Compute time to event study
Usage
computeTimeToEventAnalyses(
connectionDetails = NULL,
targetDatabaseSchema,
targetTable,
outcomeDatabaseSchema = targetDatabaseSchema,
outcomeTable = targetTable,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
cdmDatabaseSchema,
settings,
databaseId = "database 1",
outputFolder,
minCellCount = 0,
...
)Arguments
- connectionDetails
An object of type `connectionDetails` as created using the [DatabaseConnector::createConnectionDetails()] function.
- targetDatabaseSchema
Schema name where your target cohort table resides. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
- targetTable
Name of the target cohort table.
- outcomeDatabaseSchema
Schema name where your outcome cohort table resides. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
- outcomeTable
Name of the outcome cohort table.
- tempEmulationSchema
Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created
- cdmDatabaseSchema
The database schema containing the OMOP CDM data
- settings
The settings for the timeToEvent study
- databaseId
An identifier for the database (string)
- outputFolder
A directory to save the results as csv files
- minCellCount
The minimum cell value to display, values less than this will be replaced by -1
- ...
extra inputs
Value
An Andromeda::andromeda() object containing the time to event results.
See also
Other TimeToEvent:
createTimeToEventSettings()
Examples
# example code
conDet <- exampleOmopConnectionDetails()
tteSet <- createTimeToEventSettings(
targetIds = c(1,2),
outcomeIds = 3
)
result <- computeTimeToEventAnalyses(
connectionDetails = conDet,
targetDatabaseSchema = 'main',
targetTable = 'cohort',
cdmDatabaseSchema = 'main',
settings = tteSet,
outputFolder = file.path(tempdir(), 'tte')
)
#> Connecting using SQLite driver
#> Uploading #cohort_settings
#> Inserting data took 0.0107 secs
#> Computing time to event results
#> | | | 0% | |=== | 4% | |====== | 8% | |========= | 12% | |============ | 17% | |=============== | 21% | |================== | 25% | |==================== | 29% | |======================= | 33% | |========================== | 38% | |============================= | 42% | |================================ | 46% | |=================================== | 50% | |====================================== | 54% | |========================================= | 58% | |============================================ | 62% | |=============================================== | 67% | |================================================== | 71% | |==================================================== | 75% | |======================================================= | 79% | |========================================================== | 83% | |============================================================= | 88% | |================================================================ | 92% | |=================================================================== | 96% | |======================================================================| 100%
#> Executing SQL took 0.0286 secs
#> Computing time-to-event for 2 T-O pairs took 0.213 secs
#> exporting to csv file