ab_property {AMR} | R Documentation |
Get Properties of an Antibiotic
Description
Use these functions to return a specific property of an antibiotic from the antimicrobials data set. All input values will be evaluated internally with as.ab()
.
Usage
ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...)
ab_cid(x, ...)
ab_synonyms(x, ...)
ab_tradenames(x, ...)
ab_group(x, language = get_AMR_locale(), ...)
ab_atc(x, only_first = FALSE, ...)
ab_atc_group1(x, language = get_AMR_locale(), ...)
ab_atc_group2(x, language = get_AMR_locale(), ...)
ab_loinc(x, ...)
ab_ddd(x, administration = "oral", ...)
ab_ddd_units(x, administration = "oral", ...)
ab_info(x, language = get_AMR_locale(), ...)
ab_url(x, open = FALSE, ...)
ab_property(x, property = "name", language = get_AMR_locale(), ...)
set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
snake_case = NULL)
Arguments
x |
Any (vector of) text that can be coerced to a valid antibiotic drug code with |
language |
Language of the returned text - the default is the current system language (see |
tolower |
A 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". |
... |
In case of |
only_first |
A logical to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group). |
administration |
Way of administration, either |
open |
Browse the URL using |
property |
One of the column names of one of the antimicrobials data set: |
data |
A data.frame of which the columns need to be renamed, or a character vector of column names. |
snake_case |
A logical to indicate whether the names should be in so-called snake case: in lower case and all spaces/slashes replaced with an underscore ( |
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 required ATC code is not available.
The function set_ab_names()
is a special column renaming function for data.frames. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If property = "atc"
is set, preference is given to ATC codes from the J-group.
Value
A named list in case of
ab_info()
and multipleab_atc()
/ab_synonyms()
/ab_tradenames()
A data.frame in case of
set_ab_names()
A character in all other cases
Source
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: https://atcddd.fhi.no/atc_ddd_index/
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm
Download Our Reference Data
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit our website for direct download links, or explore the actual files in our GitHub repository.
See Also
Examples
# all properties:
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 transformation
ab_name(x = c("AMC", "PLB"))
ab_name(x = c("AMC", "PLB"), tolower = TRUE)
# defined daily doses (DDD)
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")
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")
ab_atc("cephtriaxone")
ab_atc("cephthriaxone")
ab_atc("seephthriaaksone")
# use set_ab_names() for renaming columns
colnames(example_isolates)
colnames(set_ab_names(example_isolates))
colnames(set_ab_names(example_isolates, NIT:VAN))
if (require("dplyr")) {
example_isolates %>%
set_ab_names()
# this does the same:
example_isolates %>%
rename_with(set_ab_names)
# set_ab_names() works with any AB property:
example_isolates %>%
set_ab_names(property = "atc")
example_isolates %>%
set_ab_names(where(is.sir)) %>%
colnames()
example_isolates %>%
set_ab_names(NIT:VAN) %>%
colnames()
}