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Implement extensive support for antiviral agents support (#77)

This commit is contained in:
Dr. Matthijs Berends
2022-11-13 08:46:10 +01:00
committed by GitHub
parent d2edcf51ad
commit 496c08d851
46 changed files with 1966 additions and 1563 deletions

View File

@ -59,38 +59,35 @@
#' @inheritSection AMR Reference Data Publicly Available
#' @examples
#' # all properties:
#' ab_name("AMX") # "Amoxicillin"
#' ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
#' ab_cid("AMX") # 33613 (Compound ID from PubChem)
#' ab_synonyms("AMX") # a list with brand names of amoxicillin
#' ab_tradenames("AMX") # same
#' ab_group("AMX") # "Beta-lactams/penicillins"
#' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
#' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
#' ab_url("AMX") # link to the official WHO page
#' ab_name("AMX")
#' ab_atc("AMX")
#' ab_cid("AMX")
#' ab_synonyms("AMX")
#' ab_tradenames("AMX")
#' ab_group("AMX")
#' ab_atc_group1("AMX")
#' ab_atc_group2("AMX")
#' ab_url("AMX")
#'
#' # smart lowercase tranformation
#' ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
#' ab_name(
#' x = c("AMC", "PLB"),
#' tolower = TRUE
#' ) # "amoxicillin/clavulanic acid" "polymyxin B"
#' ab_name(x = c("AMC", "PLB"))
#' ab_name(x = c("AMC", "PLB"), tolower = TRUE)
#'
#' # defined daily doses (DDD)
#' ab_ddd("AMX", "oral") # 1.5
#' ab_ddd_units("AMX", "oral") # "g"
#' ab_ddd("AMX", "iv") # 3
#' ab_ddd_units("AMX", "iv") # "g"
#' ab_ddd("AMX", "oral")
#' ab_ddd_units("AMX", "oral")
#' ab_ddd("AMX", "iv")
#' ab_ddd_units("AMX", "iv")
#'
#' ab_info("AMX") # all properties as a list
#'
#' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
#' ab_atc("AMP") # ATC code of AMP (ampicillin)
#' ab_group("J01CA01") # Drug group of ampicillins ATC code
#' ab_loinc("ampicillin") # LOINC codes of ampicillin
#' ab_name("21066-6") # "Ampicillin" (using LOINC)
#' ab_name(6249) # "Ampicillin" (using CID)
#' ab_name("J01CA01") # "Ampicillin" (using ATC)
#' ab_atc("AMP")
#' ab_group("J01CA01")
#' ab_loinc("ampicillin")
#' ab_name("21066-6")
#' ab_name(6249)
#' ab_name("J01CA01")
#'
#' # spelling from different languages and dyslexia are no problem
#' ab_atc("ceftriaxon")
@ -244,20 +241,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
x <- as.ab(x, ...)
ddd_prop <- administration
# 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")
}
ddd_prop <- paste0(administration, "_ddd")
out <- ab_validate(x = x, property = ddd_prop)
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)
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_(
"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",
"www.whocc.no/ddd/list_of_ddds_combined_products/"
)
}
ddd_prop <- paste0(administration, "_units")
ab_validate(x = x, property = ddd_prop)
out
}
#' @rdname ab_property