Transform to antibiotic ID

Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names).

as.ab(x)

is.ab(x)

Arguments

x	character vector to determine to antibiotic ID

Value

Character (vector) with class "ab". Unknown values will return NA.

Details

All entries in the antibiotics data set have three different identifiers: a human readable EARS-Net code (column ab, used by ECDC and WHONET), an ATC code (column atc, used by WHO), and a CID code (column cid, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.

Use the ab_property functions to get properties based on the returned antibiotic ID, see Examples.

In the ATC classification system, the active substances are classified in a hierarchy with five different levels. The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups. The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups. Source: https://www.whocc.no/atc/structure_and_principles/

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

WHOCC

This package contains all ~450 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.

See also

antibiotics for the dataframe that is being used to determine ATCs.

Examples

# NOT RUN {
# These examples all return "ERY", the ID of Erythromycin:
as.ab("J01FA01")
as.ab("J 01 FA 01")
as.ab("Erythromycin")
as.ab("eryt")
as.ab("   eryt 123")
as.ab("ERYT")
as.ab("ERY")
as.ab("eritromicine") # spelled wrong, yet works
as.ab("Erythrocin")   # trade name
as.ab("Romycin")      # trade name

# Use ab_* functions to get a specific properties (see ?ab_property);
# they use as.ab() internally:
ab_name("J01FA01")    # "Erythromycin"
ab_name("eryt")       # "Erythromycin"
# }