Property of an antibiotic

Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab().

ab_name(x, language = get_locale(), tolower = FALSE, ...)

ab_atc(x, ...)

ab_cid(x, ...)

ab_synonyms(x, ...)

ab_tradenames(x, ...)

ab_group(x, language = get_locale(), ...)

ab_atc_group1(x, language = get_locale(), ...)

ab_atc_group2(x, language = get_locale(), ...)

ab_loinc(x, ...)

ab_ddd(x, administration = "oral", units = FALSE, ...)

ab_info(x, language = get_locale(), ...)

ab_url(x, open = FALSE, ...)

ab_property(x, property = "name", language = get_locale(), ...)

Arguments

x	any (vector of) text that can be coerced to a valid microorganism code with `as.ab()`
language	language of the returned text, defaults to system language (see `get_locale()`) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
tolower	logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
...	other parameters passed on to `as.ab()`
administration	way of administration, either `"oral"` or `"iv"`
units	a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples
property	one of the column names of one of the antibiotics data set

Value

An integer in case of ab_cid()
A named list in case of ab_info() and multiple ab_synonyms()/ab_tradenames()
A double in case of ab_ddd()
A character in all other cases

Details

All output will be translated where possible.

The function ab_url() will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.

Maturing lifecycle

The lifecycle of this function is maturing. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.

Source

World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: https://www.whocc.no/atc_ddd_index/

WHONET 2019 software: http://www.whonet.org/software.html

European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: http://ec.europa.eu/health/documents/community-register/html/atc.htm

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

# 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
ab_ddd("AMX", "iv", units = TRUE)   # "g"

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)

# spelling from different languages and dyslexia are no problem
ab_atc("ceftriaxon")
ab_atc("cephtriaxone")
ab_atc("cephthriaxone")
ab_atc("seephthriaaksone")