Show mappings from non-standard vocabularies to standard

Usage

getMappings(
  candidateCodelist,
  cdm = NULL,
  nonStandardVocabularies = c("ATC", "ICD10CM", "ICD10PCS", "ICD9CM", "ICD9Proc",
    "LOINC", "OPCS4", "Read", "RxNorm", "RxNorm Extension", "SNOMED")
)

Arguments

candidateCodelist: Dataframe
cdm: cdm_reference via CDMConnector::cdm_from_con()
nonStandardVocabularies: Character vector

Value

tibble

Examples

# \donttest{
cdm <- CodelistGenerator::mockVocabRef()
#> 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: ! 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: ! 4 column in drug_strength do not match expected column type:
#> • `amount_value` is logical but expected numeric
#> • `box_size` is logical but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> Warning: ! 7 column in achilles_analysis do not match expected column type:
#> • `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: ! 5 column in achilles_results do not match expected column type:
#> • `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
#> Warning: ! 14 column in achilles_results_dist do not match expected column type:
#> • `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
#> Warning: There are observation period end dates after the current date: 2024-11-26
#> ℹ The latest max observation period end date found is 2025-12-31
codes <- CodelistGenerator::getCandidateCodes(
  cdm = cdm,
  keywords = "osteoarthritis"
)
#> Limiting to domains of interest
#> Getting concepts to include
#> Adding descendants
#> Search completed. Finishing up.
#> ✔ 2 candidate concepts identified
#> Time taken: 0 minutes and 0 seconds
CodelistGenerator::getMappings(
  cdm = cdm,
  candidateCodelist = codes,
  nonStandardVocabularies = "READ"
)
#> # A tibble: 1 × 7
#>   standard_concept_id standard_concept_name  standard_vocabulary_id
#>                 <int> <chr>                  <chr>                 
#> 1                   4 Osteoarthritis of knee SNOMED                
#> # ℹ 4 more variables: non_standard_concept_id <int>,
#> #   non_standard_concept_name <chr>, non_standard_concept_code <chr>,
#> #   non_standard_vocabulary_id <chr>
# }