R/RunCharacterization.R
runCharacterizationAnalyses.Rd
Specify the database connection containing the CDM data, the cohort database schemas/tables, the characterization settings and the directory to save the results to
runCharacterizationAnalyses(
connectionDetails,
targetDatabaseSchema,
targetTable,
outcomeDatabaseSchema,
outcomeTable,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
cdmDatabaseSchema,
characterizationSettings,
outputDirectory,
executionPath = file.path(outputDirectory, "execution"),
csvFilePrefix = "c_",
databaseId = "1",
showSubjectId = F,
minCellCount = 0,
incremental = T,
threads = 1,
minCharacterizationMean = 0.01
)
The connection details to the database containing the OMOP CDM data
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'.
Name of the target cohort table.
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'.
Name of the outcome cohort table.
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
The schema with the OMOP CDM data
The study settings created using createCharacterizationSettings
The location to save the final csv files to
The location where intermediate results are saved to
A string to append the csv files in the outputDirectory
The unique identifier for the cdm database
Whether to include subjectId of failed rechallenge case series or hide
The minimum count value that is calculated
If TRUE then skip previously executed analyses that completed
The number of threads to use when running aggregate covariates
The minimum mean threshold to extract when running aggregate covariates
Multiple csv files in the outputDirectory.
The results of the characterization will be saved into an sqlite database inside the specified saveDirectory
Other LargeScale:
createCharacterizationSettings()
,
loadCharacterizationSettings()
,
saveCharacterizationSettings()