This function retrieves the data from the cohort statistics tables and writes them to the inclusion statistics folder specified in the function call. NOTE: inclusion rule names are handled in one of two ways:
1. You can specify the cohortDefinitionSet parameter and the inclusion rule names will be extracted from the data.frame. 2. You can insert the inclusion rule names into the database using the insertInclusionRuleNames function of this package.
The first approach is preferred as to avoid the warning emitted.
exportCohortStatsTables(
connectionDetails,
connection = NULL,
cohortDatabaseSchema,
cohortTableNames = getCohortTableNames(),
cohortStatisticsFolder,
snakeCaseToCamelCase = TRUE,
fileNamesInSnakeCase = FALSE,
incremental = FALSE,
databaseId = NULL,
minCellCount = 5,
cohortDefinitionSet = NULL,
tablePrefix = ""
)An object of type connectionDetails as created using the
createConnectionDetails function in the
DatabaseConnector package. Can be left NULL if connection is
provided.
An object of type connection as created using the
connect function in the
DatabaseConnector package. Can be left NULL if connectionDetails
is provided, in which case a new connection will be opened at the start
of the function, and closed when the function finishes.
Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
The names of the cohort tables. See getCohortTableNames
for more details.
The path to the folder where the cohort statistics folder where the results will be written
Should column names in the exported files convert from snake_case to camelCase? Default is FALSE
Should the exported files use snake_case? Default is FALSE
If incremental = TRUE, results are written to update values instead of
overwriting an existing results (deprecated)
Optional - when specified, the databaseId will be added to the exported results
To preserve privacy: the minimum number of subjects contributing to a count before it can be included in the results. If the count is below this threshold, it will be set to `-minCellCount`.
The cohortDefinitionSet argument must be a data frame with
the following columns:
The unique integer identifier of the cohort
The cohort's name
The OHDSI-SQL used to generate the cohort
Optionally, this data frame may contain:
The Circe JSON representation of the cohort
Optional - allows to append a prefix to the exported file names.