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unit tests
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@ -59,38 +59,35 @@
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#' @inheritSection AMR Reference Data Publicly Available
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#' @examples
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#' # all properties:
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#' ab_name("AMX") # "Amoxicillin"
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#' ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
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#' ab_cid("AMX") # 33613 (Compound ID from PubChem)
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#' ab_synonyms("AMX") # a list with brand names of amoxicillin
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#' ab_tradenames("AMX") # same
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#' ab_group("AMX") # "Beta-lactams/penicillins"
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#' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
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#' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
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#' ab_url("AMX") # link to the official WHO page
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#' ab_name("AMX")
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#' ab_atc("AMX")
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#' ab_cid("AMX")
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#' ab_synonyms("AMX")
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#' ab_tradenames("AMX")
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#' ab_group("AMX")
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#' ab_atc_group1("AMX")
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#' ab_atc_group2("AMX")
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#' ab_url("AMX")
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#'
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#' # smart lowercase tranformation
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#' ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
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#' ab_name(
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#' x = c("AMC", "PLB"),
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#' tolower = TRUE
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#' ) # "amoxicillin/clavulanic acid" "polymyxin B"
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#' ab_name(x = c("AMC", "PLB"))
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#' ab_name(x = c("AMC", "PLB"), tolower = TRUE)
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#'
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#' # defined daily doses (DDD)
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#' ab_ddd("AMX", "oral") # 1.5
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#' ab_ddd_units("AMX", "oral") # "g"
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#' ab_ddd("AMX", "iv") # 3
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#' ab_ddd_units("AMX", "iv") # "g"
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#' ab_ddd("AMX", "oral")
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#' ab_ddd_units("AMX", "oral")
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#' ab_ddd("AMX", "iv")
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#' ab_ddd_units("AMX", "iv")
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#'
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#' ab_info("AMX") # all properties as a list
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#'
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#' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
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#' ab_atc("AMP") # ATC code of AMP (ampicillin)
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#' ab_group("J01CA01") # Drug group of ampicillins ATC code
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#' ab_loinc("ampicillin") # LOINC codes of ampicillin
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#' ab_name("21066-6") # "Ampicillin" (using LOINC)
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#' ab_name(6249) # "Ampicillin" (using CID)
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#' ab_name("J01CA01") # "Ampicillin" (using ATC)
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#' ab_atc("AMP")
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#' ab_group("J01CA01")
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#' ab_loinc("ampicillin")
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#' ab_name("21066-6")
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#' ab_name(6249)
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#' ab_name("J01CA01")
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#'
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#' # spelling from different languages and dyslexia are no problem
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#' ab_atc("ceftriaxon")
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7
R/av.R
7
R/av.R
@ -383,13 +383,8 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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next
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}
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# first 5 except for cephalosporins, then first 7 (those cephalosporins all start quite the same!)
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# first 5
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found <- suppressWarnings(as.av(substr(x[i], 1, 5), initial_search = FALSE))
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if (!is.na(found) && av_group(found, initial_search = FALSE) %unlike% "cephalosporins") {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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}
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found <- suppressWarnings(as.av(substr(x[i], 1, 7), initial_search = FALSE))
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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@ -53,44 +53,33 @@
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#' @inheritSection AMR Reference Data Publicly Available
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#' @examples
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#' # all properties:
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#' av_name("AMX") # "Amoxicillin"
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#' av_atc("AMX") # "J01CA04" (ATC code from the WHO)
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#' av_cid("AMX") # 33613 (Compound ID from PubChem)
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#' av_synonyms("AMX") # a list with brand names of amoxicillin
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#' av_tradenames("AMX") # same
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#' av_group("AMX") # "Beta-lactams/penicillins"
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#' av_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
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#' av_atc_group2("AMX") # "Penicillins with extended spectrum"
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#' av_url("AMX") # link to the official WHO page
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#' av_name("ACI")
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#' av_atc("ACI")
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#' av_cid("ACI")
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#' av_synonyms("ACI")
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#' av_tradenames("ACI")
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#' av_group("ACI")
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#' av_url("ACI")
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#'
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#' # smart lowercase tranformation
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#' av_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
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#' av_name(
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#' x = c("AMC", "PLB"),
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#' tolower = TRUE
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#' ) # "amoxicillin/clavulanic acid" "polymyxin B"
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#' av_name(x = c("ACI", "VALA"))
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#' av_name(x = c("ACI", "VALA"), tolower = TRUE)
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#'
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#' # defined daily doses (DDD)
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#' av_ddd("AMX", "oral") # 1.5
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#' av_ddd_units("AMX", "oral") # "g"
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#' av_ddd("AMX", "iv") # 3
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#' av_ddd_units("AMX", "iv") # "g"
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#' av_ddd("ACI", "oral")
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#' av_ddd_units("ACI", "oral")
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#' av_ddd("ACI", "iv")
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#' av_ddd_units("ACI", "iv")
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#'
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#' av_info("AMX") # all properties as a list
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#' av_info("ACI") # all properties as a list
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#'
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#' # all av_* functions use as.av() internally, so you can go from 'any' to 'any':
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#' av_atc("AMP") # ATC code of AMP (ampicillin)
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#' av_group("J01CA01") # Drug group of ampicillins ATC code
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#' av_loinc("ampicillin") # LOINC codes of ampicillin
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#' av_name("21066-6") # "Ampicillin" (using LOINC)
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#' av_name(6249) # "Ampicillin" (using CID)
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#' av_name("J01CA01") # "Ampicillin" (using ATC)
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#'
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#' # spelling from different languages and dyslexia are no problem
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#' av_atc("ceftriaxon")
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#' av_atc("cephtriaxone")
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#' av_atc("cephthriaxone")
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#' av_atc("seephthriaaksone")
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#' av_atc("ACI")
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#' av_group("J05AB01")
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#' av_loinc("abacavir")
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#' av_name("29113-8")
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#' av_name(135398513)
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#' av_name("J05AB01")
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av_name <- function(x, language = get_AMR_locale(), tolower = FALSE, ...) {
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meet_criteria(x, allow_NA = TRUE)
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language <- validate_language(language)
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@ -137,7 +126,7 @@ av_tradenames <- function(x, ...) {
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av_group <- function(x, language = get_AMR_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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language <- validate_language(language)
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translate_into_language(av_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
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translate_into_language(av_validate(x = x, property = "atc_group", ...), language = language, only_affect_ab_names = TRUE)
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}
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#' @rdname av_property
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