Get concept ids from a provided path to json files

Usage

codesFromConceptSet(path, cdm, type = c("codelist"))

Arguments

path: Path to a file or folder containing JSONs of concept sets
cdm: A cdm reference created with CDMConnector
type: Can be "codelist", "codelist_with_details", or "concept_set_expression"

Value

Named list with concept_ids for each concept set

Examples

# \donttest{
cdm <- mockVocabRef("database")
#> 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
#> Note: method with signature ‘DBIConnection#Id’ chosen for function ‘dbExistsTable’,
#>  target signature ‘duckdb_connection#Id’.
#>  "duckdb_connection#ANY" would also be valid
#> 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: 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
x <- codesFromConceptSet(cdm = cdm,
                         path =  system.file(package = "CodelistGenerator",
                         "concepts_for_mock"))
#> Warning: ! `codelist` contains numeric values, they are casted to integers.
x
#> 
#> ── 2 codelists ─────────────────────────────────────────────────────────────────
#> 
#> - oa_desc (3 codes)
#> - oa_no_desc (1 codes)
CDMConnector::cdmDisconnect(cdm)
# }