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.
This package uses the DatabaseConnector package and the SqlRender package. It also requires an instance of the OMOP vocabulary.
The file extras/TestCode.R
shows an example of how to run this builder.
DatabaseConnector
package set the connection details to the servercdmDatabaseSchema
, sourceDatabaseSchema
and vocabDatabaseSchema
a. In this example the cdm schema, source schema and vocab schema all exist on the same serverchunkData()
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 processinggetIteraterNum()
function. This will find how many chunks the code has to runcreateVocabTables()
function to create the vocabulary mapping tables.createAllLookupTables()
function to create the LOCATION, PERSON, CARE_SITE and PROVIDER tablescreateObservationPeriodTable()
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 WebMDcreatePayerPlanPeriodTable()
function to create the PAYER_PLAN_PERIOD table.createVisitOccurrenceTable()
function to create the VISIT_OCCURRENCE table. Be sure to set runAllParts
to TRUEcreateSTEMTable()
function to create the STEM tablecreateEventTables()
function to create the following tables from the STEM table:
CONDITION_OCCURRENCE,
PROCEDURE_OCCURRENCE,
DRUG_EXPOSURE,
DEVICE_EXPOSURE,
MEASUREMENT,
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