README.md

In OHDSI/ETL-HealthVerityBuilder: A Builder for Converting the HealthVerity Data Model to the OMOP CDM

ETL and builder for HealthVerity data

Note: This builder was written for a data cut containing data from an open claims datasource and a closed claims datasource and is still under development.

• The ETL document in located in the docs folder

Dependencies

This package uses the DatabaseConnector package and the SqlRender package. It also requires an instance of the OMOP vocabulary.

How to run

The file extras/TestCode.R shows an example of how to run this builder.

1. Using the DatabaseConnector package set the connection details to the server
2. Set the variables cdmDatabaseSchema, sourceDatabaseSchema and vocabDatabaseSchema a. In this example the cdm schema, source schema and vocab schema all exist on the same server
3. Run the chunkData() function. This will create a dataframe with a list of all the first digits of the HVIDs (set by nSubstring argument) in order to chunk the data to allow for more efficient processing
4. Run the getIteraterNum() function. This will find how many chunks the code has to run
5. Run the createVocabTables() function to create the vocabulary mapping tables.
6. Run the createAllLookupTables() function to create the LOCATION, PERSON, CARE_SITE and PROVIDER tables
7. Run the createObservationPeriodTable() function to create the OBSERVATION_PERIOD table. If createWebmdObsPeriod is set to TRUE then a separate OBSERVATION_PERIOD table will be created just for the time period the patients were in WebMD
8. Run the createPayerPlanPeriodTable() function to create the PAYER_PLAN_PERIOD table.
9. Run the createVisitOccurrenceTable() function to create the VISIT_OCCURRENCE table. Be sure to set runAllParts to TRUE
10. Run the createSTEMTable() function to create the STEM table
11. Run the createEventTables() function to create the following tables from the STEM table: CONDITION_OCCURRENCE, PROCEDURE_OCCURRENCE, DRUG_EXPOSURE, DEVICE_EXPOSURE, MEASUREMENT, OBSERVATION

OHDSI/ETL-HealthVerityBuilder documentation built on May 19, 2019, 12:40 a.m.