CodelistGenerator (version 4.0.0)

getATCCodes: Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes

Description

Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes

Usage

getATCCodes(
  cdm,
  level = c("ATC 1st"),
  name = NULL,
  nameStyle = "{concept_code}_{concept_name}",
  doseForm = NULL,
  doseUnit = NULL,
  routeCategory = NULL,
  type = "codelist"
)

Value

Concepts with their format based on the type argument

Arguments

cdm

A cdm reference to an OMOP CDM dataset. If data is held within a database, the vocabulary tables should be in the same schema as the clinical tables (person, observation period, and so on).

level

ATC level. Can be one or more of "ATC 1st", "ATC 2nd", "ATC 3rd", "ATC 4th", and "ATC 5th".

name

ATC name of interest. For example, c("Dermatologicals", "Nervous System"), would result in a list of length two with the descendant concepts for these two particular ATC groups.

nameStyle

Name style to apply to returned list. Can be one of "{concept_code}","{concept_id}", "{concept_name}", or a combination (i.e., "{concept_code}_{concept_name}").

doseForm

Only codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form. Use 'doseForms()' to see the available dose forms.

doseUnit

Only codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit Use 'availableDoseUnits()' to see the available dose units.

routeCategory

Only codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of route category. Use getRoutes() to find the available route categories.

type

Can be "codelist" or "codelist_with_details".

Examples

# \donttest{
library(CodelistGenerator)
library(omock)

# Create CDM object
cdm <- mockCdmReference()

# Create a codelist with 1st level ATC codes available in the CDM
codelist <- getATCCodes(cdm = cdm,
                        level = "ATC 1st")
codelist

# Tune the name of the generated codelists
codelist <- getATCCodes(cdm = cdm,
                        level = "ATC 1st",
                        nameStyle = "{concept_name}_{concept_code}")
codelist

# Search for a specific ATC name of interest
codelist <- getATCCodes(cdm = cdm,
                        level = "ATC 2nd",
                        name = "immunostimulants")
codelist

# Restrict concepts to specific dose forms, dose units, or route categories.
# Remember that you can use `availableDoseForm()`, `availableDoseUnit()` and
# `availableRouteCategory()` to explore your codelist.
codelist <- getATCCodes(cdm = cdm,
                        level = "ATC 2nd",
                        doseForm = NULL,
                        doseUnit = NULL,
                        routeCategory = NULL,)
codelist

# You can also create directly a codelist_with_details using the argument `type`
codelist <- getATCCodes(cdm = cdm,
                        level = "ATC 1st",
                        type = "codelist_with_details")
codelist
# }