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 )
drug | A string, e.g., "simvastatin" |
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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') |
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