-10 20:27:14 +02:00
<!DOCTYPE html>
2023-01-24 10:29:55 +01:00
<!-- 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 = "With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes." > < title > Add Custom Antimicrobials — add_custom_antimicrobials • 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-0.4.5/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 = "Add Custom Antimicrobials — add_custom_antimicrobials" > < meta property = "og:description" content = "With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes." > < meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" > < meta name = "twitter:card" content = "summary_large_image" > < meta name = "twitter:creator" content = "@msberends" > < meta name = "twitter:site" content = "@msberends" > <!-- mathjax --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity = "sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSS
2022-10-10 20:27:14 +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 >
2023-04-19 00:44:09 +02:00
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.0.0.9011< / small >
2022-10-10 20:27:14 +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" >
< ul class = "navbar-nav me-auto" > < li class = "nav-item" >
< a class = "nav-link" href = "../index.html" >
< span class = "fa fa-home" > < / span >
Home
< / a >
< / li >
< 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--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
2022-10-10 20:27:14 +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 >
2022-10-10 20:27:14 +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
2022-10-10 20:27:14 +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
2022-10-10 20:27:14 +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
2022-10-10 20:27:14 +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)
2022-10-10 20:27:14 +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
2022-10-10 20:27:14 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
2023-01-23 20:14:37 +01:00
Import Data From SPSS/SAS/Stata
2022-10-10 20:27:14 +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
2022-10-10 20:27:14 +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
2022-10-10 20:27:14 +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
2022-10-10 20:27:14 +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 >
2022-10-10 20:27:14 +02:00
< / div >
< / li >
< li class = "active 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 >
< li class = "nav-item" >
< a class = "nav-link" href = "../news/index.html" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< / 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" >
< 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" >
2023-01-14 20:00:10 +01:00
< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Add Custom Antimicrobials< / h1 >
2023-01-14 17:20:52 +01:00
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/custom_antimicrobials.R" class = "external-link" > < code > R/custom_antimicrobials.R< / code > < / a > < / small >
2022-10-10 20:27:14 +02:00
< div class = "d-none name" > < code > add_custom_antimicrobials.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
2023-01-14 20:00:10 +01:00
< p > With < code > add_custom_antimicrobials()< / code > you can add your own custom antimicrobial drug names and codes.< / p >
2022-10-10 20:27:14 +02:00
< / 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" > add_custom_antimicrobials< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > clear_custom_antimicrobials< / span > < span class = "op" > (< / 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 >
< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > resembling the < a href = "antibiotics.html" > antibiotics< / a > data set, at least containing columns "ab" and "name"< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
2022-12-27 16:14:41 +01:00
< p > < strong > Important:< / strong > Due to how < span style = "R" > R< / span > works, the < code > add_custom_antimicrobials()< / code > function has to be run in every < span style = "R" > R< / span > session - added antimicrobials are not stored between sessions and are thus lost when < span style = "R" > R< / span > is exited.< / p >
2023-03-12 13:10:15 +01:00
< p > There are two ways to circumvent this and automate the process of adding antimicrobials:< / p >
2023-02-22 14:47:35 +01:00
< p > < strong > Method 1:< / strong > Using the < a href = "AMR-options.html" > package option< / a > < code > < a href = "AMR-options.html" > AMR_custom_ab< / a > < / code > , which is the preferred method. To use this method:< / p > < ol > < li > < p > Create a data set in the structure of the < a href = "antibiotics.html" > antibiotics< / a > data set (containing at the very least columns "ab" and "name") and save it with < code > < a href = "https://rdrr.io/r/base/readRDS.html" class = "external-link" > saveRDS()< / a > < / code > to a location of choice, e.g. < code > "~/my_custom_ab.rds"< / code > , or any remote location.< / p > < / li >
< li > < p > Set the file location to the < a href = "AMR-options.html" > package option< / a > < code > < a href = "AMR-options.html" > AMR_custom_ab< / a > < / code > : < code > options(AMR_custom_ab = "~/my_custom_ab.rds")< / code > . This can even be a remote file location, such as an https URL. Since options are not saved between < span style = "R" > R< / span > sessions, it is best to save this option to the < code > .Rprofile< / code > file so that it will be loaded on start-up of < span style = "R" > R< / span > . To do this, open the < code > .Rprofile< / code > file using e.g. < code > utils::file.edit("~/.Rprofile")< / code > , add this text and save the file:< / p >
2023-01-23 20:14:37 +01:00
< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "co" > # Add custom antimicrobial codes:< / span > < / span >
2022-12-27 16:14:41 +01:00
< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/options.html" class = "external-link" > options< / a > < / span > < span class = "op" > (< / span > AMR_custom_ab < span class = "op" > =< / span > < span class = "st" > "~/my_custom_ab.rds"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div >
< p > Upon package load, this file will be loaded and run through the < code > add_custom_antimicrobials()< / code > function.< / p > < / li >
2023-03-12 13:10:15 +01:00
< / ol > < p > < strong > Method 2:< / strong > Loading the antimicrobial additions directly from your < code > .Rprofile< / code > file. Note that the definitions will be stored in a user-specific < span style = "R" > R< / span > file, which is a suboptimal workflow. To use this method:< / p > < ol > < li > < p > Edit the < code > .Rprofile< / code > file using e.g. < code > utils::file.edit("~/.Rprofile")< / code > .< / p > < / li >
2022-12-27 16:14:41 +01:00
< li > < p > Add a text like below and save the file:< / p >
< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "co" > # Add custom antibiotic drug codes:< / span > < / span >
2023-01-23 20:14:37 +01:00
< span > < span class = "fu" > AMR< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "../reference/add_custom_antimicrobials.html" > add_custom_antimicrobials< / a > < / span > < span class = "op" > (< / span > < / span >
2022-12-27 16:14:41 +01:00
< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > ab < span class = "op" > =< / span > < span class = "st" > "TESTAB"< / span > ,< / span >
< span > name < span class = "op" > =< / span > < span class = "st" > "Test Antibiotic"< / span > ,< / span >
< span > group < span class = "op" > =< / span > < span class = "st" > "Test Group"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div > < / li >
< / ol > < p > Use < code > clear_custom_antimicrobials()< / code > to clear the previously added antimicrobials.< / p >
< / div >
< div class = "section level2" >
< h2 id = "see-also" > See also< a class = "anchor" aria-label = "anchor" href = "#see-also" > < / a > < / h2 >
2023-01-14 20:00:10 +01:00
< div class = "dont-index" > < p > < code > < a href = "add_custom_microorganisms.html" > add_custom_microorganisms()< / a > < / code > to add custom microorganisms.< / p > < / div >
2022-10-10 20:27:14 +02:00
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
2022-10-15 15:28:27 +02:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
2023-01-14 20:00:10 +01:00
< span class = "r-in" > < span > < span class = "co" > # returns NA and throws a warning (which is suppressed here):< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/warning.html" class = "external-link" > suppressWarnings< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
2022-10-30 21:14:42 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "as.ab.html" > as.ab< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-10-19 11:58:58 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Class 'ab'< / span >
2022-10-30 21:14:42 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] < NA> < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # now add a custom entry - it will be considered by as.ab() and< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # all ab_*() functions< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > add_custom_antimicrobials< / span > < span class = "op" > (< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
2022-10-30 21:14:42 +01:00
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "TESTAB"< / span > ,< / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > name < span class = "op" > =< / span > < span class = "st" > "Test Antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # you can add any property present in the< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # 'antibiotics' data set, such as 'group':< / span > < / span > < / span >
< span class = "r-in" > < span > group < span class = "op" > =< / span > < span class = "st" > "Test Group"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-11-24 20:37:19 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-in" > < span > < / span > < / span >
2022-10-30 21:14:42 +01:00
< span class = "r-in" > < span > < span class = "co" > # "testab" is now a new antibiotic:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "as.ab.html" > as.ab< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-19 11:58:58 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Class 'ab'< / span >
2022-10-30 21:14:42 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] TESTAB< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Antibiotic"< / span >
2022-10-30 21:14:42 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_group< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Group"< / span >
< span class = "r-in" > < span > < / span > < / span >
2022-10-30 21:14:42 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_info< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ab< / span >
2022-10-30 21:14:42 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "TESTAB"< / span >
2022-10-10 21:46:42 +02:00
< 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] NA< / 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] "Test Antibiotic"< / 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] "Test Group"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc< / span >
2022-10-22 10:25:54 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
2022-10-10 21:46:42 +02:00
< 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] NA< / 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] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $tradenames< / span >
2022-10-22 10:25:54 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
2022-10-10 21:46:42 +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 >
2022-10-22 10:25:54 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
2022-10-10 21:46:42 +02:00
< 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] NA< / 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] NA< / 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] NA< / 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] NA< / 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 >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Add Co-fluampicil, which is one of the many J01CR50 codes, see< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # https://www.whocc.no/ddd/list_of_ddds_combined_products/< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > add_custom_antimicrobials< / span > < span class = "op" > (< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "COFLU"< / span > ,< / span > < / span >
< span class = "r-in" > < span > name < span class = "op" > =< / span > < span class = "st" > "Co-fluampicil"< / span > ,< / span > < / span >
< span class = "r-in" > < span > atc < span class = "op" > =< / span > < span class = "st" > "J01CR50"< / span > ,< / span > < / span >
2022-12-27 16:14:41 +01:00
< span class = "r-in" > < span > group < span class = "op" > =< / span > < span class = "st" > "Beta-lactams/penicillins"< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-11-24 20:37:19 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_atc< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Co-fluampicil"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CR50"< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "J01CR50"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Co-fluampicil"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # even antibiotic selectors work< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
2022-10-30 21:14:42 +01:00
< span class = "r-in" > < span > random_column < span class = "op" > =< / span > < span class = "st" > "some value"< / span > ,< / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-in" > < span > coflu < span class = "op" > =< / span > < span class = "fu" > < a href = "as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > ampicillin < span class = "op" > =< / span > < span class = "fu" > < a href = "as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "va" > x< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > random_column coflu ampicillin< / span >
2022-10-30 21:14:42 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 some value S R< / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > [< / span > , < span class = "fu" > < a href = "antibiotic_class_selectors.html" > betalactams< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span > < / span > < / span >
2022-11-24 20:37:19 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'ampicillin'< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > coflu ampicillin< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 S R< / span >
2022-10-15 15:28:27 +02:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< / code > < / pre > < / div >
2022-10-10 20:27:14 +02:00
< / 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 >
2022-10-10 20:27:14 +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 >
2022-10-10 20:27:14 +02:00
< / div >
< / footer > < / div >
< / body > < / html >
