getCohortStats: Get Cohort Inclusion Stats Table Data

In CohortGenerator: Cohort Generation for the OMOP Common Data Model

Get Cohort Inclusion Stats Table Data

Description

This function returns a data frame of the data in the Cohort Inclusion Tables. Results are organized in to a list with 5 different data frames:

• cohortInclusionTable

• cohortInclusionResultTable

• cohortInclusionStatsTable

• cohortSummaryStatsTable

• cohortCensorStatsTable

These can be optionally specified with the outputTables. See exportCohortStatsTables function for saving data to csv.

Usage

getCohortStats(
  connectionDetails,
  connection = NULL,
  cohortDatabaseSchema,
  databaseId = NULL,
  snakeCaseToCamelCase = TRUE,
  outputTables = c("cohortInclusionTable", "cohortInclusionResultTable",
    "cohortInclusionStatsTable", "cohortInclusionStatsTable", "cohortSummaryStatsTable",
    "cohortCensorStatsTable"),
  cohortTableNames = getCohortTableNames()
)

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'.
databaseId	Optional - when specified, the databaseId will be added to the exported results
snakeCaseToCamelCase	Convert column names from snake case to camel case.
outputTables	Character vector. One or more of "cohortInclusionTable", "cohortInclusionResultTable", "cohortInclusionStatsTable", "cohortInclusionStatsTable", "cohortSummaryStatsTable" or "cohortCensorStatsTable". Output is limited to these tables. Cannot export, for, example, the cohort table. Defaults to all stats tables.
cohortTableNames	The names of the cohort tables. See getCohortTableNames for more details.

CohortGenerator documentation built on Oct. 1, 2024, 1:09 a.m.