exportCohortStatsTables: Export the cohort statistics tables to the file system
In CohortGenerator: Cohort Generation for the OMOP Common Data Model

exportCohortStatsTables

R Documentation

Export the cohort statistics tables to the file system

Description

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.

Usage

exportCohortStatsTables(
  connectionDetails,
  connection = NULL,
  cohortDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  cohortStatisticsFolder,
  snakeCaseToCamelCase = TRUE,
  fileNamesInSnakeCase = FALSE,
  incremental = FALSE,
  databaseId = NULL,
  minCellCount = 5,
  cohortDefinitionSet = NULL,
  tablePrefix = ""
)

Arguments

`connectionDetails`	An object of type `connectionDetails` as created using the `createConnectionDetails` function in the DatabaseConnector package. Can be left NULL if `connection` is provided.
`connection`	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.
`cohortDatabaseSchema`	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'.
`cohortTableNames`	The names of the cohort tables. See `getCohortTableNames` for more details.
`cohortStatisticsFolder`	The path to the folder where the cohort statistics folder where the results will be written
`snakeCaseToCamelCase`	Should column names in the exported files convert from snake_case to camelCase? Default is FALSE
`fileNamesInSnakeCase`	Should the exported files use snake_case? Default is FALSE
`incremental`	If `incremental = TRUE`, results are written to update values instead of overwriting an existing results
`databaseId`	Optional - when specified, the databaseId will be added to the exported results
`minCellCount`	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'.
`cohortDefinitionSet`	The `cohortDefinitionSet` argument must be a data frame with the following columns: cohortId The unique integer identifier of the cohort cohortName The cohort's name sql The OHDSI-SQL used to generate the cohort Optionally, this data frame may contain: json The Circe JSON representation of the cohort
`tablePrefix`	Optional - allows to append a prefix to the exported file names.