abname: Name of an antibiotic

Description Usage Arguments Details WHOCC Read more on our website! Source Examples

View source: R/abname.R

Description

Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from antibiotics.

Usage

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abname(abcode, from = c("guess", "atc", "certe", "umcg"),
  to = "official", textbetween = " + ", tolower = FALSE)

Arguments

abcode

a code or name, like "AMOX", "AMCL" or "J01CA04"

from, to

type to transform from and to. See antibiotics for its column names. WIth from = "guess" the from will be guessed from "atc", "certe" and "umcg". When using to = "atc", the ATC code will be searched using as.atc.

textbetween

text to put between multiple returned texts

tolower

return output as lower case with function tolower.

Details

The ab_property functions are faster and more concise, but do not support concatenated strings, like abname("AMCL+GENT".

WHOCC


This package contains all ~500 antimicrobial drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the Pharmaceuticals Community Register of the European Commission (http://ec.europa.eu/health/documents/community-register/html/atc.htm).

These have become the gold standard for international drug utilisation monitoring and research.

The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.

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.

Source

antibiotics

Examples

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abname("AMCL")
# "Amoxicillin and beta-lactamase inhibitor"

# It is quite flexible at default (having `from = "guess"`)
abname(c("amox", "J01CA04", "Trimox", "dispermox", "Amoxil"))
# "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"

# Multiple antibiotics can be combined with "+".
# The second antibiotic will be set to lower case when `tolower` was not set:
abname("AMCL+GENT", textbetween = "/")
# "amoxicillin and enzyme inhibitor/gentamicin"

abname(c("AMCL", "GENT"))
# "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"

abname("AMCL", to = "trivial_nl")
# "Amoxicilline/clavulaanzuur"

abname("AMCL", to = "atc")
# "J01CR02"

# specific codes for University Medical Center Groningen (UMCG):
abname("J01CR02", from = "atc", to = "umcg")
# "AMCL"

# specific codes for Certe:
abname("J01CR02", from = "atc", to = "certe")
# "amcl"

msberends/AMR documentation built on Feb. 15, 2019, 3:43 a.m.