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(v0.9.0.9012) Support for LOINC codes

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dr. M.S. (Matthijs) Berends
2020-01-26 20:20:00 +01:00
parent 19172b1d48
commit 449d9bde35
35 changed files with 92866 additions and 295 deletions
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29
R/ab_property.R
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@ -47,18 +47,18 @@
#' 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"
#'
#' # 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"
#'
#' # defined daily doses (DDD)
#' ab_ddd("AMX", "oral") # 1
#' ab_ddd("AMX", "oral", units = TRUE) # "g"
#' ab_ddd("AMX", "iv") # 1
@ -66,12 +66,13 @@
#'
#' ab_info("AMX") # all properties as a list
#'
#' # all ab_* functions use as.ab() internally:
#' ab_name("Fluclox") # "Flucloxacillin"
#' ab_name("fluklox") # "Flucloxacillin"
#' ab_name("floxapen") # "Flucloxacillin"
#' ab_name(21319) # "Flucloxacillin" (using CID)
#' ab_name("J01CF05") # "Flucloxacillin" (using ATC)
#' # 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)
#'
#' # spelling from different languages and dyslexia are no problem
#' ab_atc("ceftriaxon")
@ -137,6 +138,18 @@ ab_atc_group2 <- function(x, language = get_locale(), ...) {
translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
}
#' @rdname ab_property
#' @export
ab_loinc <- function(x, ...) {
loincs <- ab_validate(x = x, property = "loinc", ...)
names(loincs) <- x
if (length(loincs) == 1) {
unname(unlist(loincs))
} else {
loincs
}
}
#' @rdname ab_property
#' @export
ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {