getDescendants
getDescendants.RdgetDescendants
Usage
getDescendants(
cdm,
conceptId,
withAncestor = FALSE,
ingredientRange = c(0, Inf),
doseForm = NULL
)Arguments
- cdm
cdm_reference via CDMConnector
- conceptId
concpet_id to search
- withAncestor
If TRUE, return column with ancestor. In case of multiple ancestors, concepts will be separated by ";"
- ingredientRange
Used to restrict descendant codes to those associated with a specific number of drug ingredients. Must be a vector of length two with the first element the minimum number of ingredients allowed and the second the maximum. A value of c(2, 2) would restrict to only concepts associated with two ingredients.
- doseForm
Only descendants codes with the specified drug dose form will be returned. If NULL, descendant codes will be returned regardless of dose form.
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
getDescendants(cdm = cdm, conceptId = 1)
#> # A tibble: 5 × 10
#> concept_id concept_name domain_id vocabulary_id standard_concept
#> <int> <chr> <chr> <chr> <chr>
#> 1 1 Musculoskeletal disorder Condition SNOMED S
#> 2 2 Osteoarthrosis Condition SNOMED S
#> 3 3 Arthritis Condition SNOMED S
#> 4 4 Osteoarthritis of knee Condition SNOMED S
#> 5 5 Osteoarthritis of hip Condition SNOMED S
#> # ℹ 5 more variables: concept_class_id <chr>, concept_code <chr>,
#> # valid_start_date <lgl>, valid_end_date <lgl>, invalid_reason <lgl>
# }