Get descendant codes for ATC levels

Usage

getATCCodes(
  cdm,
  level = c("ATC 1st"),
  name = NULL,
  doseForm = NULL,
  doseUnit = NULL,
  routeCategory = NULL,
  type = "codelist"
)

Arguments

cdm: cdm_reference via CDMConnector
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.
doseForm: Only descendants codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form.
doseUnit: Only descendants codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit
routeCategory: Only descendants codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of dose form.
type: Can be "codelist", "codelist_with_details", or "concept_set_expression"

Value

Concepts with their format based on the type argument.

Examples

# \donttest{
cdm <- mockVocabRef()
#> Warning: ! 5 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> Warning: ! 3 column in observation_period do not match expected column type:
#> • `observation_period_id` is numeric but expected integer
#> • `person_id` is numeric but expected integer
#> • `period_type_concept_id` is numeric but expected integer
#> Warning: ! 8 column in cdm_source do not match expected column type:
#> • `cdm_source_abbreviation` is logical but expected character
#> • `cdm_holder` is logical but expected character
#> • `source_description` is logical but expected character
#> • `source_documentation_reference` is logical but expected character
#> • `cdm_etl_reference` is logical but expected character
#> • `source_release_date` is logical but expected date
#> • `cdm_release_date` is logical but expected date
#> • `vocabulary_version` is logical but expected character
#> Warning: ! 3 column in concept do not match expected column type:
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 1 column in vocabulary do not match expected column type:
#> • `vocabulary_concept_id` is numeric but expected integer
#> Warning: ! 3 column in concept_relationship do not match expected column type:
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 1 column in concept_synonym do not match expected column type:
#> • `language_concept_id` is logical but expected integer
#> Warning: ! 2 column in concept_ancestor do not match expected column type:
#> • `min_levels_of_separation` is numeric but expected integer
#> • `max_levels_of_separation` is numeric but expected integer
#> Warning: ! 7 column in drug_strength do not match expected column type:
#> • `amount_value` is logical but expected numeric
#> • `amount_unit_concept_id` is numeric but expected integer
#> • `numerator_unit_concept_id` is numeric but expected integer
#> • `denominator_unit_concept_id` is numeric but expected integer
#> • `box_size` is logical but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> Warning: ! 8 column in achilles_analysis do not match expected column type:
#> • `analysis_id` is numeric but expected integer
#> • `analysis_name` is numeric but expected character
#> • `stratum_1_name` is logical but expected character
#> • `stratum_2_name` is logical but expected character
#> • `stratum_3_name` is logical but expected character
#> • `stratum_4_name` is logical but expected character
#> • `stratum_5_name` is logical but expected character
#> • `category` is logical but expected character
#> Warning: ! 7 column in achilles_results do not match expected column type:
#> • `analysis_id` is numeric but expected integer
#> • `stratum_1` is numeric but expected character
#> • `stratum_2` is logical but expected character
#> • `stratum_3` is logical but expected character
#> • `stratum_4` is logical but expected character
#> • `stratum_5` is logical but expected character
#> • `count_value` is numeric but expected integer
#> Warning: ! 16 column in achilles_results_dist do not match expected column type:
#> • `analysis_id` is numeric but expected integer
#> • `stratum_1` is logical but expected character
#> • `stratum_2` is logical but expected character
#> • `stratum_3` is logical but expected character
#> • `stratum_4` is logical but expected character
#> • `stratum_5` is logical but expected character
#> • `min_value` is logical but expected integer
#> • `max_value` is logical but expected integer
#> • `avg_value` is logical but expected numeric
#> • `stdev_value` is logical but expected numeric
#> • `median_value` is logical but expected numeric
#> • `p10_value` is logical but expected numeric
#> • `p25_value` is logical but expected numeric
#> • `p75_value` is logical but expected numeric
#> • `p90_value` is logical but expected numeric
#> • `count_value` is numeric but expected integer
#> Warning: There are observation period end dates after the current date: 2024-11-11
#> ℹ The latest max observation period end date found is 2025-12-31
getATCCodes(cdm = cdm, level = "ATC 1st")
#> 
#> ── 1 codelist ──────────────────────────────────────────────────────────────────
#> 
#> - 1234_alimentary_tract_and_metabolism (2 codes)
# }