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"
)

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 'availableDoseForms()' to see the available dose forms in the database, or 'associatedDoseForms()' to see the associated dose forms in a codelist.
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, or 'associatedDoseUnits()' to see the associated dose forms in a codelist.
routeCategory: Only codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of route category. Use 'availableRouteCategories()' to find the available route categories in the database, and 'associatedRouteCategories()' to get drug routs associated with a codelist.
type: Can be "codelist" or "codelist_with_details".

Value

Concepts with their format based on the type argument

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
#> 
#> ── 2 codelists ─────────────────────────────────────────────────────────────────
#> 
#> - L_antineoplastic_and_immunomodulating_agents (5 codes)
#> - R_respiratory_system (7 codes)

# Tune the name of the generated codelists
codelist <- getATCCodes(cdm = cdm,
                        level = "ATC 1st",
                        nameStyle = "{concept_name}_{concept_code}")
codelist
#> 
#> ── 2 codelists ─────────────────────────────────────────────────────────────────
#> 
#> - antineoplastic_and_immunomodulating_agents_L (5 codes)
#> - respiratory_system_R (7 codes)

# Search for a specific ATC name of interest
codelist <- getATCCodes(cdm = cdm,
                        level = "ATC 2nd",
                        name = "immunostimulants")
codelist
#> 
#> ── 1 codelist ──────────────────────────────────────────────────────────────────
#> 
#> - L03_immunostimulants (1 codes)

# 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
#> 
#> ── 10 codelists ────────────────────────────────────────────────────────────────
#> 
#> - L01_antineoplastic_agents (1 codes)
#> - L02_endocrine_therapy (1 codes)
#> - L03_immunostimulants (1 codes)
#> - L04_immunosuppressants (1 codes)
#> - R01_nasal_preparations (1 codes)
#> - R02_throat_preparations (1 codes)
#> along with 4 more codelists

# 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
#> 
#> ── 2 codelists with details ────────────────────────────────────────────────────
#> 
#> - L_antineoplastic_and_immunomodulating_agents (5 codes)
#> - R_respiratory_system (7 codes)
# }