clean_process_clinical_data cleans and processes clinical EHR data.

clean_process_clinical_data(
  drug,
  phenotype,
  biomarker,
  indication_drugs,
  concept_id_exclusions,
  r_covariates,
  r_drugs,
  r_biomarkers
)

Arguments

drug

A string, e.g., "simvastatin"

phenotype

A string, e.g., "Hyperlipidemia"

biomarker

A string, e.g., "LDL Cholesterol"

indication_drugs

A tibble with columns c('rxcui_in', 'drug_desc', 'indication'), eg, DrugRepurposingToolKit::drugsHyperlipidemia

concept_id_exclusions

A vector, e.g., c(2212451). Used for excluding concept_ids which may not contain the correct values

r_covariates

A tibble with columns c('person_id','dob','gender_concept_id', 'race_concept_id', drug_concept_id', 'first_drug_exposure','last_drug_exposure')

r_drugs

A tibble with columns c('person_id','start_date','end_date', 'drug_exposure_start_date','drug_concept_id')

r_biomarkers

A tibble with columns c('person_id','start_date','measurement_date', 'end_date', 'measurement_concept_id', 'value_as_number')

Details

This function cleans and processes clinical data from electronic health record (EHR) databases that have adopted the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) format.

Updated: 2021-03-27