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_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.

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. We will strive to maintain backward compatibility, but the 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

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

See also

antibiotics

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"

# 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")