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.
generateNegativeControlOutcomeCohorts(
connectionDetails = NULL,
connection = NULL,
cdmDatabaseSchema,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
cohortDatabaseSchema = cdmDatabaseSchema,
cohortTable = getCohortTableNames()$cohortTable,
negativeControlOutcomeCohortSet,
occurrenceType = "all",
detectOnDescendants = FALSE
)
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 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'.
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.
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'.
Name of the cohort table.
The negativeControlOutcomeCohortSet
argument must be a data frame with
the following columns:
The unique integer identifier of the cohort
The cohort's name
The concept_id in the condition domain to use for the negative control outcome.
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'.
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.
Invisibly returns an empty negative control outcome cohort set data.frame