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Generate a set of negative control outcome cohorts

Source: R/NegativeControlCohorts.R
generateNegativeControlOutcomeCohorts.Rd

This function generate a set of negative control outcome cohorts. For more information please see [Chapter 12 - Population Level Estimation](https://ohdsi.github.io/TheBookOfOhdsi/PopulationLevelEstimation.html) for more information how these cohorts are utilized in a study design.

Usage

generateNegativeControlOutcomeCohorts(
  connectionDetails = NULL,
  connection = NULL,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = getCohortTableNames()$cohortTable,
  negativeControlOutcomeCohortSet,
  occurrenceType = "all",
  incremental = FALSE,
  incrementalFolder = NULL,
  detectOnDescendants = FALSE
)

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.

cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.

tempEmulationSchema

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.

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'.

cohortTable

Name of the cohort table.

negativeControlOutcomeCohortSet

The negativeControlOutcomeCohortSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

outcomeConceptId

The concept_id in the condition domain to use for the negative control outcome.

occurrenceType

The occurrenceType will detect either: the first time an outcomeConceptId occurs or all times the outcomeConceptId occurs for a person. Values accepted: 'all' or 'first'.

incremental

Create only cohorts that haven't been created before?

incrementalFolder

If incremental = TRUE, specify a folder where records are kept of which definition has been executed.

detectOnDescendants

When set to TRUE, detectOnDescendants will use the vocabulary to find negative control outcomes using the outcomeConceptId and all descendants via the concept_ancestor table. When FALSE, only the exact outcomeConceptId will be used to detect the outcome.

Value

Invisibly returns an empty negative control outcome cohort set data.frame