mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
Implement extensive support for antiviral agents support (#77)
This commit is contained in:
Dr. Matthijs Berends
GitHub
parent
d2edcf51ad
commit
496c08d851
@ -1,6 +1,6 @@
|
|||||||
Package: AMR
|
Package: AMR
|
||||||
Version: 1.8.2.9047
|
Version: 1.8.2.9049
|
||||||
Date: 2022-11-12
|
Date: 2022-11-13
|
||||||
Title: Antimicrobial Resistance Data Analysis
|
Title: Antimicrobial Resistance Data Analysis
|
||||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||||
data analysis and to work with microbial and antimicrobial properties by
|
data analysis and to work with microbial and antimicrobial properties by
|
||||||
|
|||||||
24
NAMESPACE
24
NAMESPACE
@ -18,19 +18,23 @@ S3method("==",mic)
|
|||||||
S3method(">",mic)
|
S3method(">",mic)
|
||||||
S3method(">=",mic)
|
S3method(">=",mic)
|
||||||
S3method("[",ab)
|
S3method("[",ab)
|
||||||
|
S3method("[",av)
|
||||||
S3method("[",disk)
|
S3method("[",disk)
|
||||||
S3method("[",mic)
|
S3method("[",mic)
|
||||||
S3method("[",mo)
|
S3method("[",mo)
|
||||||
S3method("[<-",ab)
|
S3method("[<-",ab)
|
||||||
|
S3method("[<-",av)
|
||||||
S3method("[<-",disk)
|
S3method("[<-",disk)
|
||||||
S3method("[<-",mic)
|
S3method("[<-",mic)
|
||||||
S3method("[<-",mo)
|
S3method("[<-",mo)
|
||||||
S3method("[<-",rsi)
|
S3method("[<-",rsi)
|
||||||
S3method("[[",ab)
|
S3method("[[",ab)
|
||||||
|
S3method("[[",av)
|
||||||
S3method("[[",disk)
|
S3method("[[",disk)
|
||||||
S3method("[[",mic)
|
S3method("[[",mic)
|
||||||
S3method("[[",mo)
|
S3method("[[",mo)
|
||||||
S3method("[[<-",ab)
|
S3method("[[<-",ab)
|
||||||
|
S3method("[[<-",av)
|
||||||
S3method("[[<-",disk)
|
S3method("[[<-",disk)
|
||||||
S3method("[[<-",mic)
|
S3method("[[<-",mic)
|
||||||
S3method("[[<-",mo)
|
S3method("[[<-",mo)
|
||||||
@ -48,6 +52,7 @@ S3method(any,ab_selector)
|
|||||||
S3method(any,ab_selector_any_all)
|
S3method(any,ab_selector_any_all)
|
||||||
S3method(any,mic)
|
S3method(any,mic)
|
||||||
S3method(as.data.frame,ab)
|
S3method(as.data.frame,ab)
|
||||||
|
S3method(as.data.frame,av)
|
||||||
S3method(as.data.frame,mo)
|
S3method(as.data.frame,mo)
|
||||||
S3method(as.double,mic)
|
S3method(as.double,mic)
|
||||||
S3method(as.list,custom_eucast_rules)
|
S3method(as.list,custom_eucast_rules)
|
||||||
@ -67,6 +72,7 @@ S3method(barplot,mic)
|
|||||||
S3method(barplot,rsi)
|
S3method(barplot,rsi)
|
||||||
S3method(c,ab)
|
S3method(c,ab)
|
||||||
S3method(c,ab_selector)
|
S3method(c,ab_selector)
|
||||||
|
S3method(c,av)
|
||||||
S3method(c,custom_eucast_rules)
|
S3method(c,custom_eucast_rules)
|
||||||
S3method(c,custom_mdro_guideline)
|
S3method(c,custom_mdro_guideline)
|
||||||
S3method(c,disk)
|
S3method(c,disk)
|
||||||
@ -113,6 +119,7 @@ S3method(plot,mic)
|
|||||||
S3method(plot,resistance_predict)
|
S3method(plot,resistance_predict)
|
||||||
S3method(plot,rsi)
|
S3method(plot,rsi)
|
||||||
S3method(print,ab)
|
S3method(print,ab)
|
||||||
|
S3method(print,av)
|
||||||
S3method(print,bug_drug_combinations)
|
S3method(print,bug_drug_combinations)
|
||||||
S3method(print,custom_eucast_rules)
|
S3method(print,custom_eucast_rules)
|
||||||
S3method(print,custom_mdro_guideline)
|
S3method(print,custom_mdro_guideline)
|
||||||
@ -127,6 +134,7 @@ S3method(prod,mic)
|
|||||||
S3method(quantile,mic)
|
S3method(quantile,mic)
|
||||||
S3method(range,mic)
|
S3method(range,mic)
|
||||||
S3method(rep,ab)
|
S3method(rep,ab)
|
||||||
|
S3method(rep,av)
|
||||||
S3method(rep,disk)
|
S3method(rep,disk)
|
||||||
S3method(rep,mic)
|
S3method(rep,mic)
|
||||||
S3method(rep,mo)
|
S3method(rep,mo)
|
||||||
@ -153,6 +161,7 @@ S3method(tanpi,mic)
|
|||||||
S3method(trigamma,mic)
|
S3method(trigamma,mic)
|
||||||
S3method(trunc,mic)
|
S3method(trunc,mic)
|
||||||
S3method(unique,ab)
|
S3method(unique,ab)
|
||||||
|
S3method(unique,av)
|
||||||
S3method(unique,disk)
|
S3method(unique,disk)
|
||||||
S3method(unique,mic)
|
S3method(unique,mic)
|
||||||
S3method(unique,mo)
|
S3method(unique,mo)
|
||||||
@ -195,6 +204,7 @@ export(antifungals)
|
|||||||
export(antimicrobials_equal)
|
export(antimicrobials_equal)
|
||||||
export(antimycobacterials)
|
export(antimycobacterials)
|
||||||
export(as.ab)
|
export(as.ab)
|
||||||
|
export(as.av)
|
||||||
export(as.disk)
|
export(as.disk)
|
||||||
export(as.mic)
|
export(as.mic)
|
||||||
export(as.mo)
|
export(as.mo)
|
||||||
@ -203,6 +213,19 @@ export(atc_online_ddd)
|
|||||||
export(atc_online_ddd_units)
|
export(atc_online_ddd_units)
|
||||||
export(atc_online_groups)
|
export(atc_online_groups)
|
||||||
export(atc_online_property)
|
export(atc_online_property)
|
||||||
|
export(av_atc)
|
||||||
|
export(av_cid)
|
||||||
|
export(av_ddd)
|
||||||
|
export(av_ddd_units)
|
||||||
|
export(av_from_text)
|
||||||
|
export(av_group)
|
||||||
|
export(av_info)
|
||||||
|
export(av_loinc)
|
||||||
|
export(av_name)
|
||||||
|
export(av_property)
|
||||||
|
export(av_synonyms)
|
||||||
|
export(av_tradenames)
|
||||||
|
export(av_url)
|
||||||
export(availability)
|
export(availability)
|
||||||
export(betalactams)
|
export(betalactams)
|
||||||
export(brmo)
|
export(brmo)
|
||||||
@ -246,6 +269,7 @@ export(glycopeptides)
|
|||||||
export(guess_ab_col)
|
export(guess_ab_col)
|
||||||
export(inner_join_microorganisms)
|
export(inner_join_microorganisms)
|
||||||
export(is.ab)
|
export(is.ab)
|
||||||
|
export(is.av)
|
||||||
export(is.disk)
|
export(is.disk)
|
||||||
export(is.mic)
|
export(is.mic)
|
||||||
export(is.mo)
|
export(is.mo)
|
||||||
|
|||||||
21
R/ab.R
21
R/ab.R
@ -82,8 +82,8 @@
|
|||||||
#'
|
#'
|
||||||
#' # use ab_* functions to get a specific properties (see ?ab_property);
|
#' # use ab_* functions to get a specific properties (see ?ab_property);
|
||||||
#' # they use as.ab() internally:
|
#' # they use as.ab() internally:
|
||||||
#' ab_name("J01FA01") # "Erythromycin"
|
#' ab_name("J01FA01")
|
||||||
#' ab_name("eryt") # "Erythromycin"
|
#' ab_name("eryt")
|
||||||
#'
|
#'
|
||||||
#' \donttest{
|
#' \donttest{
|
||||||
#' if (require("dplyr")) {
|
#' if (require("dplyr")) {
|
||||||
@ -650,3 +650,20 @@ generalise_antibiotic_name <- function(x) {
|
|||||||
x <- gsub("(/| AND | WITH | W/|[+]|[-])+", " ", x, perl = TRUE)
|
x <- gsub("(/| AND | WITH | W/|[+]|[-])+", " ", x, perl = TRUE)
|
||||||
x
|
x
|
||||||
}
|
}
|
||||||
|
|
||||||
|
get_translate_ab <- function(translate_ab) {
|
||||||
|
translate_ab <- as.character(translate_ab)[1L]
|
||||||
|
if (translate_ab %in% c("TRUE", "official")) {
|
||||||
|
return("name")
|
||||||
|
} else if (translate_ab %in% c(NA_character_, "FALSE")) {
|
||||||
|
return(FALSE)
|
||||||
|
} else {
|
||||||
|
translate_ab <- tolower(translate_ab)
|
||||||
|
stop_ifnot(translate_ab %in% colnames(AMR::antibiotics),
|
||||||
|
"invalid value for 'translate_ab', this must be a column name of the antibiotics data set\n",
|
||||||
|
"or TRUE (equals 'name') or FALSE to not translate at all.",
|
||||||
|
call = FALSE
|
||||||
|
)
|
||||||
|
translate_ab
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|||||||
@ -59,7 +59,7 @@
|
|||||||
#' @examples
|
#' @examples
|
||||||
#' # mind the bad spelling of amoxicillin in this line,
|
#' # mind the bad spelling of amoxicillin in this line,
|
||||||
#' # straight from a true health care record:
|
#' # straight from a true health care record:
|
||||||
#' ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")
|
#' ab_from_text("28/03/2020 regular amoxicilliin 500mg po tid")
|
||||||
#'
|
#'
|
||||||
#' ab_from_text("500 mg amoxi po and 400mg cipro iv")
|
#' ab_from_text("500 mg amoxi po and 400mg cipro iv")
|
||||||
#' ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "dose")
|
#' ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "dose")
|
||||||
|
|||||||
@ -59,38 +59,35 @@
|
|||||||
#' @inheritSection AMR Reference Data Publicly Available
|
#' @inheritSection AMR Reference Data Publicly Available
|
||||||
#' @examples
|
#' @examples
|
||||||
#' # all properties:
|
#' # all properties:
|
||||||
#' ab_name("AMX") # "Amoxicillin"
|
#' ab_name("AMX")
|
||||||
#' ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
|
#' ab_atc("AMX")
|
||||||
#' ab_cid("AMX") # 33613 (Compound ID from PubChem)
|
#' ab_cid("AMX")
|
||||||
#' ab_synonyms("AMX") # a list with brand names of amoxicillin
|
#' ab_synonyms("AMX")
|
||||||
#' ab_tradenames("AMX") # same
|
#' ab_tradenames("AMX")
|
||||||
#' ab_group("AMX") # "Beta-lactams/penicillins"
|
#' ab_group("AMX")
|
||||||
#' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
|
#' ab_atc_group1("AMX")
|
||||||
#' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
|
#' ab_atc_group2("AMX")
|
||||||
#' ab_url("AMX") # link to the official WHO page
|
#' ab_url("AMX")
|
||||||
#'
|
#'
|
||||||
#' # smart lowercase tranformation
|
#' # smart lowercase tranformation
|
||||||
#' ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
|
#' ab_name(x = c("AMC", "PLB"))
|
||||||
#' ab_name(
|
#' ab_name(x = c("AMC", "PLB"), tolower = TRUE)
|
||||||
#' x = c("AMC", "PLB"),
|
|
||||||
#' tolower = TRUE
|
|
||||||
#' ) # "amoxicillin/clavulanic acid" "polymyxin B"
|
|
||||||
#'
|
#'
|
||||||
#' # defined daily doses (DDD)
|
#' # defined daily doses (DDD)
|
||||||
#' ab_ddd("AMX", "oral") # 1.5
|
#' ab_ddd("AMX", "oral")
|
||||||
#' ab_ddd_units("AMX", "oral") # "g"
|
#' ab_ddd_units("AMX", "oral")
|
||||||
#' ab_ddd("AMX", "iv") # 3
|
#' ab_ddd("AMX", "iv")
|
||||||
#' ab_ddd_units("AMX", "iv") # "g"
|
#' ab_ddd_units("AMX", "iv")
|
||||||
#'
|
#'
|
||||||
#' ab_info("AMX") # all properties as a list
|
#' ab_info("AMX") # all properties as a list
|
||||||
#'
|
#'
|
||||||
#' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
|
#' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
|
||||||
#' ab_atc("AMP") # ATC code of AMP (ampicillin)
|
#' ab_atc("AMP")
|
||||||
#' ab_group("J01CA01") # Drug group of ampicillins ATC code
|
#' ab_group("J01CA01")
|
||||||
#' ab_loinc("ampicillin") # LOINC codes of ampicillin
|
#' ab_loinc("ampicillin")
|
||||||
#' ab_name("21066-6") # "Ampicillin" (using LOINC)
|
#' ab_name("21066-6")
|
||||||
#' ab_name(6249) # "Ampicillin" (using CID)
|
#' ab_name(6249)
|
||||||
#' ab_name("J01CA01") # "Ampicillin" (using ATC)
|
#' ab_name("J01CA01")
|
||||||
#'
|
#'
|
||||||
#' # spelling from different languages and dyslexia are no problem
|
#' # spelling from different languages and dyslexia are no problem
|
||||||
#' ab_atc("ceftriaxon")
|
#' ab_atc("ceftriaxon")
|
||||||
@ -244,20 +241,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
|
|||||||
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
||||||
|
|
||||||
x <- as.ab(x, ...)
|
x <- as.ab(x, ...)
|
||||||
ddd_prop <- administration
|
ddd_prop <- paste0(administration, "_ddd")
|
||||||
# old behaviour
|
|
||||||
units <- list(...)$units
|
|
||||||
if (!is.null(units) && isTRUE(units)) {
|
|
||||||
if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
|
|
||||||
warning_(
|
|
||||||
"in `ab_ddd()`: using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead.",
|
|
||||||
"This warning will be shown once per session."
|
|
||||||
)
|
|
||||||
}
|
|
||||||
ddd_prop <- paste0(ddd_prop, "_units")
|
|
||||||
} else {
|
|
||||||
ddd_prop <- paste0(ddd_prop, "_ddd")
|
|
||||||
}
|
|
||||||
out <- ab_validate(x = x, property = ddd_prop)
|
out <- ab_validate(x = x, property = ddd_prop)
|
||||||
|
|
||||||
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
|
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
|
||||||
@ -277,16 +261,17 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
|
|||||||
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
||||||
|
|
||||||
x <- as.ab(x, ...)
|
x <- as.ab(x, ...)
|
||||||
if (any(ab_name(x, language = NULL) %like% "/")) {
|
ddd_prop <- paste0(administration, "_units")
|
||||||
|
out <- ab_validate(x = x, property = ddd_prop)
|
||||||
|
|
||||||
|
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
|
||||||
warning_(
|
warning_(
|
||||||
"in `ab_ddd_units()`: DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package.",
|
"in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
|
||||||
"Please refer to the WHOCC website:\n",
|
"Please refer to the WHOCC website:\n",
|
||||||
"www.whocc.no/ddd/list_of_ddds_combined_products/"
|
"www.whocc.no/ddd/list_of_ddds_combined_products/"
|
||||||
)
|
)
|
||||||
}
|
}
|
||||||
|
out
|
||||||
ddd_prop <- paste0(administration, "_units")
|
|
||||||
ab_validate(x = x, property = ddd_prop)
|
|
||||||
}
|
}
|
||||||
|
|
||||||
#' @rdname ab_property
|
#' @rdname ab_property
|
||||||
|
|||||||
2
R/amr.R
2
R/amr.R
@ -36,7 +36,7 @@
|
|||||||
#'
|
#'
|
||||||
#' This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
|
#' This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
|
||||||
#'
|
#'
|
||||||
#' After installing this package, \R knows `r format_included_data_number(microorganisms)` distinct microbial species and all `r format_included_data_number(rbind(antibiotics[, "atc", drop = FALSE], antivirals[, "atc", drop = FALSE]))` antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
|
#' After installing this package, \R knows `r format_included_data_number(microorganisms)` distinct microbial species and all `r format_included_data_number(rbind(antibiotics[, "name", drop = FALSE], antivirals[, "name", drop = FALSE]))` antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
|
||||||
#'
|
#'
|
||||||
#' This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
|
#' This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
|
||||||
#'
|
#'
|
||||||
|
|||||||
613
R/av.R
Executable file
613
R/av.R
Executable file
@ -0,0 +1,613 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||||
|
# #
|
||||||
|
# SOURCE #
|
||||||
|
# https://github.com/msberends/AMR #
|
||||||
|
# #
|
||||||
|
# CITE AS #
|
||||||
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||||
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||||
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||||
|
# doi:10.18637/jss.v104.i03 #
|
||||||
|
# #
|
||||||
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
# #
|
||||||
|
# This R package is free software; you can freely use and distribute #
|
||||||
|
# it for both personal and commercial purposes under the terms of the #
|
||||||
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||||
|
# the Free Software Foundation. #
|
||||||
|
# We created this package for both routine data analysis and academic #
|
||||||
|
# research and it was publicly released in the hope that it will be #
|
||||||
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||||
|
# #
|
||||||
|
# Visit our website for the full manual and a complete tutorial about #
|
||||||
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
#' Transform Input to an Antiviral Agent ID
|
||||||
|
#'
|
||||||
|
#' Use this function to determine the antiviral agent code of one or more antiviral agents. The data set [antivirals] will be searched for abbreviations, official names and synonyms (brand names).
|
||||||
|
#' @param x a [character] vector to determine to antiviral agent ID
|
||||||
|
#' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antiviral agent code or name can be retrieved from a single input value.
|
||||||
|
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
|
||||||
|
#' @param ... arguments passed on to internal functions
|
||||||
|
#' @rdname as.av
|
||||||
|
#' @inheritSection WHOCC WHOCC
|
||||||
|
#' @details All entries in the [antivirals] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
|
||||||
|
#'
|
||||||
|
#' All these properties will be searched for the user input. The [as.av()] can correct for different forms of misspelling:
|
||||||
|
#'
|
||||||
|
#' * Wrong spelling of drug names (such as "acyclovir"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.
|
||||||
|
#' * Too few or too many vowels or consonants
|
||||||
|
#' * Switching two characters (such as "aycclovir", often the case in clinical data, when doctors typed too fast)
|
||||||
|
#' * Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
|
||||||
|
#'
|
||||||
|
#' Use the [`av_*`][av_property()] functions to get properties based on the returned antiviral agent ID, see *Examples*.
|
||||||
|
#'
|
||||||
|
#' Note: the [as.av()] and [`av_*`][av_property()] functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
|
||||||
|
#' @section Source:
|
||||||
|
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
|
||||||
|
#'
|
||||||
|
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
|
||||||
|
#' @aliases av
|
||||||
|
#' @return A [character] [vector] with additional class [`ab`]
|
||||||
|
#' @seealso
|
||||||
|
#' * [antivirals] for the [data.frame] that is being used to determine ATCs
|
||||||
|
#' * [av_from_text()] for a function to retrieve antimicrobial drugs from clinical text (from health care records)
|
||||||
|
#' @inheritSection AMR Reference Data Publicly Available
|
||||||
|
#' @export
|
||||||
|
#' @examples
|
||||||
|
#' # these examples all return "ACI", the ID of aciclovir:
|
||||||
|
#' as.av("J05AB01")
|
||||||
|
#' as.av("J 05 AB 01")
|
||||||
|
#' as.av("Aciclovir")
|
||||||
|
#' as.av("aciclo")
|
||||||
|
#' as.av(" aciclo 123")
|
||||||
|
#' as.av("ACICL")
|
||||||
|
#' as.av("ACI")
|
||||||
|
#' as.av("Virorax") # trade name
|
||||||
|
#' as.av("Zovirax") # trade name
|
||||||
|
#'
|
||||||
|
#' as.av("acyklofir") # severe spelling error, yet works
|
||||||
|
#'
|
||||||
|
#' # use av_* functions to get a specific properties (see ?av_property);
|
||||||
|
#' # they use as.av() internally:
|
||||||
|
#' av_name("J05AB01")
|
||||||
|
#' av_name("acicl")
|
||||||
|
as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||||
|
meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
|
||||||
|
meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
|
||||||
|
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||||
|
|
||||||
|
if (is.av(x)) {
|
||||||
|
return(x)
|
||||||
|
}
|
||||||
|
if (all(x %in% c(AMR_env$AV_lookup$av, NA))) {
|
||||||
|
# all valid AB codes, but not yet right class
|
||||||
|
return(set_clean_class(x,
|
||||||
|
new_class = c("av", "character")
|
||||||
|
))
|
||||||
|
}
|
||||||
|
|
||||||
|
initial_search <- is.null(list(...)$initial_search)
|
||||||
|
already_regex <- isTRUE(list(...)$already_regex)
|
||||||
|
fast_mode <- isTRUE(list(...)$fast_mode)
|
||||||
|
|
||||||
|
x_bak <- x
|
||||||
|
x <- toupper(x)
|
||||||
|
|
||||||
|
# remove diacritics
|
||||||
|
x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
|
||||||
|
x <- gsub('"', "", x, fixed = TRUE)
|
||||||
|
x <- gsub("(specimen|specimen date|specimen_date|spec_date|gender|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
|
||||||
|
x_bak_clean <- x
|
||||||
|
if (already_regex == FALSE) {
|
||||||
|
x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
|
||||||
|
}
|
||||||
|
|
||||||
|
x <- unique(x_bak_clean) # this means that every x is in fact generalise_antibiotic_name(x)
|
||||||
|
x_new <- rep(NA_character_, length(x))
|
||||||
|
x_unknown <- character(0)
|
||||||
|
x_unknown_ATCs <- character(0)
|
||||||
|
|
||||||
|
note_if_more_than_one_found <- function(found, index, from_text) {
|
||||||
|
if (initial_search == TRUE && isTRUE(length(from_text) > 1)) {
|
||||||
|
avnames <- av_name(from_text, tolower = TRUE, initial_search = FALSE)
|
||||||
|
if (av_name(found[1L], language = NULL) %like% "(clavulanic acid|avibactam)") {
|
||||||
|
avnames <- avnames[!avnames %in% c("clavulanic acid", "avibactam")]
|
||||||
|
}
|
||||||
|
if (length(avnames) > 1) {
|
||||||
|
warning_(
|
||||||
|
"More than one result was found for item ", index, ": ",
|
||||||
|
vector_and(avnames, quotes = FALSE)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
found[1L]
|
||||||
|
}
|
||||||
|
|
||||||
|
# Fill in names, AB codes, CID codes and ATC codes directly (`x` is already clean and uppercase)
|
||||||
|
known_names <- x %in% AMR_env$AV_lookup$generalised_name
|
||||||
|
x_new[known_names] <- AMR_env$AV_lookup$av[match(x[known_names], AMR_env$AV_lookup$generalised_name)]
|
||||||
|
known_codes_av <- x %in% AMR_env$AV_lookup$av
|
||||||
|
known_codes_atc <- vapply(FUN.VALUE = logical(1), x, function(x_) x_ %in% unlist(AMR_env$AV_lookup$atc), USE.NAMES = FALSE)
|
||||||
|
known_codes_cid <- x %in% AMR_env$AV_lookup$cid
|
||||||
|
x_new[known_codes_av] <- AMR_env$AV_lookup$av[match(x[known_codes_av], AMR_env$AV_lookup$av)]
|
||||||
|
x_new[known_codes_atc] <- AMR_env$AV_lookup$av[vapply(
|
||||||
|
FUN.VALUE = integer(1),
|
||||||
|
x[known_codes_atc],
|
||||||
|
function(x_) {
|
||||||
|
which(vapply(
|
||||||
|
FUN.VALUE = logical(1),
|
||||||
|
AMR_env$AV_lookup$atc,
|
||||||
|
function(atc) x_ %in% atc
|
||||||
|
))[1L]
|
||||||
|
},
|
||||||
|
USE.NAMES = FALSE
|
||||||
|
)]
|
||||||
|
x_new[known_codes_cid] <- AMR_env$AV_lookup$av[match(x[known_codes_cid], AMR_env$AV_lookup$cid)]
|
||||||
|
previously_coerced <- x %in% AMR_env$av_previously_coerced$x
|
||||||
|
x_new[previously_coerced & is.na(x_new)] <- AMR_env$av_previously_coerced$av[match(x[is.na(x_new) & x %in% AMR_env$av_previously_coerced$x], AMR_env$av_previously_coerced$x)]
|
||||||
|
already_known <- known_names | known_codes_av | known_codes_atc | known_codes_cid | previously_coerced
|
||||||
|
|
||||||
|
# fix for NAs
|
||||||
|
x_new[is.na(x)] <- NA
|
||||||
|
already_known[is.na(x)] <- FALSE
|
||||||
|
|
||||||
|
if (initial_search == TRUE && sum(already_known) < length(x)) {
|
||||||
|
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
|
||||||
|
on.exit(close(progress))
|
||||||
|
}
|
||||||
|
|
||||||
|
for (i in which(!already_known)) {
|
||||||
|
if (initial_search == TRUE) {
|
||||||
|
progress$tick()
|
||||||
|
}
|
||||||
|
|
||||||
|
if (is.na(x[i]) || is.null(x[i])) {
|
||||||
|
next
|
||||||
|
}
|
||||||
|
if (identical(x[i], "") ||
|
||||||
|
# prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it:
|
||||||
|
identical(tolower(x[i]), "bacteria")) {
|
||||||
|
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
|
||||||
|
next
|
||||||
|
}
|
||||||
|
if (x[i] %like_case% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]") {
|
||||||
|
# seems an ATC code, but the available ones are in `already_known`, so:
|
||||||
|
x_unknown <- c(x_unknown, x[i])
|
||||||
|
x_unknown_ATCs <- c(x_unknown_ATCs, x[i])
|
||||||
|
x_new[i] <- NA_character_
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
|
||||||
|
from_text <- tryCatch(suppressWarnings(av_from_text(x[i], initial_search = FALSE, translate_av = FALSE)[[1]]),
|
||||||
|
error = function(e) character(0)
|
||||||
|
)
|
||||||
|
} else {
|
||||||
|
from_text <- character(0)
|
||||||
|
}
|
||||||
|
|
||||||
|
# old code for phenoxymethylpenicillin (Peni V)
|
||||||
|
if (x[i] == "PNV") {
|
||||||
|
x_new[i] <- "PHN"
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# exact LOINC code
|
||||||
|
loinc_found <- unlist(lapply(
|
||||||
|
AMR_env$AV_lookup$generalised_loinc,
|
||||||
|
function(s) x[i] %in% s
|
||||||
|
))
|
||||||
|
found <- AMR_env$AV_lookup$av[loinc_found == TRUE]
|
||||||
|
if (length(found) > 0) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# exact synonym
|
||||||
|
synonym_found <- unlist(lapply(
|
||||||
|
AMR_env$AV_lookup$generalised_synonyms,
|
||||||
|
function(s) x[i] %in% s
|
||||||
|
))
|
||||||
|
found <- AMR_env$AV_lookup$av[synonym_found == TRUE]
|
||||||
|
if (length(found) > 0) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# length of input is quite long, and Levenshtein distance is only max 2
|
||||||
|
if (nchar(x[i]) >= 10) {
|
||||||
|
levenshtein <- as.double(utils::adist(x[i], AMR_env$AV_lookup$generalised_name))
|
||||||
|
if (any(levenshtein <= 2)) {
|
||||||
|
found <- AMR_env$AV_lookup$av[which(levenshtein <= 2)]
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# allow characters that resemble others, but only continue when having more than 3 characters
|
||||||
|
if (nchar(x[i]) <= 3) {
|
||||||
|
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
|
||||||
|
next
|
||||||
|
}
|
||||||
|
x_spelling <- x[i]
|
||||||
|
if (already_regex == FALSE) {
|
||||||
|
x_spelling <- gsub("[IY]+", "[IY]+", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("(C|K|Q|QU|S|Z|X|KS)+", "(C|K|Q|QU|S|Z|X|KS)+", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("(PH|F|V)+", "(PH|F|V)+", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("(TH|T)+", "(TH|T)+", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("A+", "A+", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("E+", "E+", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("O+", "O+", x_spelling, perl = TRUE)
|
||||||
|
# allow any ending of -in/-ine and -im/-ime
|
||||||
|
x_spelling <- gsub("(\\[IY\\]\\+(N|M)|\\[IY\\]\\+(N|M)E\\+?)$", "[IY]+(N|M)E*", x_spelling, perl = TRUE)
|
||||||
|
# allow any ending of -ol/-ole
|
||||||
|
x_spelling <- gsub("(O\\+L|O\\+LE\\+)$", "O+LE*", x_spelling, perl = TRUE)
|
||||||
|
# allow any ending of -on/-one
|
||||||
|
x_spelling <- gsub("(O\\+N|O\\+NE\\+)$", "O+NE*", x_spelling, perl = TRUE)
|
||||||
|
# replace multiple same characters to single one with '+', like "ll" -> "l+"
|
||||||
|
x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling, perl = TRUE)
|
||||||
|
# replace spaces and slashes with a possibility on both
|
||||||
|
x_spelling <- gsub("[ /]", "( .*|.*/)", x_spelling, perl = TRUE)
|
||||||
|
# correct for digital reading text (OCR)
|
||||||
|
x_spelling <- gsub("[NRD8B]", "[NRD8B]", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("(O|0)", "(O|0)+", x_spelling, perl = TRUE)
|
||||||
|
x_spelling <- gsub("++", "+", x_spelling, fixed = TRUE)
|
||||||
|
}
|
||||||
|
|
||||||
|
# try if name starts with it
|
||||||
|
found <- AMR_env$AV_lookup[which(AMR_env$AV_lookup$generalised_name %like% paste0("^", x_spelling)), "av", drop = TRUE]
|
||||||
|
if (length(found) > 0) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
# try if name ends with it
|
||||||
|
found <- AMR_env$AV_lookup[which(AMR_env$AV_lookup$generalised_name %like% paste0(x_spelling, "$")), "av", drop = TRUE]
|
||||||
|
if (nchar(x[i]) >= 4 && length(found) > 0) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# and try if any synonym starts with it
|
||||||
|
synonym_found <- unlist(lapply(
|
||||||
|
AMR_env$AV_lookup$generalised_synonyms,
|
||||||
|
function(s) any(s %like% paste0("^", x_spelling))
|
||||||
|
))
|
||||||
|
found <- AMR_env$AV_lookup$av[synonym_found == TRUE]
|
||||||
|
if (length(found) > 0) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# INITIAL SEARCH - More uncertain results ----
|
||||||
|
|
||||||
|
if (initial_search == TRUE && fast_mode == FALSE) {
|
||||||
|
# only run on first try
|
||||||
|
|
||||||
|
# try by removing all spaces
|
||||||
|
if (x[i] %like% " ") {
|
||||||
|
found <- suppressWarnings(as.av(gsub(" +", "", x[i], perl = TRUE), initial_search = FALSE))
|
||||||
|
if (length(found) > 0 && !is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# try by removing all spaces and numbers
|
||||||
|
if (x[i] %like% " " || x[i] %like% "[0-9]") {
|
||||||
|
found <- suppressWarnings(as.av(gsub("[ 0-9]", "", x[i], perl = TRUE), initial_search = FALSE))
|
||||||
|
if (length(found) > 0 && !is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# transform back from other languages and try again
|
||||||
|
x_translated <- paste(lapply(
|
||||||
|
strsplit(x[i], "[^A-Z0-9]"),
|
||||||
|
function(y) {
|
||||||
|
for (i in seq_len(length(y))) {
|
||||||
|
for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
|
||||||
|
y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
|
||||||
|
TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
|
||||||
|
!isFALSE(TRANSLATIONS$fixed)), "pattern"],
|
||||||
|
y[i]
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
generalise_antibiotic_name(y)
|
||||||
|
}
|
||||||
|
)[[1]],
|
||||||
|
collapse = "/"
|
||||||
|
)
|
||||||
|
x_translated_guess <- suppressWarnings(as.av(x_translated, initial_search = FALSE))
|
||||||
|
if (!is.na(x_translated_guess)) {
|
||||||
|
x_new[i] <- x_translated_guess
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# now also try to coerce brandname combinations like "Amoxy/clavulanic acid"
|
||||||
|
x_translated <- paste(lapply(
|
||||||
|
strsplit(x_translated, "[^A-Z0-9 ]"),
|
||||||
|
function(y) {
|
||||||
|
for (i in seq_len(length(y))) {
|
||||||
|
y_name <- suppressWarnings(av_name(y[i], language = NULL, initial_search = FALSE))
|
||||||
|
y[i] <- ifelse(!is.na(y_name),
|
||||||
|
y_name,
|
||||||
|
y[i]
|
||||||
|
)
|
||||||
|
}
|
||||||
|
generalise_antibiotic_name(y)
|
||||||
|
}
|
||||||
|
)[[1]],
|
||||||
|
collapse = "/"
|
||||||
|
)
|
||||||
|
x_translated_guess <- suppressWarnings(as.av(x_translated, initial_search = FALSE))
|
||||||
|
if (!is.na(x_translated_guess)) {
|
||||||
|
x_new[i] <- x_translated_guess
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# try by removing all trailing capitals
|
||||||
|
if (x[i] %like_case% "[a-z]+[A-Z]+$") {
|
||||||
|
found <- suppressWarnings(as.av(gsub("[A-Z]+$", "", x[i], perl = TRUE), initial_search = FALSE))
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# keep only letters
|
||||||
|
found <- suppressWarnings(as.av(gsub("[^A-Z]", "", x[i], perl = TRUE), initial_search = FALSE))
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# try from a bigger text, like from a health care record, see ?av_from_text
|
||||||
|
# already calculated above if flag_multiple_results = TRUE
|
||||||
|
if (flag_multiple_results == TRUE) {
|
||||||
|
found <- from_text[1L]
|
||||||
|
} else {
|
||||||
|
found <- tryCatch(suppressWarnings(av_from_text(x[i], initial_search = FALSE, translate_av = FALSE)[[1]][1L]),
|
||||||
|
error = function(e) NA_character_
|
||||||
|
)
|
||||||
|
}
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# first 5
|
||||||
|
found <- suppressWarnings(as.av(substr(x[i], 1, 5), initial_search = FALSE))
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# make all consonants facultative
|
||||||
|
search_str <- gsub("([BCDFGHJKLMNPQRSTVWXZ])", "\\1*", x[i], perl = TRUE)
|
||||||
|
found <- suppressWarnings(as.av(search_str, initial_search = FALSE, already_regex = TRUE))
|
||||||
|
# keep at least 4 normal characters
|
||||||
|
if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 4) {
|
||||||
|
found <- NA
|
||||||
|
}
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# make all vowels facultative
|
||||||
|
search_str <- gsub("([AEIOUY])", "\\1*", x[i], perl = TRUE)
|
||||||
|
found <- suppressWarnings(as.av(search_str, initial_search = FALSE, already_regex = TRUE))
|
||||||
|
# keep at least 5 normal characters
|
||||||
|
if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 5) {
|
||||||
|
found <- NA
|
||||||
|
}
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# allow misspelling of vowels
|
||||||
|
x_spelling <- gsub("A+", "[AEIOU]+", x_spelling, fixed = TRUE)
|
||||||
|
x_spelling <- gsub("E+", "[AEIOU]+", x_spelling, fixed = TRUE)
|
||||||
|
x_spelling <- gsub("I+", "[AEIOU]+", x_spelling, fixed = TRUE)
|
||||||
|
x_spelling <- gsub("O+", "[AEIOU]+", x_spelling, fixed = TRUE)
|
||||||
|
x_spelling <- gsub("U+", "[AEIOU]+", x_spelling, fixed = TRUE)
|
||||||
|
found <- suppressWarnings(as.av(x_spelling, initial_search = FALSE, already_regex = TRUE))
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||||
|
next
|
||||||
|
}
|
||||||
|
|
||||||
|
# try with switched character, like "mreopenem"
|
||||||
|
for (j in seq_len(nchar(x[i]))) {
|
||||||
|
x_switched <- paste0(
|
||||||
|
# beginning part:
|
||||||
|
substr(x[i], 1, j - 1),
|
||||||
|
# here is the switching of 2 characters:
|
||||||
|
substr(x[i], j + 1, j + 1),
|
||||||
|
substr(x[i], j, j),
|
||||||
|
# ending part:
|
||||||
|
substr(x[i], j + 2, nchar(x[i]))
|
||||||
|
)
|
||||||
|
found <- suppressWarnings(as.av(x_switched, initial_search = FALSE))
|
||||||
|
if (!is.na(found)) {
|
||||||
|
break
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (!is.na(found)) {
|
||||||
|
x_new[i] <- found[1L]
|
||||||
|
next
|
||||||
|
}
|
||||||
|
} # end of initial_search = TRUE
|
||||||
|
|
||||||
|
# not found
|
||||||
|
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
|
||||||
|
}
|
||||||
|
|
||||||
|
if (initial_search == TRUE && sum(already_known) < length(x)) {
|
||||||
|
close(progress)
|
||||||
|
}
|
||||||
|
|
||||||
|
# save to package env to save time for next time
|
||||||
|
if (initial_search == TRUE) {
|
||||||
|
AMR_env$av_previously_coerced <- AMR_env$av_previously_coerced[which(!AMR_env$av_previously_coerced$x %in% x), , drop = FALSE]
|
||||||
|
AMR_env$av_previously_coerced <- unique(rbind(AMR_env$av_previously_coerced,
|
||||||
|
data.frame(
|
||||||
|
x = x,
|
||||||
|
av = x_new,
|
||||||
|
x_bak = x_bak[match(x, x_bak_clean)],
|
||||||
|
stringsAsFactors = FALSE
|
||||||
|
),
|
||||||
|
stringsAsFactors = FALSE
|
||||||
|
))
|
||||||
|
}
|
||||||
|
|
||||||
|
# take failed ATC codes apart from rest
|
||||||
|
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
|
||||||
|
warning_(
|
||||||
|
"in `as.av()`: these ATC codes are not (yet) in the antivirals data set: ",
|
||||||
|
vector_and(x_unknown_ATCs), "."
|
||||||
|
)
|
||||||
|
}
|
||||||
|
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
|
||||||
|
x_unknown <- c(x_unknown,
|
||||||
|
AMR_env$av_previously_coerced$x_bak[which(AMR_env$av_previously_coerced$x %in% x & is.na(AMR_env$av_previously_coerced$av))])
|
||||||
|
if (length(x_unknown) > 0 && fast_mode == FALSE) {
|
||||||
|
warning_(
|
||||||
|
"in `as.av()`: these values could not be coerced to a valid antiviral agent ID: ",
|
||||||
|
vector_and(x_unknown), "."
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
x_result <- x_new[match(x_bak_clean, x)]
|
||||||
|
if (length(x_result) == 0) {
|
||||||
|
x_result <- NA_character_
|
||||||
|
}
|
||||||
|
|
||||||
|
set_clean_class(x_result,
|
||||||
|
new_class = c("av", "character")
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname as.av
|
||||||
|
#' @export
|
||||||
|
is.av <- function(x) {
|
||||||
|
inherits(x, "av")
|
||||||
|
}
|
||||||
|
|
||||||
|
# will be exported using s3_register() in R/zzz.R
|
||||||
|
pillar_shaft.av <- function(x, ...) {
|
||||||
|
out <- trimws(format(x))
|
||||||
|
out[!is.na(x)] <- gsub("+", font_subtle("+"), out[!is.na(x)], fixed = TRUE)
|
||||||
|
out[is.na(x)] <- font_na(NA)
|
||||||
|
create_pillar_column(out, align = "left", min_width = 4)
|
||||||
|
}
|
||||||
|
|
||||||
|
# will be exported using s3_register() in R/zzz.R
|
||||||
|
type_sum.av <- function(x, ...) {
|
||||||
|
"av"
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @method print av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
print.av <- function(x, ...) {
|
||||||
|
cat("Class 'av'\n")
|
||||||
|
print(as.character(x), quote = FALSE)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @method as.data.frame av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
as.data.frame.av <- function(x, ...) {
|
||||||
|
nm <- deparse1(substitute(x))
|
||||||
|
if (!"nm" %in% names(list(...))) {
|
||||||
|
as.data.frame.vector(as.av(x), ..., nm = nm)
|
||||||
|
} else {
|
||||||
|
as.data.frame.vector(as.av(x), ...)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
#' @method [ av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
"[.av" <- function(x, ...) {
|
||||||
|
y <- NextMethod()
|
||||||
|
attributes(y) <- attributes(x)
|
||||||
|
y
|
||||||
|
}
|
||||||
|
#' @method [[ av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
"[[.av" <- function(x, ...) {
|
||||||
|
y <- NextMethod()
|
||||||
|
attributes(y) <- attributes(x)
|
||||||
|
y
|
||||||
|
}
|
||||||
|
#' @method [<- av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
"[<-.av" <- function(i, j, ..., value) {
|
||||||
|
y <- NextMethod()
|
||||||
|
attributes(y) <- attributes(i)
|
||||||
|
return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av)
|
||||||
|
}
|
||||||
|
#' @method [[<- av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
"[[<-.av" <- function(i, j, ..., value) {
|
||||||
|
y <- NextMethod()
|
||||||
|
attributes(y) <- attributes(i)
|
||||||
|
return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av)
|
||||||
|
}
|
||||||
|
#' @method c av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
c.av <- function(...) {
|
||||||
|
x <- list(...)[[1L]]
|
||||||
|
y <- NextMethod()
|
||||||
|
attributes(y) <- attributes(x)
|
||||||
|
return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @method unique av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
unique.av <- function(x, incomparables = FALSE, ...) {
|
||||||
|
y <- NextMethod()
|
||||||
|
attributes(y) <- attributes(x)
|
||||||
|
y
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @method rep av
|
||||||
|
#' @export
|
||||||
|
#' @noRd
|
||||||
|
rep.av <- function(x, ...) {
|
||||||
|
y <- NextMethod()
|
||||||
|
attributes(y) <- attributes(x)
|
||||||
|
y
|
||||||
|
}
|
||||||
|
|
||||||
|
get_translate_av <- function(translate_av) {
|
||||||
|
translate_av <- as.character(translate_av)[1L]
|
||||||
|
if (translate_av %in% c("TRUE", "official")) {
|
||||||
|
return("name")
|
||||||
|
} else if (translate_av %in% c(NA_character_, "FALSE")) {
|
||||||
|
return(FALSE)
|
||||||
|
} else {
|
||||||
|
translate_av <- tolower(translate_av)
|
||||||
|
stop_ifnot(translate_av %in% colnames(AMR::antivirals),
|
||||||
|
"invalid value for 'translate_av', this must be a column name of the antivirals data set\n",
|
||||||
|
"or TRUE (equals 'name') or FALSE to not translate at all.",
|
||||||
|
call = FALSE
|
||||||
|
)
|
||||||
|
translate_av
|
||||||
|
}
|
||||||
|
}
|
||||||
186
R/av_from_text.R
Normal file
186
R/av_from_text.R
Normal file
@ -0,0 +1,186 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||||
|
# #
|
||||||
|
# SOURCE #
|
||||||
|
# https://github.com/msberends/AMR #
|
||||||
|
# #
|
||||||
|
# CITE AS #
|
||||||
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||||
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||||
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||||
|
# doi:10.18637/jss.v104.i03 #
|
||||||
|
# #
|
||||||
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
# #
|
||||||
|
# This R package is free software; you can freely use and distribute #
|
||||||
|
# it for both personal and commercial purposes under the terms of the #
|
||||||
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||||
|
# the Free Software Foundation. #
|
||||||
|
# We created this package for both routine data analysis and academic #
|
||||||
|
# research and it was publicly released in the hope that it will be #
|
||||||
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||||
|
# #
|
||||||
|
# Visit our website for the full manual and a complete tutorial about #
|
||||||
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
#' Retrieve Antiviral Drug Names and Doses from Clinical Text
|
||||||
|
#'
|
||||||
|
#' Use this function on e.g. clinical texts from health care records. It returns a [list] with all antiviral drugs, doses and forms of administration found in the texts.
|
||||||
|
#' @param text text to analyse
|
||||||
|
#' @param type type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
|
||||||
|
#' @param collapse a [character] to pass on to `paste(, collapse = ...)` to only return one [character] per element of `text`, see *Examples*
|
||||||
|
#' @param translate_av if `type = "drug"`: a column name of the [antivirals] data set to translate the antibiotic abbreviations to, using [av_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
|
||||||
|
#' @param thorough_search a [logical] to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
|
||||||
|
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
|
||||||
|
#' @param ... arguments passed on to [as.av()]
|
||||||
|
#' @details This function is also internally used by [as.av()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.av()] function may use very long regular expression to match brand names of antiviral agents. This may fail on some systems.
|
||||||
|
#'
|
||||||
|
#' ### Argument `type`
|
||||||
|
#' At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.av()] internally, it will correct for misspelling.
|
||||||
|
#'
|
||||||
|
#' With `type = "dose"` (or similar, like "dosing", "doses"), all text elements will be searched for [numeric] values that are higher than 100 and do not resemble years. The output will be [numeric]. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see *Examples*.
|
||||||
|
#'
|
||||||
|
#' With `type = "administration"` (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see *Examples*.
|
||||||
|
#'
|
||||||
|
#' ### Argument `collapse`
|
||||||
|
#' Without using `collapse`, this function will return a [list]. This can be convenient to use e.g. inside a `mutate()`):\cr
|
||||||
|
#' `df %>% mutate(avx = av_from_text(clinical_text))`
|
||||||
|
#'
|
||||||
|
#' The returned AV codes can be transformed to official names, groups, etc. with all [`av_*`][av_property()] functions such as [av_name()] and [av_group()], or by using the `translate_av` argument.
|
||||||
|
#'
|
||||||
|
#' With using `collapse`, this function will return a [character]:\cr
|
||||||
|
#' `df %>% mutate(avx = av_from_text(clinical_text, collapse = "|"))`
|
||||||
|
#' @export
|
||||||
|
#' @return A [list], or a [character] if `collapse` is not `NULL`
|
||||||
|
#' @examples
|
||||||
|
#' av_from_text("28/03/2020 valaciclovir po tid")
|
||||||
|
#' av_from_text("28/03/2020 valaciclovir po tid", type = "admin")
|
||||||
|
av_from_text <- function(text,
|
||||||
|
type = c("drug", "dose", "administration"),
|
||||||
|
collapse = NULL,
|
||||||
|
translate_av = FALSE,
|
||||||
|
thorough_search = NULL,
|
||||||
|
info = interactive(),
|
||||||
|
...) {
|
||||||
|
if (missing(type)) {
|
||||||
|
type <- type[1L]
|
||||||
|
}
|
||||||
|
|
||||||
|
meet_criteria(text)
|
||||||
|
meet_criteria(type, allow_class = "character", has_length = 1)
|
||||||
|
meet_criteria(collapse, has_length = 1, allow_NULL = TRUE)
|
||||||
|
meet_criteria(translate_av, allow_NULL = FALSE) # get_translate_av() will be more informative about what's allowed
|
||||||
|
meet_criteria(thorough_search, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
|
||||||
|
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||||
|
|
||||||
|
type <- tolower(trimws2(type))
|
||||||
|
|
||||||
|
text <- tolower(as.character(text))
|
||||||
|
text_split_all <- strsplit(text, "[ ;.,:\\|]")
|
||||||
|
progress <- progress_ticker(n = length(text_split_all), n_min = 5, print = info)
|
||||||
|
on.exit(close(progress))
|
||||||
|
|
||||||
|
if (type %like% "(drug|ab|anti)") {
|
||||||
|
translate_av <- get_translate_av(translate_av)
|
||||||
|
|
||||||
|
if (isTRUE(thorough_search) ||
|
||||||
|
(isTRUE(is.null(thorough_search)) && max(vapply(FUN.VALUE = double(1), text_split_all, length), na.rm = TRUE) <= 3)) {
|
||||||
|
text_split_all <- text_split_all[nchar(text_split_all) >= 4 & grepl("[a-z]+", text_split_all)]
|
||||||
|
result <- lapply(text_split_all, function(text_split) {
|
||||||
|
progress$tick()
|
||||||
|
suppressWarnings(
|
||||||
|
as.av(text_split, ...)
|
||||||
|
)
|
||||||
|
})
|
||||||
|
} else {
|
||||||
|
# no thorough search
|
||||||
|
names_atc <- substr(c(AMR::antivirals$name, AMR::antivirals$atc), 1, 5)
|
||||||
|
synonyms <- unlist(AMR::antivirals$synonyms)
|
||||||
|
synonyms <- synonyms[nchar(synonyms) >= 4]
|
||||||
|
# regular expression must not be too long, so split synonyms in two:
|
||||||
|
synonyms_part1 <- synonyms[seq_len(0.5 * length(synonyms))]
|
||||||
|
synonyms_part2 <- synonyms[!synonyms %in% synonyms_part1]
|
||||||
|
to_regex <- function(x) {
|
||||||
|
paste0(
|
||||||
|
"^(",
|
||||||
|
paste0(unique(gsub("[^a-z0-9]+", "", sort(tolower(x)))), collapse = "|"),
|
||||||
|
").*"
|
||||||
|
)
|
||||||
|
}
|
||||||
|
result <- lapply(text_split_all, function(text_split) {
|
||||||
|
progress$tick()
|
||||||
|
suppressWarnings(
|
||||||
|
as.av(
|
||||||
|
unique(c(
|
||||||
|
text_split[text_split %like_case% to_regex(names_atc)],
|
||||||
|
text_split[text_split %like_case% to_regex(synonyms_part1)],
|
||||||
|
text_split[text_split %like_case% to_regex(synonyms_part2)]
|
||||||
|
)),
|
||||||
|
...
|
||||||
|
)
|
||||||
|
)
|
||||||
|
})
|
||||||
|
}
|
||||||
|
|
||||||
|
close(progress)
|
||||||
|
|
||||||
|
result <- lapply(result, function(out) {
|
||||||
|
out <- out[!is.na(out)]
|
||||||
|
if (length(out) == 0) {
|
||||||
|
as.av(NA)
|
||||||
|
} else {
|
||||||
|
if (!isFALSE(translate_av)) {
|
||||||
|
out <- av_property(out, property = translate_av, initial_search = FALSE)
|
||||||
|
}
|
||||||
|
out
|
||||||
|
}
|
||||||
|
})
|
||||||
|
} else if (type %like% "dos") {
|
||||||
|
text_split_all <- strsplit(text, " ", fixed = TRUE)
|
||||||
|
result <- lapply(text_split_all, function(text_split) {
|
||||||
|
text_split <- text_split[text_split %like% "^[0-9]{2,}(/[0-9]+)?[a-z]*$"]
|
||||||
|
# only left part of "/", like 500 in "500/125"
|
||||||
|
text_split <- gsub("/.*", "", text_split)
|
||||||
|
text_split <- gsub(",", ".", text_split, fixed = TRUE) # foreign system using comma as decimal sep
|
||||||
|
text_split <- as.double(gsub("[^0-9.]", "", text_split))
|
||||||
|
# minimal 100 units/mg and no years that unlikely doses
|
||||||
|
text_split <- text_split[text_split >= 100 & !text_split %in% c(1951:1999, 2001:2049)]
|
||||||
|
|
||||||
|
if (length(text_split) > 0) {
|
||||||
|
text_split
|
||||||
|
} else {
|
||||||
|
NA_real_
|
||||||
|
}
|
||||||
|
})
|
||||||
|
} else if (type %like% "adm") {
|
||||||
|
result <- lapply(text_split_all, function(text_split) {
|
||||||
|
text_split <- text_split[text_split %like% "(^iv$|intraven|^po$|per os|oral|implant|inhal|instill|nasal|paren|rectal|sublingual|buccal|trans.*dermal|vaginal)"]
|
||||||
|
if (length(text_split) > 0) {
|
||||||
|
text_split <- gsub("(^po$|.*per os.*)", "oral", text_split)
|
||||||
|
text_split <- gsub("(^iv$|.*intraven.*)", "iv", text_split)
|
||||||
|
text_split
|
||||||
|
} else {
|
||||||
|
NA_character_
|
||||||
|
}
|
||||||
|
})
|
||||||
|
} else {
|
||||||
|
stop_("`type` must be either 'drug', 'dose' or 'administration'")
|
||||||
|
}
|
||||||
|
|
||||||
|
# collapse text if needed
|
||||||
|
if (!is.null(collapse)) {
|
||||||
|
result <- vapply(FUN.VALUE = character(1), result, function(x) {
|
||||||
|
if (length(x) == 1 & all(is.na(x))) {
|
||||||
|
NA_character_
|
||||||
|
} else {
|
||||||
|
paste0(x, collapse = collapse)
|
||||||
|
}
|
||||||
|
})
|
||||||
|
}
|
||||||
|
|
||||||
|
result
|
||||||
|
}
|
||||||
290
R/av_property.R
Normal file
290
R/av_property.R
Normal file
@ -0,0 +1,290 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||||
|
# #
|
||||||
|
# SOURCE #
|
||||||
|
# https://github.com/msberends/AMR #
|
||||||
|
# #
|
||||||
|
# CITE AS #
|
||||||
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||||
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||||
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||||
|
# doi:10.18637/jss.v104.i03 #
|
||||||
|
# #
|
||||||
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
# #
|
||||||
|
# This R package is free software; you can freely use and distribute #
|
||||||
|
# it for both personal and commercial purposes under the terms of the #
|
||||||
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||||
|
# the Free Software Foundation. #
|
||||||
|
# We created this package for both routine data analysis and academic #
|
||||||
|
# research and it was publicly released in the hope that it will be #
|
||||||
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||||
|
# #
|
||||||
|
# Visit our website for the full manual and a complete tutorial about #
|
||||||
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
#' Get Properties of an Antiviral Agent
|
||||||
|
#'
|
||||||
|
#' Use these functions to return a specific property of an antiviral agent from the [antivirals] data set. All input values will be evaluated internally with [as.av()].
|
||||||
|
#' @param x any (vector of) text that can be coerced to a valid antiviral agent code with [as.av()]
|
||||||
|
#' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character].
|
||||||
|
#' @param property one of the column names of one of the [antivirals] data set: `vector_or(colnames(antivirals), sort = FALSE)`.
|
||||||
|
#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
|
||||||
|
#' @param administration way of administration, either `"oral"` or `"iv"`
|
||||||
|
#' @param open browse the URL using [utils::browseURL()]
|
||||||
|
#' @param ... other arguments passed on to [as.av()]
|
||||||
|
#' @details All output [will be translated][translate] where possible.
|
||||||
|
#'
|
||||||
|
#' The function [av_url()] will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
|
||||||
|
#' @inheritSection as.av Source
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @name av_property
|
||||||
|
#' @return
|
||||||
|
#' - An [integer] in case of [av_cid()]
|
||||||
|
#' - A named [list] in case of [av_info()] and multiple [av_atc()]/[av_synonyms()]/[av_tradenames()]
|
||||||
|
#' - A [double] in case of [av_ddd()]
|
||||||
|
#' - A [character] in all other cases
|
||||||
|
#' @export
|
||||||
|
#' @seealso [antivirals]
|
||||||
|
#' @inheritSection AMR Reference Data Publicly Available
|
||||||
|
#' @examples
|
||||||
|
#' # all properties:
|
||||||
|
#' av_name("ACI")
|
||||||
|
#' av_atc("ACI")
|
||||||
|
#' av_cid("ACI")
|
||||||
|
#' av_synonyms("ACI")
|
||||||
|
#' av_tradenames("ACI")
|
||||||
|
#' av_group("ACI")
|
||||||
|
#' av_url("ACI")
|
||||||
|
#'
|
||||||
|
#' # smart lowercase tranformation
|
||||||
|
#' av_name(x = c("ACI", "VALA"))
|
||||||
|
#' av_name(x = c("ACI", "VALA"), tolower = TRUE)
|
||||||
|
#'
|
||||||
|
#' # defined daily doses (DDD)
|
||||||
|
#' av_ddd("ACI", "oral")
|
||||||
|
#' av_ddd_units("ACI", "oral")
|
||||||
|
#' av_ddd("ACI", "iv")
|
||||||
|
#' av_ddd_units("ACI", "iv")
|
||||||
|
#'
|
||||||
|
#' av_info("ACI") # all properties as a list
|
||||||
|
#'
|
||||||
|
#' # all av_* functions use as.av() internally, so you can go from 'any' to 'any':
|
||||||
|
#' av_atc("ACI")
|
||||||
|
#' av_group("J05AB01")
|
||||||
|
#' av_loinc("abacavir")
|
||||||
|
#' av_name("29113-8")
|
||||||
|
#' av_name(135398513)
|
||||||
|
#' av_name("J05AB01")
|
||||||
|
av_name <- function(x, language = get_AMR_locale(), tolower = FALSE, ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
language <- validate_language(language)
|
||||||
|
meet_criteria(tolower, allow_class = "logical", has_length = 1)
|
||||||
|
|
||||||
|
x <- translate_into_language(av_validate(x = x, property = "name", ...), language = language, only_affect_ab_names = TRUE)
|
||||||
|
if (tolower == TRUE) {
|
||||||
|
# use perl to only transform the first character
|
||||||
|
# as we want "polymyxin B", not "polymyxin b"
|
||||||
|
x <- gsub("^([A-Z])", "\\L\\1", x, perl = TRUE)
|
||||||
|
}
|
||||||
|
x
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_cid <- function(x, ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
av_validate(x = x, property = "cid", ...)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_synonyms <- function(x, ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
syns <- av_validate(x = x, property = "synonyms", ...)
|
||||||
|
names(syns) <- x
|
||||||
|
if (length(syns) == 1) {
|
||||||
|
unname(unlist(syns))
|
||||||
|
} else {
|
||||||
|
syns
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_tradenames <- function(x, ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
av_synonyms(x, ...)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_group <- function(x, language = get_AMR_locale(), ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
language <- validate_language(language)
|
||||||
|
translate_into_language(av_validate(x = x, property = "atc_group", ...), language = language, only_affect_ab_names = TRUE)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_atc <- function(x, ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
# ATCs in the antivirals data set are not a list
|
||||||
|
av_validate(x = x, property = "atc", ...)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_loinc <- function(x, ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
loincs <- av_validate(x = x, property = "loinc", ...)
|
||||||
|
names(loincs) <- x
|
||||||
|
if (length(loincs) == 1) {
|
||||||
|
unname(unlist(loincs))
|
||||||
|
} else {
|
||||||
|
loincs
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_ddd <- function(x, administration = "oral", ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
||||||
|
|
||||||
|
x <- as.av(x, ...)
|
||||||
|
ddd_prop <- paste0(administration, "_ddd")
|
||||||
|
out <- av_validate(x = x, property = ddd_prop)
|
||||||
|
|
||||||
|
if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
|
||||||
|
warning_(
|
||||||
|
"in `av_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
|
||||||
|
"Please refer to the WHOCC website:\n",
|
||||||
|
"www.whocc.no/ddd/list_of_ddds_combined_products/"
|
||||||
|
)
|
||||||
|
}
|
||||||
|
out
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_ddd_units <- function(x, administration = "oral", ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
||||||
|
|
||||||
|
x <- as.av(x, ...)
|
||||||
|
ddd_prop <- paste0(administration, "_units")
|
||||||
|
out <- av_validate(x = x, property = ddd_prop)
|
||||||
|
|
||||||
|
if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
|
||||||
|
warning_(
|
||||||
|
"in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
|
||||||
|
"Please refer to the WHOCC website:\n",
|
||||||
|
"www.whocc.no/ddd/list_of_ddds_combined_products/"
|
||||||
|
)
|
||||||
|
}
|
||||||
|
out
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_info <- function(x, language = get_AMR_locale(), ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
language <- validate_language(language)
|
||||||
|
|
||||||
|
x <- as.av(x, ...)
|
||||||
|
list(
|
||||||
|
av = as.character(x),
|
||||||
|
cid = av_cid(x),
|
||||||
|
name = av_name(x, language = language),
|
||||||
|
group = av_group(x, language = language),
|
||||||
|
atc = av_atc(x),
|
||||||
|
tradenames = av_tradenames(x),
|
||||||
|
loinc = av_loinc(x),
|
||||||
|
ddd = list(
|
||||||
|
oral = list(
|
||||||
|
amount = av_ddd(x, administration = "oral"),
|
||||||
|
units = av_ddd_units(x, administration = "oral")
|
||||||
|
),
|
||||||
|
iv = list(
|
||||||
|
amount = av_ddd(x, administration = "iv"),
|
||||||
|
units = av_ddd_units(x, administration = "iv")
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_url <- function(x, open = FALSE, ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||||
|
|
||||||
|
av <- as.av(x = x, ...)
|
||||||
|
atcs <- av_atc(av, only_first = TRUE)
|
||||||
|
u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
|
||||||
|
u[is.na(atcs)] <- NA_character_
|
||||||
|
names(u) <- av_name(av)
|
||||||
|
|
||||||
|
NAs <- av_name(av, tolower = TRUE, language = NULL)[!is.na(av) & is.na(atcs)]
|
||||||
|
if (length(NAs) > 0) {
|
||||||
|
warning_("in `av_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
|
||||||
|
}
|
||||||
|
|
||||||
|
if (open == TRUE) {
|
||||||
|
if (length(u) > 1 && !is.na(u[1L])) {
|
||||||
|
warning_("in `av_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||||
|
}
|
||||||
|
if (!is.na(u[1L])) {
|
||||||
|
utils::browseURL(u[1L])
|
||||||
|
}
|
||||||
|
}
|
||||||
|
u
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname av_property
|
||||||
|
#' @export
|
||||||
|
av_property <- function(x, property = "name", language = get_AMR_locale(), ...) {
|
||||||
|
meet_criteria(x, allow_NA = TRUE)
|
||||||
|
meet_criteria(property, is_in = colnames(AMR::antivirals), has_length = 1)
|
||||||
|
meet_criteria(language, is_in = c(LANGUAGES_SUPPORTED, ""), has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||||
|
translate_into_language(av_validate(x = x, property = property, ...), language = language)
|
||||||
|
}
|
||||||
|
|
||||||
|
av_validate <- function(x, property, ...) {
|
||||||
|
if (tryCatch(all(x[!is.na(x)] %in% AMR_env$AV_lookup$av), error = function(e) FALSE)) {
|
||||||
|
# special case for av_* functions where class is already 'av'
|
||||||
|
x <- AMR_env$AV_lookup[match(x, AMR_env$AV_lookup$av), property, drop = TRUE]
|
||||||
|
} else {
|
||||||
|
# try to catch an error when inputting an invalid argument
|
||||||
|
# so the 'call.' can be set to FALSE
|
||||||
|
tryCatch(x[1L] %in% AMR_env$AV_lookup[1, property, drop = TRUE],
|
||||||
|
error = function(e) stop(e$message, call. = FALSE)
|
||||||
|
)
|
||||||
|
|
||||||
|
if (!all(x %in% AMR_env$AV_lookup[, property, drop = TRUE])) {
|
||||||
|
x <- as.av(x, ...)
|
||||||
|
if (all(is.na(x)) && is.list(AMR_env$AV_lookup[, property, drop = TRUE])) {
|
||||||
|
x <- rep(NA_character_, length(x))
|
||||||
|
} else {
|
||||||
|
x <- AMR_env$AV_lookup[match(x, AMR_env$AV_lookup$av), property, drop = TRUE]
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (property == "av") {
|
||||||
|
return(set_clean_class(x, new_class = c("av", "character")))
|
||||||
|
} else if (property == "cid") {
|
||||||
|
return(as.integer(x))
|
||||||
|
} else if (property %like% "ddd") {
|
||||||
|
return(as.double(x))
|
||||||
|
} else {
|
||||||
|
x[is.na(x)] <- NA
|
||||||
|
return(x)
|
||||||
|
}
|
||||||
|
}
|
||||||
4
R/data.R
4
R/data.R
@ -48,15 +48,17 @@
|
|||||||
#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
|
#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
|
||||||
#'
|
#'
|
||||||
#' ### For the [antivirals] data set: a [tibble][tibble::tibble] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
|
#' ### For the [antivirals] data set: a [tibble][tibble::tibble] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
|
||||||
|
#' - `av`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
|
||||||
|
#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
|
||||||
#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
|
#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
|
||||||
#' - `cid`\cr Compound ID as found in PubChem
|
#' - `cid`\cr Compound ID as found in PubChem
|
||||||
#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
|
|
||||||
#' - `atc_group`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
|
#' - `atc_group`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
|
||||||
#' - `synonyms`\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
|
#' - `synonyms`\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
|
||||||
#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment
|
#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment
|
||||||
#' - `oral_units`\cr Units of `oral_ddd`
|
#' - `oral_units`\cr Units of `oral_ddd`
|
||||||
#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
|
#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
|
||||||
#' - `iv_units`\cr Units of `iv_ddd`
|
#' - `iv_units`\cr Units of `iv_ddd`
|
||||||
|
#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent.
|
||||||
#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
|
#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
|
||||||
#'
|
#'
|
||||||
#' Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and consequently only available where a CID is available.
|
#' Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and consequently only available where a CID is available.
|
||||||
|
|||||||
5
R/mdro.R
5
R/mdro.R
@ -248,11 +248,6 @@ mdro <- function(x = NULL,
|
|||||||
pct_required_classes <- pct_required_classes / 100
|
pct_required_classes <- pct_required_classes / 100
|
||||||
}
|
}
|
||||||
|
|
||||||
if (!is.null(list(...)$country)) {
|
|
||||||
warning_("in `mdro()`: using `country` is deprecated, use `guideline` instead. See ?mdro")
|
|
||||||
guideline <- list(...)$country
|
|
||||||
}
|
|
||||||
|
|
||||||
guideline.bak <- guideline
|
guideline.bak <- guideline
|
||||||
if (is.list(guideline)) {
|
if (is.list(guideline)) {
|
||||||
# Custom MDRO guideline ---------------------------------------------------
|
# Custom MDRO guideline ---------------------------------------------------
|
||||||
|
|||||||
17
R/rsi_calc.R
17
R/rsi_calc.R
@ -375,20 +375,3 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
|
|||||||
out <- as_original_data_class(out, class(data.bak))
|
out <- as_original_data_class(out, class(data.bak))
|
||||||
structure(out, class = c("rsi_df", class(out)))
|
structure(out, class = c("rsi_df", class(out)))
|
||||||
}
|
}
|
||||||
|
|
||||||
get_translate_ab <- function(translate_ab) {
|
|
||||||
translate_ab <- as.character(translate_ab)[1L]
|
|
||||||
if (translate_ab %in% c("TRUE", "official")) {
|
|
||||||
return("name")
|
|
||||||
} else if (translate_ab %in% c(NA_character_, "FALSE")) {
|
|
||||||
return(FALSE)
|
|
||||||
} else {
|
|
||||||
translate_ab <- tolower(translate_ab)
|
|
||||||
stop_ifnot(translate_ab %in% colnames(AMR::antibiotics),
|
|
||||||
"invalid value for 'translate_ab', this must be a column name of the antibiotics data set\n",
|
|
||||||
"or TRUE (equals 'name') or FALSE to not translate at all.",
|
|
||||||
call = FALSE
|
|
||||||
)
|
|
||||||
translate_ab
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|||||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
14
R/vctrs.R
14
R/vctrs.R
@ -70,6 +70,20 @@ vec_cast.ab.character <- function(x, to, ...) {
|
|||||||
return_after_integrity_check(x, "antimicrobial code", as.character(AMR_env$AB_lookup$ab))
|
return_after_integrity_check(x, "antimicrobial code", as.character(AMR_env$AB_lookup$ab))
|
||||||
}
|
}
|
||||||
|
|
||||||
|
# S3: av
|
||||||
|
vec_ptype2.character.av <- function(x, y, ...) {
|
||||||
|
x
|
||||||
|
}
|
||||||
|
vec_ptype2.av.character <- function(x, y, ...) {
|
||||||
|
y
|
||||||
|
}
|
||||||
|
vec_cast.character.av <- function(x, to, ...) {
|
||||||
|
as.character(x)
|
||||||
|
}
|
||||||
|
vec_cast.av.character <- function(x, to, ...) {
|
||||||
|
return_after_integrity_check(x, "antiviral agent code", as.character(AMR_env$AV_lookup$av))
|
||||||
|
}
|
||||||
|
|
||||||
# S3: mo
|
# S3: mo
|
||||||
vec_ptype2.character.mo <- function(x, y, ...) {
|
vec_ptype2.character.mo <- function(x, y, ...) {
|
||||||
x
|
x
|
||||||
|
|||||||
17
R/zzz.R
17
R/zzz.R
@ -50,6 +50,11 @@ AMR_env$ab_previously_coerced <- data.frame(
|
|||||||
ab = character(0),
|
ab = character(0),
|
||||||
stringsAsFactors = FALSE
|
stringsAsFactors = FALSE
|
||||||
)
|
)
|
||||||
|
AMR_env$av_previously_coerced <- data.frame(
|
||||||
|
x = character(0),
|
||||||
|
av = character(0),
|
||||||
|
stringsAsFactors = FALSE
|
||||||
|
)
|
||||||
AMR_env$rsi_interpretation_history <- data.frame(
|
AMR_env$rsi_interpretation_history <- data.frame(
|
||||||
datetime = Sys.time()[0],
|
datetime = Sys.time()[0],
|
||||||
index = integer(0),
|
index = integer(0),
|
||||||
@ -87,11 +92,13 @@ if (utf8_supported && !is_latex) {
|
|||||||
# developers of the vctrs package:
|
# developers of the vctrs package:
|
||||||
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
|
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
|
||||||
s3_register("pillar::pillar_shaft", "ab")
|
s3_register("pillar::pillar_shaft", "ab")
|
||||||
|
s3_register("pillar::pillar_shaft", "av")
|
||||||
s3_register("pillar::pillar_shaft", "mo")
|
s3_register("pillar::pillar_shaft", "mo")
|
||||||
s3_register("pillar::pillar_shaft", "rsi")
|
s3_register("pillar::pillar_shaft", "rsi")
|
||||||
s3_register("pillar::pillar_shaft", "mic")
|
s3_register("pillar::pillar_shaft", "mic")
|
||||||
s3_register("pillar::pillar_shaft", "disk")
|
s3_register("pillar::pillar_shaft", "disk")
|
||||||
s3_register("tibble::type_sum", "ab")
|
s3_register("tibble::type_sum", "ab")
|
||||||
|
s3_register("tibble::type_sum", "av")
|
||||||
s3_register("tibble::type_sum", "mo")
|
s3_register("tibble::type_sum", "mo")
|
||||||
s3_register("tibble::type_sum", "rsi")
|
s3_register("tibble::type_sum", "rsi")
|
||||||
s3_register("tibble::type_sum", "mic")
|
s3_register("tibble::type_sum", "mic")
|
||||||
@ -129,6 +136,11 @@ if (utf8_supported && !is_latex) {
|
|||||||
s3_register("vctrs::vec_ptype2", "ab.character")
|
s3_register("vctrs::vec_ptype2", "ab.character")
|
||||||
s3_register("vctrs::vec_cast", "character.ab")
|
s3_register("vctrs::vec_cast", "character.ab")
|
||||||
s3_register("vctrs::vec_cast", "ab.character")
|
s3_register("vctrs::vec_cast", "ab.character")
|
||||||
|
# S3: av
|
||||||
|
s3_register("vctrs::vec_ptype2", "character.av")
|
||||||
|
s3_register("vctrs::vec_ptype2", "av.character")
|
||||||
|
s3_register("vctrs::vec_cast", "character.av")
|
||||||
|
s3_register("vctrs::vec_cast", "av.character")
|
||||||
# S3: mo
|
# S3: mo
|
||||||
s3_register("vctrs::vec_ptype2", "character.mo")
|
s3_register("vctrs::vec_ptype2", "character.mo")
|
||||||
s3_register("vctrs::vec_ptype2", "mo.character")
|
s3_register("vctrs::vec_ptype2", "mo.character")
|
||||||
@ -168,6 +180,7 @@ if (utf8_supported && !is_latex) {
|
|||||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||||
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
|
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
|
||||||
AMR_env$AB_lookup <- create_AB_lookup()
|
AMR_env$AB_lookup <- create_AB_lookup()
|
||||||
|
AMR_env$AV_lookup <- create_AV_lookup()
|
||||||
AMR_env$MO_lookup <- create_MO_lookup()
|
AMR_env$MO_lookup <- create_MO_lookup()
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -190,6 +203,10 @@ create_AB_lookup <- function() {
|
|||||||
cbind(AMR::antibiotics, AB_LOOKUP)
|
cbind(AMR::antibiotics, AB_LOOKUP)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
create_AV_lookup <- function() {
|
||||||
|
cbind(AMR::antivirals, AV_LOOKUP)
|
||||||
|
}
|
||||||
|
|
||||||
create_MO_lookup <- function() {
|
create_MO_lookup <- function() {
|
||||||
MO_lookup <- AMR::microorganisms
|
MO_lookup <- AMR::microorganisms
|
||||||
|
|
||||||
|
|||||||
19
_pkgdown.yml
19
_pkgdown.yml
@ -102,9 +102,9 @@ navbar:
|
|||||||
- text: "Get properties of an antibiotic"
|
- text: "Get properties of an antibiotic"
|
||||||
icon: "fa-capsules"
|
icon: "fa-capsules"
|
||||||
href: "reference/ab_property.html" # reference instead of an article
|
href: "reference/ab_property.html" # reference instead of an article
|
||||||
# - text: "Other: benchmarks"
|
- text: "Get properties of an antiviral agent"
|
||||||
# icon: "fa-shipping-fast"
|
icon: "fa-capsules"
|
||||||
# href: "articles/benchmarks.html"
|
href: "reference/av_property.html" # reference instead of an article
|
||||||
- text: "Manual"
|
- text: "Manual"
|
||||||
icon: "fa-book-open"
|
icon: "fa-book-open"
|
||||||
href: "reference/index.html"
|
href: "reference/index.html"
|
||||||
@ -176,7 +176,18 @@ reference:
|
|||||||
- "`resistance_predict`"
|
- "`resistance_predict`"
|
||||||
- "`guess_ab_col`"
|
- "`guess_ab_col`"
|
||||||
|
|
||||||
- title: "Background information on included data"
|
- title: "Other: antiviral drugs"
|
||||||
|
desc: >
|
||||||
|
This package also provides extensive support for antiviral agents, even though it is not the primary
|
||||||
|
scope of this package. Working with data containing information about antiviral drugs was never easier.
|
||||||
|
Use these functions to get valid properties of antiviral drugs from any input or to clean your input.
|
||||||
|
You can even retrieve drug names and doses from clinical text records, using `av_from_text()`.
|
||||||
|
contents:
|
||||||
|
- "`as.av`"
|
||||||
|
- "`av_property`"
|
||||||
|
- "`av_from_text`"
|
||||||
|
|
||||||
|
- title: "Other: background information on included data"
|
||||||
desc: >
|
desc: >
|
||||||
Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
|
Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
|
||||||
for more information about how to work with functions in this package.
|
for more information about how to work with functions in this package.
|
||||||
|
|||||||
@ -267,17 +267,19 @@ AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
|
|||||||
# this will be used for documentation:
|
# this will be used for documentation:
|
||||||
DEFINED_AB_GROUPS <- ls(envir = globalenv())
|
DEFINED_AB_GROUPS <- ls(envir = globalenv())
|
||||||
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
|
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
|
||||||
create_AB_lookup <- function() {
|
create_AB_AV_lookup <- function(df) {
|
||||||
AMR_env$AB_lookup <- AMR::antibiotics
|
new_df <- df
|
||||||
AMR_env$AB_lookup$generalised_name <- generalise_antibiotic_name(AMR_env$AB_lookup$name)
|
new_df$generalised_name <- generalise_antibiotic_name(new_df$name)
|
||||||
AMR_env$AB_lookup$generalised_synonyms <- lapply(AMR_env$AB_lookup$synonyms, generalise_antibiotic_name)
|
new_df$generalised_synonyms <- lapply(new_df$synonyms, generalise_antibiotic_name)
|
||||||
AMR_env$AB_lookup$generalised_abbreviations <- lapply(AMR_env$AB_lookup$abbreviations, generalise_antibiotic_name)
|
if ("abbreviations" %in% colnames(df)) {
|
||||||
AMR_env$AB_lookup$generalised_loinc <- lapply(AMR_env$AB_lookup$loinc, generalise_antibiotic_name)
|
new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
|
||||||
AMR_env$AB_lookup$generalised_all <- unname(lapply(
|
}
|
||||||
as.list(as.data.frame(t(AMR_env$AB_lookup[,
|
new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
|
||||||
|
new_df$generalised_all <- unname(lapply(
|
||||||
|
as.list(as.data.frame(t(new_df[,
|
||||||
c(
|
c(
|
||||||
"ab", "atc", "cid", "name",
|
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
|
||||||
colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "generalised"]
|
colnames(new_df)[colnames(new_df) %like% "generalised"]
|
||||||
),
|
),
|
||||||
drop = FALSE
|
drop = FALSE
|
||||||
]),
|
]),
|
||||||
@ -288,9 +290,10 @@ create_AB_lookup <- function() {
|
|||||||
x[x != ""]
|
x[x != ""]
|
||||||
}
|
}
|
||||||
))
|
))
|
||||||
AMR_env$AB_lookup[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "^generalised"]]
|
new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
|
||||||
}
|
}
|
||||||
AB_LOOKUP <- create_AB_lookup()
|
AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
|
||||||
|
AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
|
||||||
|
|
||||||
# Export to package as internal data ----
|
# Export to package as internal data ----
|
||||||
usethis::ui_info(paste0("Updating internal package data"))
|
usethis::ui_info(paste0("Updating internal package data"))
|
||||||
@ -304,6 +307,7 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
|
|||||||
MO_FULLNAME_LOWER,
|
MO_FULLNAME_LOWER,
|
||||||
MO_PREVALENT_GENERA,
|
MO_PREVALENT_GENERA,
|
||||||
AB_LOOKUP,
|
AB_LOOKUP,
|
||||||
|
AV_LOOKUP,
|
||||||
AB_AMINOGLYCOSIDES,
|
AB_AMINOGLYCOSIDES,
|
||||||
AB_AMINOPENICILLINS,
|
AB_AMINOPENICILLINS,
|
||||||
AB_ANTIFUNGALS,
|
AB_ANTIFUNGALS,
|
||||||
|
|||||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -1,103 +1,121 @@
|
|||||||
"atc" "cid" "name" "atc_group" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units"
|
"av" "name" "atc" "cid" "atc_group" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc"
|
||||||
"J05AF06" 441300 "Abacavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Abacavir,Abacavir sulfate,Ziagen" 0.6 "g"
|
"ABA" "Abacavir" "J05AF06" 441300 "Nucleoside and nucleotide reverse transcriptase inhibitors" "abacavir sulfate,avacavir,ziagen" 0.6 "g" "29113-8,78772-1,78773-9,79134-3,80118-3"
|
||||||
"J05AB01" 135398513 "Aciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Acicloftal,Aciclovier,Aciclovir,Aciclovirum,Activir,AcycloFoam,Acycloguanosine,Acyclovir,Acyclovir Lauriad,ACYCLOVIR SODIUM,Avirax,Cargosil,Cyclovir,Genvir,Gerpevir,Hascovir,Herpevir,Maynar,Poviral,Sitavig,Sitavir,Vipral,Virolex,Viropump,Virorax,Zovirax,Zovirax topical,Zyclir" 4 "g" 4 "g"
|
"ACI" "Aciclovir" "J05AB01" 135398513 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "acicloftal,aciclovier,aciclovirum,activir,acyclofoam,acycloguanosine,acyclovir,acyclovir lauriad,avaclyr,cargosil,cyclovir,genvir,gerpevir,hascovir,maynar,novirus,poviral,sitavig,sitavir,vipral,viropump,virorax,zovirax,zyclir" 4 "g" 4 "g" ""
|
||||||
"J05AF08" 60871 "Adefovir dipivoxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Adefovir di ester,Adefovir dipivoxil,Adefovir Dipivoxil,Adefovir dipivoxyl,Adefovir pivoxil,Adefovirdipivoxl,Bisadenine,BISADENINE,BisPMEA,Hepsera,Preveon,YouHeDing" 10 "mg"
|
"ADD" "Adefovir dipivoxil" "J05AF08" 60871 "Nucleoside and nucleotide reverse transcriptase inhibitors" "adefovir di,adefovir di ester,adefovir dipivoxyl,adefovir pivoxil,adefovirdipivoxl,bisadenine,bispmea,hepsera,preveon,youheding" 10 "mg" ""
|
||||||
"J05AE05" 65016 "Amprenavir" "Protease inhibitors" "Agenerase,Amprenavir,Amprenavirum,Prozei,Vertex" 1.2 "g"
|
"AME" "Amenamevir" "J05AX26" 11397521 "Other antivirals" "amenalief" 0.4 "g" ""
|
||||||
"J05AP06" 16076883 "Asunaprevir" "Antivirals for treatment of HCV infections" "Asunaprevir,Sunvepra"
|
"AMP" "Amprenavir" "J05AE05" 65016 "Protease inhibitors" "agenerase,carbamate,prozei" 1.2 "g" "29114-6,31028-4,78791-1"
|
||||||
"J05AE08" 148192 "Atazanavir" "Protease inhibitors" "Atazanavir,Atazanavir Base,Latazanavir,Reyataz,Zrivada" 0.3 "g"
|
"ASU" "Asunaprevir" "J05AP06" 16076883 "Antivirals for treatment of HCV infections" "sunvepra,sunvepratrade" 0.2 "g" ""
|
||||||
"J05AR15" 86583336 "Atazanavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
|
"ATA" "Atazanavir" "J05AE08" 148192 "Protease inhibitors" "atazanavir base,latazanavir,reyataz,zrivada" 0.3 "g" "41470-6,78796-0,78797-8,80142-3,80143-1"
|
||||||
"J05AR23" "Atazanavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "" 0.3 "g"
|
"ATA+COBI" "Atazanavir/cobicistat" "J05AR15" 86583336 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AP03" 10324367 "Boceprevir" "Antivirals for treatment of HCV infections" "Bocepravir,Boceprevir,Victrelis" 2.4 "g"
|
"ATA+RIT" "Atazanavir/ritonavir" "J05AR23" 25134325 "Antivirals for treatment of HIV infections, combinations" "" 0.3 "g" ""
|
||||||
"J05AB15" 446727 "Brivudine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Bridic,Brivox,Brivudin,Brivudina,Brivudine,Brivudinum,BrVdUrd,Helpin,Zerpex,Zostex" 0.125 "g"
|
"BAM" "Baloxavir marboxil" "J05AX25" 124081896 "Other antivirals" "xofluza" 40 "mg" ""
|
||||||
"J05AB12" 60613 "Cidofovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Cidofovir,Cidofovir anhydrous,Cidofovir gel,Cidofovirum,Forvade,Vistide" 25 "mg"
|
"BOC" "Boceprevir" "J05AP03" 10324367 "Antivirals for treatment of HCV infections" "victrelis" 2.4 "g" ""
|
||||||
"J05AF12" 73115 "Clevudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Clevudine,Levovir,Revovir" 30 "mg"
|
"BRIN" "Brincidofovir" "J05AB17" 483477 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "cidofovir prodrug,tembexa" ""
|
||||||
"J05AP07" 25154714 "Daclatasvir" "Antivirals for treatment of HCV infections" "Daclatasvir,Daklinza" 60 "mg"
|
"BRIV" "Brivudine" "J05AB15" 446727 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "bridic,brivox,brivudin,brivudina,brivudinum,brvdurd,helpin,zerpex,zostex" 0.125 "g" ""
|
||||||
"J05AE10" 213039 "Darunavir" "Protease inhibitors" "Darunavir,Darunavirum,Prezista,Prezista Naive" 1.2 "g"
|
"BUL" "Bulevirtide" "J05AX28" "Other antivirals" "" ""
|
||||||
"J05AR14" "Darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
|
"CAB" "Cabotegravir" "J05AJ04" 54713659 "Integrase inhibitors" "cabenuva" 30 "mg" 10 "mg" ""
|
||||||
"J05AP09" 56640146 "Dasabuvir" "Antivirals for treatment of HCV infections" "Dasabuvir" 0.5 "g"
|
"CID" "Cidofovir" "J05AB12" 60613 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "cidofovir anhydrous,cidofovir gel,cidofovir hydrate,cidofovirum,forvade,hpmpc dihydrate,phosphonic acid,vistide" 25 "mg" ""
|
||||||
"J05AP52" "Dasabuvir, ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
|
"CLE" "Clevudine" "J05AF12" 73115 "Nucleoside and nucleotide reverse transcriptase inhibitors" "levovir,revovir" 30 "mg" ""
|
||||||
"J05AG02" 5625 "Delavirdine" "Non-nucleoside reverse transcriptase inhibitors" "BHAP der,Delavirdin,Delavirdina,Delavirdine,Delavirdinum,PIPERAZINE,Rescriptor" 1.2 "g"
|
"COBL" "Coblopasvir" "J05AP12" 58316387 "Antivirals for treatment of HCV infections" "" ""
|
||||||
"J05AF02" 135398739 "Didanosine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Didanosina,Didanosine,Didanosinum,Dideoxyinosine,DIDEOXYINOSINE,Hypoxanthine ddN,Videx,Videx EC" 0.4 "g"
|
"DAC" "Daclatasvir" "J05AP07" 25154714 "Antivirals for treatment of HCV infections" "daklinza" 60 "mg" ""
|
||||||
"J05AX12" 54726191 "Dolutegravir" "Other antivirals" "Dolutegravir,Dolutegravir Sodium,Soltegravir,Tivicay" 50 "mg"
|
"DAC+ASU+BEC" "Daclatasvir/asunaprevir/beclabuvir" "J05AP58" "Antivirals for treatment of HCV infections" "" ""
|
||||||
"J05AR21" 131801472 "Dolutegravir and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
|
"DAR" "Darunavir" "J05AE10" 213039 "Protease inhibitors" "carbamate,darunavirum,derunavir,prezista,prezista naive" 1.2 "g" "57954-0"
|
||||||
"J05AG06" 58460047 "Doravirine" "Non-nucleoside reverse transcriptase inhibitors" "Doravirine,Pifeltro"
|
"DAR+COBI" "Darunavir/cobicistat" "J05AR14" 57327017 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AG03" 64139 "Efavirenz" "Non-nucleoside reverse transcriptase inhibitors" "Efavirenz,Efavirenzum,Eravirenz,Stocrin,Strocin,Sustiva" 0.6 "g"
|
"DAR+RIT" "Darunavir/ritonavir" "J05AR26" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AP54" 91669168 "Elbasvir and grazoprevir" "Antivirals for treatment of HCV infections" ""
|
"DAS" "Dasabuvir" "J05AP09" 56640146 "Antivirals for treatment of HCV infections" "" 0.5 "g" ""
|
||||||
"J05AX11" 5277135 "Elvitegravir" "Other antivirals" "Elvitegravir,Vitekta"
|
"DAS+OMB+PAR+RIT" "Dasabuvir/ombitasvir/paritaprevir/ritonavir" "J05AP52" "Antivirals for treatment of HCV infections" "" ""
|
||||||
"J05AF09" 60877 "Emtricitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Coviracil,Emtricitabin,Emtricitabina,Emtricitabine,Emtricitabinum,Emtritabine,Emtriva,Racivir" 0.2 "g"
|
"DEL" "Delavirdine" "J05AG02" 5625 "Non-nucleoside reverse transcriptase inhibitors" "piperazine,rescriptor" 1.2 "g" "27082-7,29115-3"
|
||||||
"J05AR17" 90469070 "Emtricitabine and tenofovir alafenamide" "Antivirals for treatment of HIV infections, combinations" ""
|
"DID" "Didanosine" "J05AF02" 135398739 "Nucleoside and nucleotide reverse transcriptase inhibitors" "didanosina,didanosinum,dideoxyinosine,hypoxanthine ddn,videx ec" 0.4 "g" "29116-1,48307-3"
|
||||||
"J05AR20" "Emtricitabine, tenofovir alafenamide and bictegravir" "Antivirals for treatment of HIV infections, combinations" ""
|
"DOL" "Dolutegravir" "J05AJ03" 54726191 "Integrase inhibitors" "dolutegravir dtg,soltegravir,tivicay" 50 "mg" ""
|
||||||
"J05AR19" "Emtricitabine, tenofovir alafenamide and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
|
"DOL+RIL" "Dolutegravir/rilpivirine" "J05AR21" 131801472 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AR22" "Emtricitabine, tenofovir alafenamide, darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
|
"DOR" "Doravirine" "J05AG06" 58460047 "Non-nucleoside reverse transcriptase inhibitors" "pifeltro" 0.1 "g" ""
|
||||||
"J05AR18" "Emtricitabine, tenofovir alafenamide, elvitegravir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
|
"EFA" "Efavirenz" "J05AG03" 64139 "Non-nucleoside reverse transcriptase inhibitors" "efavirenz teva,efavirenzum,eravirenz,stocrin,strocin,sustiva,viraday" 0.6 "g" "29117-9,33928-3,51907-4,51908-2"
|
||||||
"J05AR06" "Emtricitabine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations" ""
|
"ELB" "Elbasvir" "J05AP10" 71661251 "Antivirals for treatment of HCV infections" "methyl carbamate" 50 "mg" ""
|
||||||
"J05AR08" "Emtricitabine, tenofovir disoproxil and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
|
"ELB+GRA" "Elbasvir/grazoprevir" "J05AP54" 91669168 "Antivirals for treatment of HCV infections" "zepatier" ""
|
||||||
"J05AR09" "Emtricitabine, tenofovir disoproxil, elvitegravir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
|
"ELV" "Elvitegravir" "J05AJ02" 5277135 "Integrase inhibitors" "vitekta" "88986-5"
|
||||||
"J05AX07" 16130199 "Enfuvirtide" "Other antivirals" "Enfurvitide,Enfuvirtide,Fuzeon,Pentafuside" 0.18 "g"
|
"EMT" "Emtricitabine" "J05AF09" 60877 "Nucleoside and nucleotide reverse transcriptase inhibitors" "coviracil,emtricitabinum,emtritabine,emtriva,racivir" 0.2 "g" ""
|
||||||
"J05AX17" 10089466 "Enisamium iodide" "Other antivirals" "Enisamium iodide" 1.5 "g"
|
"EMT+TEA" "Emtricitabine/tenofovir alafenamide" "J05AR17" 90469070 "Antivirals for treatment of HIV infections, combinations" "descovy" ""
|
||||||
"J05AF10" 135398508 "Entecavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Baraclude,Entecavir,Entecavir anhydrous,Entecavirum" 0.5 "mg"
|
"EMT+TEA+BIC" "Emtricitabine/tenofovir alafenamide/bictegravir" "J05AR20" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AG04" 193962 "Etravirine" "Non-nucleoside reverse transcriptase inhibitors" "DAPY deriv,Etravine,Etravirine,Intelence" 0.4 "g"
|
"EMT+TEA+RIL" "Emtricitabine/tenofovir alafenamide/rilpivirine" "J05AR19" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AP04" 42601552 "Faldaprevir" "Antivirals for treatment of HCV infections" "Faldaprevir"
|
"EMT+TEA+DAR+COBI" "Emtricitabine/tenofovir alafenamide/darunavir/cobicistat" "J05AR22" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AB09" 3324 "Famciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Famciclovir,Famciclovirum,Famvir,Oravir" 0.75 "g"
|
"EMT+TEA+ELV+COBI" "Emtricitabine/tenofovir alafenamide/elvitegravir/cobicistat" "J05AR18" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AE07" 131536 "Fosamprenavir" "Protease inhibitors" "Amprenavir phosphate,Fosamprenavir,Lexiva,Telzir" 1.4 "g"
|
"EMT+TED+EFA" "Emtricitabine/tenofovir disoproxil/efavirenz" "J05AR06" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AD01" 3415 "Foscarnet" "Phosphonic acid derivatives" "Forscarnet,Forscarnet sodium,Foscarmet,Foscarnet,Phosphonoformate,Phosphonoformic acid" 6.5 "g"
|
"EMT+TED+RIL" "Emtricitabine/tenofovir disoproxil/rilpivirine" "J05AR08" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AD02" 546 "Fosfonet" "Phosphonic acid derivatives" "Fosfonet,Fosfonet sodium,Fosfonet Sodium,Fosfonoacetate,Fosfonoacetic acid,Phosphonacetate,Phosphonacetic acid"
|
"EMT+TED+ELV+COBI" "Emtricitabine/tenofovir disoproxil/elvitegravir/cobicistat" "J05AR09" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AB06" 135398740 "Ganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Citovirax,Cymevan,Cymeven,Cymevene,Cytovene,Cytovene IV,Ganciclovir,Ganciclovirum,Gancyclovir,Hydroxyacyclovir,Virgan,Vitrasert,Zirgan" 3 "g" 0.5 "g"
|
"ENF" "Enfuvirtide" "J05AX07" 16130199 "Other antivirals" "enfurvitide,fuzeon,pentafuside" 0.18 "g" ""
|
||||||
"J05AP57" "Glecaprevir and pibrentasvir" "Antivirals for treatment of HCV infections" ""
|
"ENI" "Enisamium iodide" "J05AX17" 10089466 "Other antivirals" "amizon" 1.5 "g" ""
|
||||||
"J05AX23" "Ibalizumab" "Other antivirals" ""
|
"ENT" "Entecavir" "J05AF10" 135398508 "Nucleoside and nucleotide reverse transcriptase inhibitors" "baraclude,entecavir anhydrous" 0.5 "mg" ""
|
||||||
"J05AB02" 5905 "Idoxuridine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Antizona,Dendrid,Emanil,Heratil,Herpesil,Herpid,Herpidu,Herplex,HERPLEX,Herplex liquifilm,Idexur,Idossuridina,Idoxene,Idoxuridin,Idoxuridina,Idoxuridine,Idoxuridinum,Idu Oculos,Iducher,Idulea,Iduoculos,Iduridin,Iduviran,Iododeoxyridine,Iododeoxyuridine,Iodoxuridine,Joddeoxiuridin,Kerecid,Kerecide,Ophthalmadine,Spectanefran,Stoxil,Synmiol,Virudox"
|
"ETR" "Etravirine" "J05AG04" 193962 "Non-nucleoside reverse transcriptase inhibitors" "dapy deriv,etravine,intelence" 0.4 "g" "57961-5"
|
||||||
"J05AE02" 5362440 "Indinavir" "Protease inhibitors" "Compound J,Crixivan,Indinavir,Indinavir anhydrous,Propolis+Indinavir" 2.4 "g"
|
"FAL" "Faldaprevir" "J05AP04" 42601552 "Antivirals for treatment of HCV infections" "" ""
|
||||||
"J05AX05" 135449284 "Inosine pranobex" "Other antivirals" "Aviral,Delimmun,Immunovir,Imunovir,Inosine pranobex,Inosiplex,Isoprinosin,Isoprinosina,Isoprinosine,Isoviral,Methisoprinol,Methysoprinol,Metisoprinol,Viruxan" 3 "g"
|
"FAM" "Famciclovir" "J05AB09" 3324 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "famciclovirum,famvir,oravir" 0.75 "g" ""
|
||||||
"J05AF05" 60825 "Lamivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Epivir,Hepitec,Heptivir,Heptodin,Heptovir,Lamivir,Lamivudin,Lamivudina,Lamivudine,Lamivudinum,Zeffix" 0.3 "g"
|
"FAV" "Favipiravir" "J05AX27" 492405 "Other antivirals" "avigan,fapilavir,favilavir" 1.6 "g" ""
|
||||||
"J05AR02" "Lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations" ""
|
"FOSA" "Fosamprenavir" "J05AE07" 131536 "Protease inhibitors" "amprenavir phosphate,carbamate,lexiva,telzir" 1.4 "g" ""
|
||||||
"J05AR16" 73386700 "Lamivudine and raltegravir" "Antivirals for treatment of HIV infections, combinations" ""
|
"FOSC" "Foscarnet" "J05AD01" 3415 "Phosphonic acid derivatives" "forscarnet,foscarmet,foscavir,phosphonoformate,phosphonoformic acid" 6.5 "g" ""
|
||||||
"J05AR12" "Lamivudine and tenofovir disoproxil" "Antivirals for treatment of HIV infections, combinations" ""
|
"FOSF" "Fosfonet" "J05AD02" 546 "Phosphonic acid derivatives" "fosfonet sodium,fosfonoacetate,fosfonoacetic acid,phosphonacetate,phosphonacetic acid,phosphonoaceticacid" ""
|
||||||
"J05AR13" "Lamivudine, abacavir and dolutegravir" "Antivirals for treatment of HIV infections, combinations" ""
|
"FOST" "Fostemsavir" "J05AX29" 11319217 "Other antivirals" "rukobia" 1.2 "g" ""
|
||||||
"J05AR24" "Lamivudine, tenofovir disoproxil and doravirine" "Antivirals for treatment of HIV infections, combinations" ""
|
"GAN" "Ganciclovir" "J05AB06" 135398740 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "citovirax,cymevan,cymeven,cymevene,cytovene,ganciclovirum,gancyclovir,hydroxyacyclovir,virgan,vitrasert,zirgan" 3 "g" 0.5 "g" "15367-6,25256-9,59798-9,59799-7,60077-5,60078-3"
|
||||||
"J05AR11" "Lamivudine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations" ""
|
"GLE+PIB" "Glecaprevir/pibrentasvir" "J05AP57" 85471918 "Antivirals for treatment of HCV infections" "" ""
|
||||||
"J05AX18" 45138674 "Letermovir" "Other antivirals" "Letermovir,Prevymis" 0.48 "g" 0.48 "g"
|
"GRA" "Grazoprevir" "J05AP11" 44603531 "Antivirals for treatment of HCV infections" "" 0.1 "g" ""
|
||||||
"J05AR10" 11979606 "Lopinavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "Aluvia,Kaletra" 0.8 "g"
|
"IBA" "Ibalizumab" "J05AX23" "Other antivirals" "" ""
|
||||||
"J05AX02" 24839946 "Lysozyme" "Other antivirals" "Lysozyme chloride,Lysozyme Chloride,Lysozyme G"
|
"IDO" "Idoxuridine" "J05AB02" 5905 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "antizona,dendrid,heratil,herplex,idossuridina,idoxene,idoxuridin,idoxuridina,idoxuridinum,iduoculos,iduridin,iododeoxyridine,iododeoxyuridine,iodoxuridine,joddeoxiuridin,kerecid,stoxil,virudox" ""
|
||||||
"J05AX09" 3002977 "Maraviroc" "Other antivirals" "Celsentri,Maraviroc,Selzentry" 0.6 "g"
|
"IND" "Indinavir" "J05AE02" 5362440 "Protease inhibitors" "compound j,crixivan,indinavir anhydrous,propolis+indinavir" 2.4 "g" "29118-7,31033-4,51918-1"
|
||||||
"J05AX10" 471161 "Maribavir" "Other antivirals" "Benzimidavir,Camvia,Maribavir"
|
"INP" "Inosine pranobex" "J05AX05" 135449284 "Other antivirals" "aviral,delimmun,groprinosin,immunovir,imunovir,imunoviral,inosiplex,isoprinosin,isoprinosina,isoprinosine,isoviral,methisoprinol,modimmunal,pranosina,pranosine,viruxan" 3 "g" ""
|
||||||
"J05AA01" 667492 "Metisazone" "Thiosemicarbazones" "Kemoviran,Marboran,Marborane,Methisazon,Methisazone,Methsazone,Metisazon,Metisazona,Metisazone,Metisazonum,Viruzona"
|
"LAM" "Lamivudine" "J05AF05" 60825 "Nucleoside and nucleotide reverse transcriptase inhibitors" "epivir,hepitec,heptivir,heptodin,heptovir,lamivir,lamivudeine,lamivudine teva,lamivudinum,virolam,zeffix" 0.3 "g" "29119-5,49226-4"
|
||||||
"J05AX01" 71655 "Moroxydine" "Other antivirals" "Bimolin,Flumidine,Influmine,Moroxidina,Moroxydine,Moroxydinum,Vironil,Virugon,Virumin,Wirumin" 0.3 "g"
|
"LAM+ABA" "Lamivudine/abacavir" "J05AR02" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AE04" 64143 "Nelfinavir" "Protease inhibitors" "Nelfinavir,Viracept" 2.25 "g"
|
"LAM+DOL" "Lamivudine/dolutegravir" "J05AR25" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AG01" 4463 "Nevirapine" "Non-nucleoside reverse transcriptase inhibitors" "Nevirapine,Nevirapine anhydrous,Viramune,Viramune IR,Viramune XR" 0.4 "g"
|
"LAM+RAL" "Lamivudine/raltegravir" "J05AR16" 73386700 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AP53" "Ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
|
"LAM+TED" "Lamivudine/tenofovir disoproxil" "J05AR12" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AH02" 65028 "Oseltamivir" "Neuraminidase inhibitors" "Agucort,Oseltamivir,Tamiflu,Tamvir" 0.15 "g"
|
"LAM+ABA+DOL" "Lamivudine/abacavir/dolutegravir" "J05AR13" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AB13" 135398748 "Penciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Adenovir,Denavir,Penciceovir,Penciclovir,Penciclovirum,Pencyclovir,Vectavir"
|
"LAM+TED+DOL" "Lamivudine/tenofovir disoproxil/dolutegravir" "J05AR27" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AX21" 9942657 "Pentanedioic acid imidazolyl ethanamide" "Other antivirals" "Ingamine" 90 "mg"
|
"LAM+TED+DOR" "Lamivudine/tenofovir disoproxil/doravirine" "J05AR24" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AH03" 154234 "Peramivir" "Neuraminidase inhibitors" "PeramiFlu,Peramivir,Rapiacta,RAPIVAB"
|
"LAM+TED+EFA" "Lamivudine/tenofovir disoproxil/efavirenz" "J05AR11" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AX06" 1684 "Pleconaril" "Other antivirals" "Picovir,Pleconaril,Pleconarilis"
|
"LAN" "Laninamivir" "J05AH04" 502272 "Neuraminidase inhibitors" "" ""
|
||||||
"J05AX08" 54671008 "Raltegravir" "Other antivirals" "Isentress,Raltegravir" 0.8 "g"
|
"LEN" "Lenacapavir" "J05AX31" 133082658 "Other antivirals" "" ""
|
||||||
"J05AP01" 37542 "Ribavirin" "Antivirals for treatment of HCV infections" "Copegus,Cotronak,Drug: Ribavirin,Ravanex,Rebetol,Rebetron,Rebretron,Ribacine,Ribamide,Ribamidil,Ribamidyl,Ribasphere,Ribavirin,Ribavirin Capsules,Ribavirina,Ribavirine,Ribavirinum,Ribovirin,Tribavirin,Varazid,Vilona,Viramid,Viramide,Virazid,Virazide,Virazole" 1 "g"
|
"LET" "Letermovir" "J05AX18" 45138674 "Other antivirals" "acetic acid,prevymis" 0.48 "g" 0.48 "g" ""
|
||||||
"J05AG05" 6451164 "Rilpivirine" "Non-nucleoside reverse transcriptase inhibitors" "Edurant,Rilpivirine" 25 "mg"
|
"LOP+RIT" "Lopinavir/ritonavir" "J05AR10" 11979606 "Antivirals for treatment of HIV infections, combinations" "aluvia,kaletra,lopimune" 0.8 "g" ""
|
||||||
"J05AC02" 5071 "Rimantadine" "Cyclic amines" "Remantadine,Riamantadine,Rimant,RIMANTADIN,Rimantadin A,Rimantadina,Rimantadine,Rimantadinum" 0.2 "g"
|
"LYS" "Lysozyme" "J05AX02" 16130991 "Other antivirals" "" ""
|
||||||
"J05AE03" 392622 "Ritonavir" "Protease inhibitors" "Norvir,Norvir Sec,Norvir Softgel,Ritonavir,Ritonavire,Ritonavirum" 1.2 "g"
|
"MARA" "Maraviroc" "J05AX09" 3002977 "Other antivirals" "celsentri,selzentry" 0.6 "g" "88987-3"
|
||||||
"J05AE01" 441243 "Saquinavir" "Protease inhibitors" "Fortovase,Invirase,Saquinavir" 1.8 "g"
|
"MARI" "Maribavir" "J05AX10" 471161 "Other antivirals" "benzimidavir,camvia" ""
|
||||||
"J05AP05" 24873435 "Simeprevir" "Antivirals for treatment of HCV infections" "Olysio,Simeprevir sodium" 0.15 "g"
|
"MET" "Metisazone" "J05AA01" 667492 "Thiosemicarbazones" "kemoviran,marboran,marborane,methisazon,methisazone,methsazone,metisazon,metisazona,metisazonum,viruzona" ""
|
||||||
"J05AP08" 45375808 "Sofosbuvir" "Antivirals for treatment of HCV infections" "Hepcinat,Hepcvir,Sofosbuvir,Sovaldi,SOVALDI,SoviHep" 0.4 "g"
|
"MOR" "Moroxydine" "J05AX01" 71655 "Other antivirals" "bimolin,moroxidina,moroxydinum,virugon,virumin,wirumin" 0.3 "g" ""
|
||||||
"J05AP51" 72734365 "Sofosbuvir and ledipasvir" "Antivirals for treatment of HCV infections" ""
|
"NEL" "Nelfinavir" "J05AE04" 64143 "Protease inhibitors" "viracept" 2.25 "g" "29120-3,32647-0,35113-0,51923-1"
|
||||||
"J05AP55" 91885554 "Sofosbuvir and velpatasvir" "Antivirals for treatment of HCV infections" "Epclusa Tablet"
|
"NEV" "Nevirapine" "J05AG01" 4463 "Non-nucleoside reverse transcriptase inhibitors" "nevirapine anhydrous,nevirapine teva,nevirapine),viramune,viramune ir,viramune xr" 0.4 "g" "29121-1,32646-2,51925-6"
|
||||||
"J05AP56" "Sofosbuvir, velpatasvir and voxilaprevir" "Antivirals for treatment of HCV infections" ""
|
"OMB+PAR+RIT" "Ombitasvir/paritaprevir/ritonavir" "J05AP53" "Antivirals for treatment of HCV infections" "" ""
|
||||||
"J05AF04" 18283 "Stavudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Estavudina,Sanilvudine,Stavudin,Stavudine,Stavudinum,Zerit Xr,Zerut XR" 80 "mg"
|
"OSE" "Oseltamivir" "J05AH02" 65028 "Neuraminidase inhibitors" "agucort,tamiflu,tamvir" 0.15 "g" ""
|
||||||
"J05AR07" 15979285 "Stavudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" "STAVUDIINE"
|
"PEN" "Penciclovir" "J05AB13" 135398748 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "adenovir,denavir,penciceovir,penciclovirum,pencyclovir,vectavir" "60140-1,60141-9"
|
||||||
"J05AP02" 3010818 "Telaprevir" "Antivirals for treatment of HCV infections" "Incivek,Incivo,Telaprevir,Telavic" 2.25 "g"
|
"PAIE" "Pentanedioic acid imidazolyl ethanamide" "J05AX21" 9942657 "Other antivirals" "ingamine" 90 "mg" ""
|
||||||
"J05AF11" 159269 "Telbivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Epavudine,Sebivo,Telbivudin,Telbivudine,Tyzeka" 0.6 "g"
|
"PER" "Peramivir" "J05AH03" 154234 "Neuraminidase inhibitors" "peramiflu,peramivir anhydrous,rapiacta,rapivab" 0.6 "g" ""
|
||||||
"J05AF13" 9574768 "Tenofovir alafenamide" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Vemlidy" 25 "mg"
|
"PLE" "Pleconaril" "J05AX06" 1684 "Other antivirals" "picovir,pleconarilis" ""
|
||||||
"J05AF07" 5481350 "Tenofovir disoproxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "BisPMPA,PMPA prodrug,Tenofovir,Viread" 0.245 "g"
|
"RAL" "Raltegravir" "J05AJ01" 54671008 "Integrase inhibitors" "isentress" 0.8 "g" "72835-2"
|
||||||
"J05AR03" "Tenofovir disoproxil and emtricitabine" "Antivirals for treatment of HIV infections, combinations" ""
|
"REM" "Remdesivir" "J05AB16" 121304016 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "veklury" 0.1 "g" ""
|
||||||
"J05AX19" 5475 "Tilorone" "Other antivirals" "Amiksin,Amixin,Amixin IC,Amyxin,Tiloron,Tilorona,Tilorone,Tiloronum" 0.125 "g"
|
"RIB" "Ribavirin" "J05AP01" 37542 "Antivirals for treatment of HCV infections" "copegus,cotronak,ravanex,rebetol,rebetron,rebretron,ribacine,ribamide,ribamidil,ribamidyl,ribasphere,ribavirin capsules,ribavirin mylan,ribavirin teva,ribavirina,ribavirine,ribavirinum,tribavirin,varazid,vilona,viramid,virazid,virazide,virazole" 1 "g" "41469-8"
|
||||||
"J05AE09" 54682461 "Tipranavir" "Protease inhibitors" "Aptivus,Tipranavir" 1 "g"
|
"RIL" "Rilpivirine" "J05AG05" 6451164 "Non-nucleoside reverse transcriptase inhibitors" "edurant,rilpivirina" 25 "mg" 15 "mg" "80547-3"
|
||||||
"J05AC03" 64377 "Tromantadine" "Cyclic amines" "Tromantadina,Tromantadine,Tromantadinum,Viruserol"
|
"RIM" "Rimantadine" "J05AC02" 5071 "Cyclic amines" "ethanamine,rimant,rimantadin,rimantadin a,rimantadina,rimantadinum" 0.2 "g" ""
|
||||||
"J05AX13" 131411 "Umifenovir" "Other antivirals" "Arbidol,Arbidol base,Umifenovir" 0.8 "g"
|
"RIT" "Ritonavir" "J05AE03" 392622 "Protease inhibitors" "empetus,norvir,norvir softgel,ritomune,ritonavirum,ritovir,viekirax,viriton" 1.2 "g" "29122-9,31027-6,51929-8,51930-6"
|
||||||
"J05AB11" 135398742 "Valaciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Talavir,Valaciclovir,Valaciclovirum,ValACV,Valcivir,Valcyclovir,Valtrex,Virval,Zelitrex" 3 "g"
|
"SAQ" "Saquinavir" "J05AE01" 441243 "Protease inhibitors" "fortovase,invirase,saquinavirum" 1.8 "g" "19051-2,29123-7,51932-2"
|
||||||
"J05AB14" 135413535 "Valganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Cymeval,Valganciclovir" 0.9 "g"
|
"SIM" "Simeprevir" "J05AP05" 24873435 "Antivirals for treatment of HCV infections" "olysio,simeprevir sodium" 0.15 "g" ""
|
||||||
"J05AB03" 21704 "Vidarabine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Adenine arabinoside,Araadenosine,Arabinoside adenine,Arabinosyl adenine,Arabinosyladenine,Spongoadenosine,Vidarabin,Vidarabina,Vidarabine,Vidarabine anhydrous,Vidarabinum,Vira A,Vira ATM"
|
"SOF" "Sofosbuvir" "J05AP08" 45375808 "Antivirals for treatment of HCV infections" "hepcinat,hepcvir,sovaldi,sovihep" 0.4 "g" ""
|
||||||
"J05AF03" 24066 "Zalcitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Dideoxycytidine,Interferon AD + ddC,Zalcitabine,Zalcitibine" 2.25 "mg"
|
"SOF+LED" "Sofosbuvir/ledipasvir" "J05AP51" 72734365 "Antivirals for treatment of HCV infections" "harvoni" ""
|
||||||
"J05AH01" 60855 "Zanamivir" "Neuraminidase inhibitors" "MODIFIED SIALIC ACID,Relenza,Zanamavir,Zanamir,Zanamivi,Zanamivir,Zanamivir hydrate"
|
"SOF+VEL" "Sofosbuvir/velpatasvir" "J05AP55" 91885554 "Antivirals for treatment of HCV infections" "epclusa,epclusa tablet" ""
|
||||||
"J05AF01" 35370 "Zidovudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Azidothymidine,AZT Antiviral,Beta interferon,Compound S,Propolis+AZT,Retrovir,Zidovudina,Zidovudine,ZIDOVUDINE,Zidovudine EP III,Zidovudinum" 0.6 "g" 0.6 "g"
|
"SOF+VEL+VOX" "Sofosbuvir/velpatasvir/voxilaprevir" "J05AP56" "Antivirals for treatment of HCV infections" "" ""
|
||||||
"J05AR01" "Zidovudine and lamivudine" "Antivirals for treatment of HIV infections, combinations" ""
|
"STA" "Stavudine" "J05AF04" 18283 "Nucleoside and nucleotide reverse transcriptase inhibitors" "estavudina,sanilvudine,stavudinum,zerit xr,zerut xr" 80 "mg" "29124-5,49227-2"
|
||||||
"J05AR04" "Zidovudine, lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations" ""
|
"STA+LAM+NEV" "Stavudine/lamivudine/nevirapine" "J05AR07" 15979285 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
"J05AR05" "Zidovudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" ""
|
"TEC" "Tecovirimat" "J05AX24" 16124688 "Other antivirals" "" ""
|
||||||
|
"TELA" "Telaprevir" "J05AP02" 3010818 "Antivirals for treatment of HCV infections" "incivek,incivo,telavic" 2.25 "g" ""
|
||||||
|
"TELB" "Telbivudine" "J05AF11" 159269 "Nucleoside and nucleotide reverse transcriptase inhibitors" "epavudine,sebivo,telbivudin,tyzeka" 0.6 "g" ""
|
||||||
|
"TEA" "Tenofovir alafenamide" "J05AF13" 9574768 "Nucleoside and nucleotide reverse transcriptase inhibitors" "vemlidy" 25 "mg" ""
|
||||||
|
"TED" "Tenofovir disoproxil" "J05AF07" 5481350 "Nucleoside and nucleotide reverse transcriptase inhibitors" "bispmpa,pmpa prodrug,tenofovir,tenofovir bis,tenofovirdisoproxil,viread" 0.245 "g" ""
|
||||||
|
"TED+EMT" "Tenofovir disoproxil/emtricitabine" "J05AR03" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
|
"TIL" "Tilorone" "J05AX19" 5475 "Other antivirals" "amixin ic,tiloron,tilorona,tiloronum" 0.125 "g" ""
|
||||||
|
"TIP" "Tipranavir" "J05AE09" 54682461 "Protease inhibitors" "aptivus" 1 "g" "57383-2"
|
||||||
|
"TRO" "Tromantadine" "J05AC03" 64377 "Cyclic amines" "tromantadina,tromantadinum" ""
|
||||||
|
"UMI" "Umifenovir" "J05AX13" 131411 "Other antivirals" "arbidol,arbidol base" 0.8 "g" ""
|
||||||
|
"VALA" "Valaciclovir" "J05AB11" 135398742 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "talavir,valacv,valacyclovir,valcivir,valcyclovir,valtrex,virval,zelitrex" 3 "g" ""
|
||||||
|
"VALG" "Valganciclovir" "J05AB14" 135413535 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "cymeval" 0.9 "g" "74960-6"
|
||||||
|
"VID" "Vidarabine" "J05AB03" 21704 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "adenine arabinoside,araadenosine,arabinoside adenine,arabinosyl adenine,arabinosyladenine,spongoadenosine,vidarabin,vidarabina,vidarabine anhydrous,vidarabinum,vira a,vira atm" 0.7 "g" ""
|
||||||
|
"ZAL" "Zalcitabine" "J05AF03" 24066 "Nucleoside and nucleotide reverse transcriptase inhibitors" "dideoxycytidine,interferon ad + ddc,zalcitibine" 2.25 "mg" "29125-2"
|
||||||
|
"ZAN" "Zanamivir" "J05AH01" 60855 "Neuraminidase inhibitors" "modified sialic acid,relenza,zanamavir,zanamivi,zanamivirhydrate" 1.2 "g" ""
|
||||||
|
"ZID" "Zidovudine" "J05AF01" 35370 "Nucleoside and nucleotide reverse transcriptase inhibitors" "azidothymidine,beta interferon,compound s,propolis+azt,retrovir,trizivir,zidovudina,zidovudinum" 0.6 "g" 0.6 "g" "29126-0,6894-0"
|
||||||
|
"ZID+LAM" "Zidovudine/lamivudine" "J05AR01" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
|
"ZID+LAM+ABA" "Zidovudine/lamivudine/abacavir" "J05AR04" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
|
"ZID+LAM+NEV" "Zidovudine/lamivudine/nevirapine" "J05AR05" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||||
|
|||||||
Binary file not shown.
@ -1 +1 @@
|
|||||||
246da79545e045edac7c3ec445b3a04e
|
009fea3738cdb6390dccd470cb27f015
|
||||||
|
|||||||
@ -62,7 +62,7 @@ for (i in seq_len(nrow(antibiotics))) {
|
|||||||
# sort and fix for empty values
|
# sort and fix for empty values
|
||||||
for (i in 1:nrow(antibiotics)) {
|
for (i in 1:nrow(antibiotics)) {
|
||||||
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc"][[1]]))))
|
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc"][[1]]))))
|
||||||
antibiotics[i, "loinc"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(loinc))
|
antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc[!loinc == ""]) == 0, list(""), list(loinc))
|
||||||
}
|
}
|
||||||
|
|
||||||
# remember to update R/aa_globals.R for the documentation
|
# remember to update R/aa_globals.R for the documentation
|
||||||
|
|||||||
@ -192,7 +192,7 @@ abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixe
|
|||||||
# vector with official names, returns vector with CIDs
|
# vector with official names, returns vector with CIDs
|
||||||
get_CID <- function(ab) {
|
get_CID <- function(ab) {
|
||||||
CID <- rep(NA_integer_, length(ab))
|
CID <- rep(NA_integer_, length(ab))
|
||||||
p <- progress_ticker(n = length(ab), min_time = 0)
|
p <- AMR:::progress_ticker(n = length(ab), min_time = 0)
|
||||||
for (i in 1:length(ab)) {
|
for (i in 1:length(ab)) {
|
||||||
p$tick()
|
p$tick()
|
||||||
|
|
||||||
@ -248,7 +248,7 @@ antibiotics[is.na(CIDs), ] %>% View()
|
|||||||
# returns list with synonyms (brand names), with CIDs as names
|
# returns list with synonyms (brand names), with CIDs as names
|
||||||
get_synonyms <- function(CID, clean = TRUE) {
|
get_synonyms <- function(CID, clean = TRUE) {
|
||||||
synonyms <- rep(NA_character_, length(CID))
|
synonyms <- rep(NA_character_, length(CID))
|
||||||
p <- progress_ticker(n = length(CID), min_time = 0)
|
p <- AMR:::progress_ticker(n = length(CID), min_time = 0)
|
||||||
|
|
||||||
for (i in 1:length(CID)) {
|
for (i in 1:length(CID)) {
|
||||||
p$tick()
|
p$tick()
|
||||||
|
|||||||
@ -27,14 +27,18 @@
|
|||||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
# ==================================================================== #
|
# ==================================================================== #
|
||||||
|
|
||||||
# get all data from the WHOCC website
|
library(dplyr)
|
||||||
|
library(tidyr)
|
||||||
|
library(rvest)
|
||||||
|
|
||||||
|
# get all data from the WHOCC website
|
||||||
get_atc_table <- function(atc_group) {
|
get_atc_table <- function(atc_group) {
|
||||||
# give as input J0XXX, like atc_group = "J05AB"
|
# give as input J0XXX, like atc_group = "J05AB"
|
||||||
downloaded <- read_html(paste0("https://www.whocc.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
|
downloaded <- read_html(paste0("https://www.whocc.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
|
||||||
table_title <- downloaded %>%
|
table_title <- downloaded %>%
|
||||||
html_nodes(paste0('a[href="./?code=', atc_group, '"]')) %>%
|
html_nodes(paste0('a[href^="./?code=', atc_group, '&"]')) %>%
|
||||||
html_text()
|
html_text()
|
||||||
|
table_title <- table_title[tolower(table_title) != "show text from guidelines"][1]
|
||||||
table_content <- downloaded %>%
|
table_content <- downloaded %>%
|
||||||
html_nodes("table") %>%
|
html_nodes("table") %>%
|
||||||
html_table(header = TRUE) %>%
|
html_table(header = TRUE) %>%
|
||||||
@ -59,12 +63,13 @@ get_atc_table <- function(atc_group) {
|
|||||||
}
|
}
|
||||||
|
|
||||||
# these are the relevant groups for input: https://www.whocc.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
|
# these are the relevant groups for input: https://www.whocc.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
|
||||||
atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AP", "J05AR", "J05AX")
|
atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AJ", "J05AP", "J05AR", "J05AX")
|
||||||
|
|
||||||
# get the first
|
# get the first
|
||||||
antivirals <- get_atc_table(atc_groups[1])
|
antivirals <- get_atc_table(atc_groups[1])
|
||||||
# bind all others to it
|
# bind all others to it
|
||||||
for (i in 2:length(atc_groups)) {
|
for (i in 2:length(atc_groups)) {
|
||||||
|
message(atc_groups[i], "...")
|
||||||
antivirals <- rbind(antivirals, get_atc_table(atc_groups[i]))
|
antivirals <- rbind(antivirals, get_atc_table(atc_groups[i]))
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -73,7 +78,8 @@ antivirals <- antivirals %>%
|
|||||||
arrange(name) %>%
|
arrange(name) %>%
|
||||||
as.data.frame(stringsAsFactors = FALSE)
|
as.data.frame(stringsAsFactors = FALSE)
|
||||||
|
|
||||||
# add PubChem Compound ID (cid) and their trade names - functions are in file to create `antibiotics` data set
|
# add PubChem Compound ID (cid) and their trade names
|
||||||
|
# see `data-raw/reproduction_of_antibiotics` for get_CID() and get_synonyms()
|
||||||
CIDs <- get_CID(antivirals$name)
|
CIDs <- get_CID(antivirals$name)
|
||||||
# these could not be found:
|
# these could not be found:
|
||||||
antivirals[is.na(CIDs), ] %>% View()
|
antivirals[is.na(CIDs), ] %>% View()
|
||||||
@ -92,7 +98,7 @@ synonyms <- lapply(
|
|||||||
|
|
||||||
antivirals <- antivirals %>%
|
antivirals <- antivirals %>%
|
||||||
transmute(atc,
|
transmute(atc,
|
||||||
cid = CIDs,
|
cid = as.double(CIDs),
|
||||||
name,
|
name,
|
||||||
atc_group,
|
atc_group,
|
||||||
synonyms = unname(synonyms),
|
synonyms = unname(synonyms),
|
||||||
@ -100,7 +106,79 @@ antivirals <- antivirals %>%
|
|||||||
oral_units,
|
oral_units,
|
||||||
iv_ddd,
|
iv_ddd,
|
||||||
iv_units
|
iv_units
|
||||||
|
) %>%
|
||||||
|
AMR:::dataset_UTF8_to_ASCII()
|
||||||
|
|
||||||
|
av_codes <- tibble(name = antivirals$name %>%
|
||||||
|
strsplit("(, | and )") %>%
|
||||||
|
unlist() %>%
|
||||||
|
unique() %>%
|
||||||
|
sort()) %>%
|
||||||
|
mutate(av_1st = toupper(abbreviate(name, minlength = 3, use.classes = FALSE))) %>%
|
||||||
|
filter(!name %in% c("acid", "dipivoxil", "disoproxil", "marboxil", "alafenamide"))
|
||||||
|
|
||||||
|
replace_with_av_code <- function(name) {
|
||||||
|
unname(av_codes$av_1st[match(name, av_codes$name)])
|
||||||
|
}
|
||||||
|
|
||||||
|
names_codes <- antivirals %>%
|
||||||
|
separate(name,
|
||||||
|
into = paste0("name", c(1:7)),
|
||||||
|
sep = "(, | and )",
|
||||||
|
remove = FALSE,
|
||||||
|
fill = "right") %>%
|
||||||
|
# remove empty columns
|
||||||
|
select(!where(function(x) all(is.na(x)))) %>%
|
||||||
|
mutate_at(vars(matches("name[1-9]")), replace_with_av_code) %>%
|
||||||
|
unite(av, matches("name[1-9]"), sep = "+", na.rm = TRUE) %>%
|
||||||
|
mutate(name = gsub("(, | and )", "/", name))
|
||||||
|
substr(names_codes$name, 1, 1) <- toupper(substr(names_codes$name, 1, 1))
|
||||||
|
|
||||||
|
antivirals <- bind_cols(
|
||||||
|
names_codes %>% select(av, name),
|
||||||
|
antivirals %>% select(-name)
|
||||||
)
|
)
|
||||||
|
class(antivirals$av) <- c("av", "character")
|
||||||
|
antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
|
||||||
|
|
||||||
|
# add loinc, see 'data-raw/loinc.R'
|
||||||
|
loinc_df <- read.csv("data-raw/Loinc.csv",
|
||||||
|
row.names = NULL,
|
||||||
|
stringsAsFactors = FALSE)
|
||||||
|
|
||||||
|
loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
|
||||||
|
av_names <- antivirals %>%
|
||||||
|
pull(name) %>%
|
||||||
|
paste0(collapse = "|") %>%
|
||||||
|
paste0("(", ., ")")
|
||||||
|
|
||||||
|
antivirals$loinc <- as.list(rep(NA_character_, nrow(antivirals)))
|
||||||
|
for (i in seq_len(nrow(antivirals))) {
|
||||||
|
message(i)
|
||||||
|
loinc_ab <- loinc_df %>%
|
||||||
|
filter(COMPONENT %like% paste0("^", antivirals$name[i])) %>%
|
||||||
|
pull(LOINC_NUM)
|
||||||
|
if (length(loinc_ab) > 0) {
|
||||||
|
antivirals$loinc[i] <- list(loinc_ab)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
# sort and fix for empty values
|
||||||
|
for (i in 1:nrow(antivirals)) {
|
||||||
|
loinc <- as.character(sort(unique(tolower(antivirals[i, "loinc", drop = TRUE][[1]]))))
|
||||||
|
antivirals[i, "loinc"][[1]] <- ifelse(length(loinc[!loinc == ""]) == 0, list(""), list(loinc))
|
||||||
|
}
|
||||||
|
|
||||||
|
# de-duplicate synonyms
|
||||||
|
for (i in 1:nrow(antivirals)) {
|
||||||
|
syn <- as.character(sort(unique(tolower(antivirals[i, "synonyms", drop = TRUE][[1]]))))
|
||||||
|
syn <- syn[!syn %in% tolower(antivirals[i, "name", drop = TRUE])]
|
||||||
|
antivirals[i, "synonyms"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(syn))
|
||||||
|
}
|
||||||
|
|
||||||
|
antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
|
||||||
|
|
||||||
|
# check it
|
||||||
|
antivirals
|
||||||
|
|
||||||
# save it
|
# save it
|
||||||
usethis::use_data(antivirals, overwrite = TRUE)
|
usethis::use_data(antivirals, overwrite = TRUE, internal = FALSE, compress = "xz", version = 2)
|
||||||
|
|||||||
Binary file not shown.
2
index.md
2
index.md
@ -6,7 +6,7 @@ The `AMR` package is a [free and open-source](#copyright) R package with [zero d
|
|||||||
|
|
||||||
This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
|
This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
|
||||||
|
|
||||||
After installing this package, R knows [**~49,000 distinct microbial species**](./reference/microorganisms.html) and all [**~570 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.
|
After installing this package, R knows [**~49,000 distinct microbial species**](./reference/microorganisms.html) and all [**~600 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.
|
||||||
|
|
||||||
##### Used in 175 countries, translated to 16 languages
|
##### Used in 175 countries, translated to 16 languages
|
||||||
|
|
||||||
|
|||||||
@ -45,10 +45,8 @@ expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
|
|||||||
expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
|
expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
|
||||||
|
|
||||||
expect_identical(ab_ddd("AMX", "oral"), 1.5)
|
expect_identical(ab_ddd("AMX", "oral"), 1.5)
|
||||||
expect_warning(ab_ddd("AMX", "oral", units = TRUE)) # old behaviour
|
|
||||||
expect_identical(ab_ddd_units("AMX", "iv"), "g")
|
expect_identical(ab_ddd_units("AMX", "iv"), "g")
|
||||||
expect_identical(ab_ddd("AMX", "iv"), 3)
|
expect_identical(ab_ddd("AMX", "iv"), 3)
|
||||||
expect_identical(ab_ddd_units("AMX", "iv"), "g")
|
|
||||||
|
|
||||||
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
|
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
|
||||||
expect_identical(
|
expect_identical(
|
||||||
|
|||||||
80
inst/tinytest/test-av.R
Executable file
80
inst/tinytest/test-av.R
Executable file
@ -0,0 +1,80 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||||
|
# #
|
||||||
|
# SOURCE #
|
||||||
|
# https://github.com/msberends/AMR #
|
||||||
|
# #
|
||||||
|
# CITE AS #
|
||||||
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||||
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||||
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||||
|
# doi:10.18637/jss.v104.i03 #
|
||||||
|
# #
|
||||||
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
# #
|
||||||
|
# This R package is free software; you can freely use and distribute #
|
||||||
|
# it for both personal and commercial purposes under the terms of the #
|
||||||
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||||
|
# the Free Software Foundation. #
|
||||||
|
# We created this package for both routine data analysis and academic #
|
||||||
|
# research and it was publicly released in the hope that it will be #
|
||||||
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||||
|
# #
|
||||||
|
# Visit our website for the full manual and a complete tutorial about #
|
||||||
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
expect_equal(
|
||||||
|
as.character(as.av(c(
|
||||||
|
"J05AB01",
|
||||||
|
"J 05 AB 01",
|
||||||
|
"Aciclovir",
|
||||||
|
"aciclo",
|
||||||
|
" aciclo 123",
|
||||||
|
"ACICL",
|
||||||
|
"ACI",
|
||||||
|
"Virorax",
|
||||||
|
"Zovirax"
|
||||||
|
))),
|
||||||
|
rep("ACI", 9)
|
||||||
|
)
|
||||||
|
|
||||||
|
expect_identical(class(as.av("acic")), c("av", "character"))
|
||||||
|
expect_identical(class(antivirals$av), c("av", "character"))
|
||||||
|
expect_true(is.av(as.av("acic")))
|
||||||
|
expect_stdout(print(as.av("acic")))
|
||||||
|
expect_stdout(print(data.frame(a = as.av("acic"))))
|
||||||
|
|
||||||
|
expect_warning(as.av("J00AA00")) # ATC not yet available in data set
|
||||||
|
expect_warning(as.av("UNKNOWN"))
|
||||||
|
|
||||||
|
expect_stdout(print(as.av("acic")))
|
||||||
|
|
||||||
|
expect_equal(
|
||||||
|
as.character(as.av("zovirax")),
|
||||||
|
"ACI"
|
||||||
|
)
|
||||||
|
|
||||||
|
expect_equal(
|
||||||
|
as.character(as.av(c("Abacaivr", "Celvudine"))),
|
||||||
|
c("ABA", "CLE")
|
||||||
|
)
|
||||||
|
|
||||||
|
expect_warning(as.av("Abacavir Clevudine"))
|
||||||
|
|
||||||
|
# based on Levenshtein distance
|
||||||
|
expect_identical(av_name("adevofir dypifo", language = NULL), "Adefovir dipivoxil")
|
||||||
|
|
||||||
|
# assigning and subsetting
|
||||||
|
x <- antivirals$av
|
||||||
|
expect_inherits(x[1], "av")
|
||||||
|
expect_inherits(x[[1]], "av")
|
||||||
|
expect_inherits(c(x[1], x[9]), "av")
|
||||||
|
expect_inherits(unique(x[1], x[9]), "av")
|
||||||
|
expect_inherits(rep(x[1], 2), "av")
|
||||||
|
expect_warning(x[1] <- "invalid code")
|
||||||
|
expect_warning(x[[1]] <- "invalid code")
|
||||||
|
expect_warning(c(x[1], "test"))
|
||||||
58
inst/tinytest/test-av_from_text.R
Normal file
58
inst/tinytest/test-av_from_text.R
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||||
|
# #
|
||||||
|
# SOURCE #
|
||||||
|
# https://github.com/msberends/AMR #
|
||||||
|
# #
|
||||||
|
# CITE AS #
|
||||||
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||||
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||||
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||||
|
# doi:10.18637/jss.v104.i03 #
|
||||||
|
# #
|
||||||
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
# #
|
||||||
|
# This R package is free software; you can freely use and distribute #
|
||||||
|
# it for both personal and commercial purposes under the terms of the #
|
||||||
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||||
|
# the Free Software Foundation. #
|
||||||
|
# We created this package for both routine data analysis and academic #
|
||||||
|
# research and it was publicly released in the hope that it will be #
|
||||||
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||||
|
# #
|
||||||
|
# Visit our website for the full manual and a complete tutorial about #
|
||||||
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
expect_identical(
|
||||||
|
av_from_text("28/03/2020 regular aciclovir 500mg po tds")[[1]],
|
||||||
|
as.av("Aciclovir")
|
||||||
|
)
|
||||||
|
expect_identical(
|
||||||
|
av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = TRUE)[[1]],
|
||||||
|
as.av("Aciclovir")
|
||||||
|
)
|
||||||
|
expect_identical(
|
||||||
|
av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = FALSE)[[1]],
|
||||||
|
as.av("Aciclovir")
|
||||||
|
)
|
||||||
|
expect_identical(
|
||||||
|
av_from_text("28/03/2020 regular aciclovir 500mg po tds", translate_av = TRUE)[[1]],
|
||||||
|
"Aciclovir"
|
||||||
|
)
|
||||||
|
expect_identical(
|
||||||
|
av_from_text("administered aciclo and valaciclo", collapse = ", ")[[1]],
|
||||||
|
"ACI, VALA"
|
||||||
|
)
|
||||||
|
|
||||||
|
expect_identical(
|
||||||
|
av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "dose")[[1]],
|
||||||
|
500
|
||||||
|
)
|
||||||
|
expect_identical(
|
||||||
|
av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "admin")[[1]],
|
||||||
|
"oral"
|
||||||
|
)
|
||||||
64
inst/tinytest/test-av_property.R
Normal file
64
inst/tinytest/test-av_property.R
Normal file
@ -0,0 +1,64 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||||
|
# #
|
||||||
|
# SOURCE #
|
||||||
|
# https://github.com/msberends/AMR #
|
||||||
|
# #
|
||||||
|
# CITE AS #
|
||||||
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||||
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||||
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||||
|
# doi:10.18637/jss.v104.i03 #
|
||||||
|
# #
|
||||||
|
# Developed at the University of Groningen, the Netherlands, in #
|
||||||
|
# collaboration with non-profit organisations Certe Medical #
|
||||||
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||||
|
# #
|
||||||
|
# This R package is free software; you can freely use and distribute #
|
||||||
|
# it for both personal and commercial purposes under the terms of the #
|
||||||
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||||
|
# the Free Software Foundation. #
|
||||||
|
# We created this package for both routine data analysis and academic #
|
||||||
|
# research and it was publicly released in the hope that it will be #
|
||||||
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||||
|
# #
|
||||||
|
# Visit our website for the full manual and a complete tutorial about #
|
||||||
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
expect_identical(av_name("ACI", language = NULL), "Aciclovir")
|
||||||
|
expect_identical(av_atc("ACI"), "J05AB01")
|
||||||
|
expect_identical(av_cid("ACI"), as.integer(135398513))
|
||||||
|
|
||||||
|
expect_inherits(av_tradenames("ACI"), "character")
|
||||||
|
expect_inherits(av_tradenames(c("ACI", "ACI")), "list")
|
||||||
|
|
||||||
|
expect_identical(av_group("ACI", language = NULL),"Nucleosides and nucleotides excl. reverse transcriptase inhibitors")
|
||||||
|
|
||||||
|
expect_identical(av_name(135398513, language = NULL), "Aciclovir")
|
||||||
|
expect_identical(av_name("J05AB01", language = NULL), "Aciclovir")
|
||||||
|
|
||||||
|
expect_identical(av_ddd("ACI", "oral"), 4)
|
||||||
|
expect_identical(av_ddd_units("ACI", "iv"), "g")
|
||||||
|
expect_identical(av_ddd("ACI", "iv"), 4)
|
||||||
|
|
||||||
|
expect_identical(
|
||||||
|
av_name(x = c("ACI", "VALA"), tolower = TRUE, language = NULL),
|
||||||
|
c("aciclovir", "valaciclovir")
|
||||||
|
)
|
||||||
|
|
||||||
|
expect_inherits(av_info("ACI"), "list")
|
||||||
|
|
||||||
|
expect_error(av_property("acic", "invalid property"))
|
||||||
|
expect_error(av_name("acic", language = "INVALID"))
|
||||||
|
expect_stdout(print(av_name("acic", language = NULL)))
|
||||||
|
|
||||||
|
expect_equal(av_name("29113-8", language = NULL), "Abacavir")
|
||||||
|
expect_equal(
|
||||||
|
av_loinc("Abacavir"),
|
||||||
|
c("29113-8", "78772-1", "78773-9", "79134-3", "80118-3")
|
||||||
|
)
|
||||||
|
|
||||||
|
expect_true(av_url("ACI") %like% "whocc.no")
|
||||||
|
expect_warning(av_url("ASP"))
|
||||||
@ -27,8 +27,6 @@
|
|||||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||||
# ==================================================================== #
|
# ==================================================================== #
|
||||||
|
|
||||||
expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
|
|
||||||
expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
|
|
||||||
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
|
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
|
||||||
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
|
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
|
||||||
|
|
||||||
|
|||||||
@ -32,7 +32,7 @@ Welcome to the \code{AMR} package.
|
|||||||
|
|
||||||
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
|
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
|
||||||
|
|
||||||
After installing this package, \R knows ~49,000 distinct microbial species and all ~580 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
|
After installing this package, \R knows ~49,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
|
||||||
|
|
||||||
This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
|
This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
|
||||||
|
|
||||||
|
|||||||
@ -60,7 +60,7 @@ With using \code{collapse}, this function will return a \link{character}:\cr
|
|||||||
\examples{
|
\examples{
|
||||||
# mind the bad spelling of amoxicillin in this line,
|
# mind the bad spelling of amoxicillin in this line,
|
||||||
# straight from a true health care record:
|
# straight from a true health care record:
|
||||||
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")
|
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tid")
|
||||||
|
|
||||||
ab_from_text("500 mg amoxi po and 400mg cipro iv")
|
ab_from_text("500 mg amoxi po and 400mg cipro iv")
|
||||||
ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "dose")
|
ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "dose")
|
||||||
|
|||||||
@ -109,38 +109,35 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/S
|
|||||||
|
|
||||||
\examples{
|
\examples{
|
||||||
# all properties:
|
# all properties:
|
||||||
ab_name("AMX") # "Amoxicillin"
|
ab_name("AMX")
|
||||||
ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
|
ab_atc("AMX")
|
||||||
ab_cid("AMX") # 33613 (Compound ID from PubChem)
|
ab_cid("AMX")
|
||||||
ab_synonyms("AMX") # a list with brand names of amoxicillin
|
ab_synonyms("AMX")
|
||||||
ab_tradenames("AMX") # same
|
ab_tradenames("AMX")
|
||||||
ab_group("AMX") # "Beta-lactams/penicillins"
|
ab_group("AMX")
|
||||||
ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
|
ab_atc_group1("AMX")
|
||||||
ab_atc_group2("AMX") # "Penicillins with extended spectrum"
|
ab_atc_group2("AMX")
|
||||||
ab_url("AMX") # link to the official WHO page
|
ab_url("AMX")
|
||||||
|
|
||||||
# smart lowercase tranformation
|
# smart lowercase tranformation
|
||||||
ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
|
ab_name(x = c("AMC", "PLB"))
|
||||||
ab_name(
|
ab_name(x = c("AMC", "PLB"), tolower = TRUE)
|
||||||
x = c("AMC", "PLB"),
|
|
||||||
tolower = TRUE
|
|
||||||
) # "amoxicillin/clavulanic acid" "polymyxin B"
|
|
||||||
|
|
||||||
# defined daily doses (DDD)
|
# defined daily doses (DDD)
|
||||||
ab_ddd("AMX", "oral") # 1.5
|
ab_ddd("AMX", "oral")
|
||||||
ab_ddd_units("AMX", "oral") # "g"
|
ab_ddd_units("AMX", "oral")
|
||||||
ab_ddd("AMX", "iv") # 3
|
ab_ddd("AMX", "iv")
|
||||||
ab_ddd_units("AMX", "iv") # "g"
|
ab_ddd_units("AMX", "iv")
|
||||||
|
|
||||||
ab_info("AMX") # all properties as a list
|
ab_info("AMX") # all properties as a list
|
||||||
|
|
||||||
# all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
|
# all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
|
||||||
ab_atc("AMP") # ATC code of AMP (ampicillin)
|
ab_atc("AMP")
|
||||||
ab_group("J01CA01") # Drug group of ampicillins ATC code
|
ab_group("J01CA01")
|
||||||
ab_loinc("ampicillin") # LOINC codes of ampicillin
|
ab_loinc("ampicillin")
|
||||||
ab_name("21066-6") # "Ampicillin" (using LOINC)
|
ab_name("21066-6")
|
||||||
ab_name(6249) # "Ampicillin" (using CID)
|
ab_name(6249)
|
||||||
ab_name("J01CA01") # "Ampicillin" (using ATC)
|
ab_name("J01CA01")
|
||||||
|
|
||||||
# spelling from different languages and dyslexia are no problem
|
# spelling from different languages and dyslexia are no problem
|
||||||
ab_atc("ceftriaxon")
|
ab_atc("ceftriaxon")
|
||||||
|
|||||||
@ -4,7 +4,7 @@
|
|||||||
\name{antibiotics}
|
\name{antibiotics}
|
||||||
\alias{antibiotics}
|
\alias{antibiotics}
|
||||||
\alias{antivirals}
|
\alias{antivirals}
|
||||||
\title{Data Sets with 585 Antimicrobial Drugs}
|
\title{Data Sets with 603 Antimicrobial Drugs}
|
||||||
\format{
|
\format{
|
||||||
\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 483 observations and 14 variables:}{
|
\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 483 observations and 14 variables:}{
|
||||||
\itemize{
|
\itemize{
|
||||||
@ -25,21 +25,23 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
\subsection{For the \link{antivirals} data set: a \link[tibble:tibble]{tibble} with 102 observations and 9 variables:}{
|
\subsection{For the \link{antivirals} data set: a \link[tibble:tibble]{tibble} with 120 observations and 11 variables:}{
|
||||||
\itemize{
|
\itemize{
|
||||||
|
\item \code{av}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
|
||||||
|
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO
|
||||||
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
|
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
|
||||||
\item \code{cid}\cr Compound ID as found in PubChem
|
\item \code{cid}\cr Compound ID as found in PubChem
|
||||||
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO
|
|
||||||
\item \code{atc_group}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
|
\item \code{atc_group}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
|
||||||
\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
|
\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
|
||||||
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment
|
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment
|
||||||
\item \code{oral_units}\cr Units of \code{oral_ddd}
|
\item \code{oral_units}\cr Units of \code{oral_ddd}
|
||||||
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
|
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
|
||||||
\item \code{iv_units}\cr Units of \code{iv_ddd}
|
\item \code{iv_units}\cr Units of \code{iv_ddd}
|
||||||
|
\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent.
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 102 rows and 9 columns.
|
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
|
||||||
}
|
}
|
||||||
\source{
|
\source{
|
||||||
\itemize{
|
\itemize{
|
||||||
|
|||||||
@ -87,8 +87,8 @@ ab_atc("seephthriaaksone") # and even this works
|
|||||||
|
|
||||||
# use ab_* functions to get a specific properties (see ?ab_property);
|
# use ab_* functions to get a specific properties (see ?ab_property);
|
||||||
# they use as.ab() internally:
|
# they use as.ab() internally:
|
||||||
ab_name("J01FA01") # "Erythromycin"
|
ab_name("J01FA01")
|
||||||
ab_name("eryt") # "Erythromycin"
|
ab_name("eryt")
|
||||||
|
|
||||||
\donttest{
|
\donttest{
|
||||||
if (require("dplyr")) {
|
if (require("dplyr")) {
|
||||||
|
|||||||
91
man/as.av.Rd
Normal file
91
man/as.av.Rd
Normal file
@ -0,0 +1,91 @@
|
|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/av.R
|
||||||
|
\name{as.av}
|
||||||
|
\alias{as.av}
|
||||||
|
\alias{av}
|
||||||
|
\alias{is.av}
|
||||||
|
\title{Transform Input to an Antiviral Agent ID}
|
||||||
|
\usage{
|
||||||
|
as.av(x, flag_multiple_results = TRUE, info = interactive(), ...)
|
||||||
|
|
||||||
|
is.av(x)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{a \link{character} vector to determine to antiviral agent ID}
|
||||||
|
|
||||||
|
\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antiviral agent code or name can be retrieved from a single input value.}
|
||||||
|
|
||||||
|
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
|
||||||
|
|
||||||
|
\item{...}{arguments passed on to internal functions}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
A \link{character} \link{vector} with additional class \code{\link{ab}}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Use this function to determine the antiviral agent code of one or more antiviral agents. The data set \link{antivirals} will be searched for abbreviations, official names and synonyms (brand names).
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
All entries in the \link{antivirals} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
|
||||||
|
|
||||||
|
All these properties will be searched for the user input. The \code{\link[=as.av]{as.av()}} can correct for different forms of misspelling:
|
||||||
|
\itemize{
|
||||||
|
\item Wrong spelling of drug names (such as "acyclovir"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.
|
||||||
|
\item Too few or too many vowels or consonants
|
||||||
|
\item Switching two characters (such as "aycclovir", often the case in clinical data, when doctors typed too fast)
|
||||||
|
\item Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
|
||||||
|
}
|
||||||
|
|
||||||
|
Use the \code{\link[=av_property]{av_*}} functions to get properties based on the returned antiviral agent ID, see \emph{Examples}.
|
||||||
|
|
||||||
|
Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
|
||||||
|
}
|
||||||
|
\section{Source}{
|
||||||
|
|
||||||
|
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
|
||||||
|
|
||||||
|
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
|
||||||
|
}
|
||||||
|
|
||||||
|
\section{WHOCC}{
|
||||||
|
|
||||||
|
\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr}
|
||||||
|
This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}).
|
||||||
|
|
||||||
|
These have become the gold standard for international drug utilisation monitoring and research.
|
||||||
|
|
||||||
|
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
|
||||||
|
|
||||||
|
\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.} See \url{https://www.whocc.no/copyright_disclaimer/.}
|
||||||
|
}
|
||||||
|
|
||||||
|
\section{Reference Data Publicly Available}{
|
||||||
|
|
||||||
|
All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/SI 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 \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||||
|
}
|
||||||
|
|
||||||
|
\examples{
|
||||||
|
# these examples all return "ACI", the ID of aciclovir:
|
||||||
|
as.av("J05AB01")
|
||||||
|
as.av("J 05 AB 01")
|
||||||
|
as.av("Aciclovir")
|
||||||
|
as.av("aciclo")
|
||||||
|
as.av(" aciclo 123")
|
||||||
|
as.av("ACICL")
|
||||||
|
as.av("ACI")
|
||||||
|
as.av("Virorax") # trade name
|
||||||
|
as.av("Zovirax") # trade name
|
||||||
|
|
||||||
|
as.av("acyklofir") # severe spelling error, yet works
|
||||||
|
|
||||||
|
# use av_* functions to get a specific properties (see ?av_property);
|
||||||
|
# they use as.av() internally:
|
||||||
|
av_name("J05AB01")
|
||||||
|
av_name("acicl")
|
||||||
|
}
|
||||||
|
\seealso{
|
||||||
|
\itemize{
|
||||||
|
\item \link{antivirals} for the \link{data.frame} that is being used to determine ATCs
|
||||||
|
\item \code{\link[=av_from_text]{av_from_text()}} for a function to retrieve antimicrobial drugs from clinical text (from health care records)
|
||||||
|
}
|
||||||
|
}
|
||||||
63
man/av_from_text.Rd
Normal file
63
man/av_from_text.Rd
Normal file
@ -0,0 +1,63 @@
|
|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/av_from_text.R
|
||||||
|
\name{av_from_text}
|
||||||
|
\alias{av_from_text}
|
||||||
|
\title{Retrieve Antiviral Drug Names and Doses from Clinical Text}
|
||||||
|
\usage{
|
||||||
|
av_from_text(
|
||||||
|
text,
|
||||||
|
type = c("drug", "dose", "administration"),
|
||||||
|
collapse = NULL,
|
||||||
|
translate_av = FALSE,
|
||||||
|
thorough_search = NULL,
|
||||||
|
info = interactive(),
|
||||||
|
...
|
||||||
|
)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{text}{text to analyse}
|
||||||
|
|
||||||
|
\item{type}{type of property to search for, either \code{"drug"}, \code{"dose"} or \code{"administration"}, see \emph{Examples}}
|
||||||
|
|
||||||
|
\item{collapse}{a \link{character} to pass on to \code{paste(, collapse = ...)} to only return one \link{character} per element of \code{text}, see \emph{Examples}}
|
||||||
|
|
||||||
|
\item{translate_av}{if \code{type = "drug"}: a column name of the \link{antivirals} data set to translate the antibiotic abbreviations to, using \code{\link[=av_property]{av_property()}}. Defaults to \code{FALSE}. Using \code{TRUE} is equal to using "name".}
|
||||||
|
|
||||||
|
\item{thorough_search}{a \link{logical} to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to \code{TRUE} will take considerably more time than when using \code{FALSE}. At default, it will turn \code{TRUE} when all input elements contain a maximum of three words.}
|
||||||
|
|
||||||
|
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
|
||||||
|
|
||||||
|
\item{...}{arguments passed on to \code{\link[=as.av]{as.av()}}}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antiviral drugs, doses and forms of administration found in the texts.
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
This function is also internally used by \code{\link[=as.av]{as.av()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.av]{as.av()}} function may use very long regular expression to match brand names of antiviral agents. This may fail on some systems.
|
||||||
|
\subsection{Argument \code{type}}{
|
||||||
|
|
||||||
|
At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.av]{as.av()}} internally, it will correct for misspelling.
|
||||||
|
|
||||||
|
With \code{type = "dose"} (or similar, like "dosing", "doses"), all text elements will be searched for \link{numeric} values that are higher than 100 and do not resemble years. The output will be \link{numeric}. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see \emph{Examples}.
|
||||||
|
|
||||||
|
With \code{type = "administration"} (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see \emph{Examples}.
|
||||||
|
}
|
||||||
|
|
||||||
|
\subsection{Argument \code{collapse}}{
|
||||||
|
|
||||||
|
Without using \code{collapse}, this function will return a \link{list}. This can be convenient to use e.g. inside a \code{mutate()}):\cr
|
||||||
|
\code{df \%>\% mutate(avx = av_from_text(clinical_text))}
|
||||||
|
|
||||||
|
The returned AV codes can be transformed to official names, groups, etc. with all \code{\link[=av_property]{av_*}} functions such as \code{\link[=av_name]{av_name()}} and \code{\link[=av_group]{av_group()}}, or by using the \code{translate_av} argument.
|
||||||
|
|
||||||
|
With using \code{collapse}, this function will return a \link{character}:\cr
|
||||||
|
\code{df \%>\% mutate(avx = av_from_text(clinical_text, collapse = "|"))}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
av_from_text("28/03/2020 valaciclovir po tid")
|
||||||
|
av_from_text("28/03/2020 valaciclovir po tid", type = "admin")
|
||||||
|
}
|
||||||
117
man/av_property.Rd
Normal file
117
man/av_property.Rd
Normal file
@ -0,0 +1,117 @@
|
|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/av_property.R
|
||||||
|
\name{av_property}
|
||||||
|
\alias{av_property}
|
||||||
|
\alias{av_name}
|
||||||
|
\alias{av_cid}
|
||||||
|
\alias{av_synonyms}
|
||||||
|
\alias{av_tradenames}
|
||||||
|
\alias{av_group}
|
||||||
|
\alias{av_atc}
|
||||||
|
\alias{av_loinc}
|
||||||
|
\alias{av_ddd}
|
||||||
|
\alias{av_ddd_units}
|
||||||
|
\alias{av_info}
|
||||||
|
\alias{av_url}
|
||||||
|
\title{Get Properties of an Antiviral Agent}
|
||||||
|
\usage{
|
||||||
|
av_name(x, language = get_AMR_locale(), tolower = FALSE, ...)
|
||||||
|
|
||||||
|
av_cid(x, ...)
|
||||||
|
|
||||||
|
av_synonyms(x, ...)
|
||||||
|
|
||||||
|
av_tradenames(x, ...)
|
||||||
|
|
||||||
|
av_group(x, language = get_AMR_locale(), ...)
|
||||||
|
|
||||||
|
av_atc(x, ...)
|
||||||
|
|
||||||
|
av_loinc(x, ...)
|
||||||
|
|
||||||
|
av_ddd(x, administration = "oral", ...)
|
||||||
|
|
||||||
|
av_ddd_units(x, administration = "oral", ...)
|
||||||
|
|
||||||
|
av_info(x, language = get_AMR_locale(), ...)
|
||||||
|
|
||||||
|
av_url(x, open = FALSE, ...)
|
||||||
|
|
||||||
|
av_property(x, property = "name", language = get_AMR_locale(), ...)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{any (vector of) text that can be coerced to a valid antiviral agent code with \code{\link[=as.av]{as.av()}}}
|
||||||
|
|
||||||
|
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||||
|
|
||||||
|
\item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}.}
|
||||||
|
|
||||||
|
\item{...}{other arguments passed on to \code{\link[=as.av]{as.av()}}}
|
||||||
|
|
||||||
|
\item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}
|
||||||
|
|
||||||
|
\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
|
||||||
|
|
||||||
|
\item{property}{one of the column names of one of the \link{antivirals} data set: \code{vector_or(colnames(antivirals), sort = FALSE)}.}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
\itemize{
|
||||||
|
\item An \link{integer} in case of \code{\link[=av_cid]{av_cid()}}
|
||||||
|
\item A named \link{list} in case of \code{\link[=av_info]{av_info()}} and multiple \code{\link[=av_atc]{av_atc()}}/\code{\link[=av_synonyms]{av_synonyms()}}/\code{\link[=av_tradenames]{av_tradenames()}}
|
||||||
|
\item A \link{double} in case of \code{\link[=av_ddd]{av_ddd()}}
|
||||||
|
\item A \link{character} in all other cases
|
||||||
|
}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Use these functions to return a specific property of an antiviral agent from the \link{antivirals} data set. All input values will be evaluated internally with \code{\link[=as.av]{as.av()}}.
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
All output \link[=translate]{will be translated} where possible.
|
||||||
|
|
||||||
|
The function \code{\link[=av_url]{av_url()}} will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
|
||||||
|
}
|
||||||
|
\section{Source}{
|
||||||
|
|
||||||
|
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
|
||||||
|
|
||||||
|
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
|
||||||
|
}
|
||||||
|
|
||||||
|
\section{Reference Data Publicly Available}{
|
||||||
|
|
||||||
|
All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/SI 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 \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||||
|
}
|
||||||
|
|
||||||
|
\examples{
|
||||||
|
# all properties:
|
||||||
|
av_name("ACI")
|
||||||
|
av_atc("ACI")
|
||||||
|
av_cid("ACI")
|
||||||
|
av_synonyms("ACI")
|
||||||
|
av_tradenames("ACI")
|
||||||
|
av_group("ACI")
|
||||||
|
av_url("ACI")
|
||||||
|
|
||||||
|
# smart lowercase tranformation
|
||||||
|
av_name(x = c("ACI", "VALA"))
|
||||||
|
av_name(x = c("ACI", "VALA"), tolower = TRUE)
|
||||||
|
|
||||||
|
# defined daily doses (DDD)
|
||||||
|
av_ddd("ACI", "oral")
|
||||||
|
av_ddd_units("ACI", "oral")
|
||||||
|
av_ddd("ACI", "iv")
|
||||||
|
av_ddd_units("ACI", "iv")
|
||||||
|
|
||||||
|
av_info("ACI") # all properties as a list
|
||||||
|
|
||||||
|
# all av_* functions use as.av() internally, so you can go from 'any' to 'any':
|
||||||
|
av_atc("ACI")
|
||||||
|
av_group("J05AB01")
|
||||||
|
av_loinc("abacavir")
|
||||||
|
av_name("29113-8")
|
||||||
|
av_name(135398513)
|
||||||
|
av_name("J05AB01")
|
||||||
|
}
|
||||||
|
\seealso{
|
||||||
|
\link{antivirals}
|
||||||
|
}
|
||||||
@ -156,7 +156,7 @@ microorganisms %>%
|
|||||||
```
|
```
|
||||||
|
|
||||||
|
|
||||||
## `antibiotics`: Antibiotic Agents
|
## `antibiotics`: Antibiotic (+Antifungal) Drugs
|
||||||
|
|
||||||
`r structure_txt(antibiotics)`
|
`r structure_txt(antibiotics)`
|
||||||
|
|
||||||
@ -173,6 +173,7 @@ This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET,
|
|||||||
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
|
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
|
||||||
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
|
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
|
||||||
* [WHONET software 2019](https://whonet.org)
|
* [WHONET software 2019](https://whonet.org)
|
||||||
|
* [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org)
|
||||||
|
|
||||||
### Example content
|
### Example content
|
||||||
|
|
||||||
@ -183,7 +184,7 @@ antibiotics %>%
|
|||||||
```
|
```
|
||||||
|
|
||||||
|
|
||||||
## `antivirals`: Antiviral Agents
|
## `antivirals`: Antiviral Drugs
|
||||||
|
|
||||||
`r structure_txt(antivirals)`
|
`r structure_txt(antivirals)`
|
||||||
|
|
||||||
@ -191,7 +192,7 @@ This data set is in R available as `antivirals`, after you load the `AMR` packag
|
|||||||
|
|
||||||
`r download_txt("antivirals")`
|
`r download_txt("antivirals")`
|
||||||
|
|
||||||
The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stata files all contain the trade names as comma separated values.
|
The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stata files all contain the trade names and LOINC codes as comma separated values.
|
||||||
|
|
||||||
### Source
|
### Source
|
||||||
|
|
||||||
@ -199,6 +200,7 @@ This data set contains all ATC codes gathered from WHO and all compound IDs from
|
|||||||
|
|
||||||
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
|
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
|
||||||
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
|
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
|
||||||
|
* [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org)
|
||||||
|
|
||||||
### Example content
|
### Example content
|
||||||
|
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user