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, ...)

ab_atc_group1(x, ...)

ab_atc_group2(x, ...)

ab_ddd(x, administration = "oral", units = 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 multiple ab_synonyms

• A double in case of ab_ddd

• A character in all other cases

Details

All output will be translated where possible.

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

# NOT RUN {
# 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_name(x = c("AMC", "PLB"))  # "Amoxicillin/clavulanic acid" "Polymyxin B"
ab_name(x = c("AMC", "PLB"),
        tolower = TRUE)       # "amoxicillin/clavulanic acid" "polymyxin B"

ab_ddd("AMX", "oral")               #  1
ab_ddd("AMX", "oral", units = TRUE) # "g"
ab_ddd("AMX", "iv")                 #  1
ab_ddd("AMX", "iv", units = TRUE)   # "g"

# 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)
# }