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ohdsi-studies / ScyllaEstimation

This OHDSI network study assesses the comparative effectiveness and safety among treatments administered during hospitalization and prior to intensive services. It also assesses the comparative effectiveness and safety among treatments administered after COVID-19 positive testing or diagnosis in the outpatient setting without prior hospitalization.
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SynthesizePositiveControls argument in 'execute' function #7

Closed tfalcs closed 3 years ago

tfalcs commented 3 years ago

@schuemie , @anthonysena

There seems to be an inconsistency with the set of arguments in the 'execute' function of the 'CodeToRun.R' file and in the construction of the function in the 'Main.R' file. The latter doesn't have the 'SynthesizePositiveControls' argument, whereas the former does. When I comment out the 'SynthesizePositiveControls' argument in the 'execute' function in the CodeToRun script, it runs just fine. Otherwise, I get the following:

execute(connectionDetails = connectionDetails,

  • cdmDatabaseSchema = cdmDatabaseSchema,
  • cohortDatabaseSchema = cohortDatabaseSchema,
  • cohortTable = cohortTable,
  • oracleTempSchema = oracleTempSchema,
  • outputFolder = outputFolder,
  • databaseId = databaseId,
  • databaseName = databaseName,
  • databaseDescription = databaseDescription,
  • createCohorts = TRUE,
  • synthesizePositiveControls = TRUE,
  • runAnalyses = TRUE,
  • packageResults = TRUE,
  • maxCores = maxCores) Error in execute(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, : unused argument (synthesizePositiveControls = TRUE) No suitable frames for recover()
schuemie commented 3 years ago

Thanks Thomas, and sorry I missed that. We're not using positive control synthesis in this study, so I decided to remove it from the code altogether.