mirror of https://github.com/msberends/AMR.git
unit tests
This commit is contained in:
parent
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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
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@ -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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19
_pkgdown.yml
19
_pkgdown.yml
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@ -102,9 +102,9 @@ navbar:
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- text: "Get properties of an antibiotic"
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icon: "fa-capsules"
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href: "reference/ab_property.html" # reference instead of an article
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# - text: "Other: benchmarks"
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# icon: "fa-shipping-fast"
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# href: "articles/benchmarks.html"
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- text: "Get properties of an antiviral agent"
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icon: "fa-capsules"
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href: "reference/av_property.html" # reference instead of an article
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- text: "Manual"
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icon: "fa-book-open"
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href: "reference/index.html"
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@ -175,8 +175,19 @@ reference:
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- "`mean_amr_distance`"
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- "`resistance_predict`"
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- "`guess_ab_col`"
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- title: "Other: antiviral drugs"
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desc: >
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This package also provides extensive support for antiviral agents, even though it is not the primary
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scope of this package. Working with data containing information about antiviral drugs was never easier.
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Use these functions to get valid properties of antiviral drugs from any input or to clean your input.
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You can even retrieve drug names and doses from clinical text records, using `av_from_text()`.
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contents:
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- "`as.av`"
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- "`av_property`"
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- "`av_from_text`"
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- title: "Background information on included data"
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- title: "Other: background information on included data"
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desc: >
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Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
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for more information about how to work with functions in this package.
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@ -0,0 +1,80 @@
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# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_equal(
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as.character(as.av(c(
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"J05AB01",
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"J 05 AB 01",
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"Aciclovir",
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"aciclo",
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" aciclo 123",
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"ACICL",
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"ACI",
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"Virorax",
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"Zovirax"
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))),
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rep("ACI", 9)
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)
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expect_identical(class(as.av("acic")), c("av", "character"))
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expect_identical(class(antivirals$av), c("av", "character"))
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expect_true(is.av(as.av("acic")))
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expect_stdout(print(as.av("acic")))
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expect_stdout(print(data.frame(a = as.av("acic"))))
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expect_warning(as.av("J00AA00")) # ATC not yet available in data set
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expect_warning(as.av("UNKNOWN"))
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expect_stdout(print(as.av("acic")))
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expect_equal(
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as.character(as.av("zovirax")),
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"ACI"
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)
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expect_equal(
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as.character(as.av(c("Abacaivr", "Celvudine"))),
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c("ABA", "CLE")
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)
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expect_warning(as.av("Abacavir Clevudine"))
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# based on Levenshtein distance
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expect_identical(av_name("adevofir dypifo", language = NULL), "Adefovir dipivoxil")
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# assigning and subsetting
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x <- antivirals$av
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expect_inherits(x[1], "av")
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expect_inherits(x[[1]], "av")
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expect_inherits(c(x[1], x[9]), "av")
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expect_inherits(unique(x[1], x[9]), "av")
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expect_inherits(rep(x[1], 2), "av")
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expect_warning(x[1] <- "invalid code")
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expect_warning(x[[1]] <- "invalid code")
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expect_warning(c(x[1], "test"))
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@ -0,0 +1,58 @@
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# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds")[[1]],
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as.av("Aciclovir")
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = TRUE)[[1]],
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as.av("Aciclovir")
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = FALSE)[[1]],
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as.av("Aciclovir")
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds", translate_ab = TRUE)[[1]],
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"Aciclovir"
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)
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expect_identical(
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av_from_text("administered aciclo and valaciclo", collapse = ", ")[[1]],
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"ACI, VALA"
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "dose")[[1]],
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500
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "admin")[[1]],
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"oral"
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)
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@ -0,0 +1,65 @@
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# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
|
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# 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 #
|
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# the Free Software Foundation. #
|
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# We created this package for both routine data analysis and academic #
|
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# research and it was publicly released in the hope that it will be #
|
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_identical(av_name("ACI", language = NULL), "Aciclovir")
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expect_identical(av_atc("ACI"), "J05AB01")
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expect_identical(av_cid("ACI"), as.integer(135398513))
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expect_inherits(av_tradenames("ACI"), "character")
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expect_inherits(av_tradenames(c("ACI", "ACI")), "list")
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expect_identical(av_group("ACI", language = NULL),"Nucleosides and nucleotides excl. reverse transcriptase inhibitors")
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expect_identical(av_name(135398513, language = NULL), "Aciclovir")
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expect_identical(av_name("J05AB01", language = NULL), "Aciclovir")
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expect_identical(av_ddd("ACI", "oral"), 4)
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expect_warning(av_ddd("ACI", "oral", units = TRUE)) # old behaviour
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expect_identical(av_ddd_units("ACI", "iv"), "g")
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expect_identical(av_ddd("ACI", "iv"), 4)
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expect_identical(
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av_name(x = c("ACI", "VALA"), tolower = TRUE, language = NULL),
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c("aciclovir", "valaciclovir")
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)
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expect_inherits(av_info("ACI"), "list")
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expect_error(av_property("acic", "invalid property"))
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expect_error(av_name("acic", language = "INVALID"))
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expect_stdout(print(av_name("acic", language = NULL)))
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expect_equal(av_name("29113-8", language = NULL), "Abacavir")
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expect_equal(
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av_loinc("Abacavir"),
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c("29113-8", "78772-1", "78773-9", "79134-3", "80118-3")
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)
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expect_true(av_url("ACI") %like% "whocc.no")
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expect_warning(av_url("ASP"))
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|
|
@ -109,38 +109,35 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/S
|
|||
|
||||
\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")
|
||||
|
|
|
|||
|
|
@ -85,44 +85,33 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/S
|
|||
|
||||
\examples{
|
||||
# all properties:
|
||||
av_name("AMX") # "Amoxicillin"
|
||||
av_atc("AMX") # "J01CA04" (ATC code from the WHO)
|
||||
av_cid("AMX") # 33613 (Compound ID from PubChem)
|
||||
av_synonyms("AMX") # a list with brand names of amoxicillin
|
||||
av_tradenames("AMX") # same
|
||||
av_group("AMX") # "Beta-lactams/penicillins"
|
||||
av_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
|
||||
av_atc_group2("AMX") # "Penicillins with extended spectrum"
|
||||
av_url("AMX") # link to the official WHO page
|
||||
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("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
|
||||
av_name(
|
||||
x = c("AMC", "PLB"),
|
||||
tolower = TRUE
|
||||
) # "amoxicillin/clavulanic acid" "polymyxin B"
|
||||
av_name(x = c("ACI", "VALA"))
|
||||
av_name(x = c("ACI", "VALA"), tolower = TRUE)
|
||||
|
||||
# defined daily doses (DDD)
|
||||
av_ddd("AMX", "oral") # 1.5
|
||||
av_ddd_units("AMX", "oral") # "g"
|
||||
av_ddd("AMX", "iv") # 3
|
||||
av_ddd_units("AMX", "iv") # "g"
|
||||
av_ddd("ACI", "oral")
|
||||
av_ddd_units("ACI", "oral")
|
||||
av_ddd("ACI", "iv")
|
||||
av_ddd_units("ACI", "iv")
|
||||
|
||||
av_info("AMX") # all properties as a list
|
||||
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("AMP") # ATC code of AMP (ampicillin)
|
||||
av_group("J01CA01") # Drug group of ampicillins ATC code
|
||||
av_loinc("ampicillin") # LOINC codes of ampicillin
|
||||
av_name("21066-6") # "Ampicillin" (using LOINC)
|
||||
av_name(6249) # "Ampicillin" (using CID)
|
||||
av_name("J01CA01") # "Ampicillin" (using ATC)
|
||||
|
||||
# spelling from different languages and dyslexia are no problem
|
||||
av_atc("ceftriaxon")
|
||||
av_atc("cephtriaxone")
|
||||
av_atc("cephthriaxone")
|
||||
av_atc("seephthriaaksone")
|
||||
av_atc("ACI")
|
||||
av_group("J05AB01")
|
||||
av_loinc("abacavir")
|
||||
av_name("29113-8")
|
||||
av_name(135398513)
|
||||
av_name("J05AB01")
|
||||
}
|
||||
\seealso{
|
||||
\link{antivirals}
|
||||
|
|
|
|||
Loading…
Reference in New Issue