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Export the cohort statistics tables to the file system

Source: R/Export.R
exportCohortStatsTables.Rd

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.