new_generated_cohort_set {CDMConnector}

R Documentation

Constructor for GeneratedCohortSet objects

Description

This constructor function is to be used by analytic package developers to create generatedCohortSet objects.

Usage

new_generated_cohort_set(
  cohort_ref,
  cohort_set_ref = NULL,
  cohort_attrition_ref = NULL,
  cohort_count_ref = NULL,
  overwrite = FALSE
)

newGeneratedCohortSet(
  cohortRef,
  cohortSetRef = NULL,
  cohortAttritionRef = NULL,
  cohortCountRef = NULL,
  overwrite = FALSE
)

Arguments

cohort_ref, cohortRef	A tbl_sql object that points to a remote cohort table with the following first four columns: cohort_definition_id, subject_id, cohort_start_date, cohort_end_date. Additional columns are optional.
cohort_set_ref, cohortSetRef	A tbl_sql object that points to a remote table with the following first two columns: cohort_definition_id, cohort_name. Additional columns are optional. cohort_definition_id should be a primary key on this table and uniquely identify rows.
cohort_attrition_ref, cohortAttritionRef	A tbl_sql object that points to an attrition table in a remote database with the first column being cohort_definition_id.
cohort_count_ref, cohortCountRef	A tbl_sql object that points to a cohort_count table in a remote database with columns cohort_definition_id, cohort_entries, cohort_subjects.
overwrite	Should tables be overwritten if they already exist? TRUE or FALSE (default)

Details

A generatedCohort is a set of person-time from an OMOP CDM database. A generatedCohort can be represented by a table with three columns: subject_id, cohort_start_date, cohort_end_date. Subject_id is the same as person_id in the OMOP CDM. A generatedCohortSet is a collection of one or more generatedCohorts and can be represented as a table with four columns: cohort_definition_id, subject_id, cohort_start_date, cohort_end_date.

This constructor function defines the generatedCohortSet object in R.

The object is an extension of a tbl_sql object defined in dplyr. This is a lazy database query that points to a cohort table in the database with at least the columns cohort_definition_id, subject_id, cohort_start_date, cohort_end_date. The table could optionally have more columns as well.

In addition the generatedCohortSet object has three optional attributes. These are: cohort_set, cohort_attrition, cohort_count. Each of these attributes is also a lazy SQL query (tbl_sql) that points to a table in a database and is described below.

cohort_set

cohort_set is a table with one row per cohort_definition_id. The first two columns of the cohort_set table are: cohort_definition_id, and cohort_name. Additional columns can be added. The cohort_set table is meant to store metadata about the cohort definition. Since this table is required it will be created if it it is not supplied.

cohort_attrition

cohort_attrition is an optional table that stores attrition information recorded during the cohort generation process such as how many persons were dropped at each step of inclusion rule application. The first column of this table should be cohort_definition_id but all other columns currently have no constraints.

cohort_count

cohort_count is a option attribute table that records the number of records and the number of unique persons in each cohort in a generatedCohortSet. It is derived metadata that can be re-derived as long as cohort_set, the complete list of cohorts in the set, is available. Column names of cohort_count are: cohort_definition_id, number_records, number_subjects. This table is required for generatedCohortSet objects and will be created if not supplied.

Value

A generatedCohortSet object that is a tbl_sql reference to a cohort table in the write_schema of an OMOP CDM

Examples

## Not run: 
 # This function is for developers who are creating generatedCohortSet
 # objects in their packages. The function should accept a cdm_reference
 # object as the first argument and return a cdm_reference object with the
 # cohort table added. The second argument should be `name` which will be
 # the prefix for the database tables, the name of the cohort table in the
 # database and the name of the cohort table in the cdm object.
 # Other optional arguments can be added after the first two.

 generateCustomCohort <- function(cdm, name, ...) {

   # accept a cdm_reference object as input
   checkmate::assertClass(cdm, "cdm_reference")
   con <- attr(cdm, "dbcon")

   # Create the tables in the database however you like
   # All the tables should be prefixed with `name`
   # The cohort table should be called `name` in the database

   # Create the dplyr table references
   cohort_ref <- dplyr::tbl(con, name)
   cohort_set <- dplyr::tbl(con, paste0(name, "_set"))
   cohort_attrition_ref <- dplyr::tbl(con, paste0(name, "_attrition"))
   cohort_count_ref <- dplyr::tbl(con, paste0(name, "_count"))

   # add to the cdm
   cdm[[name]] <- cohort_ref

   # create the generated cohort set object using the constructor
   cdm[[name]] <- new_generated_cohort_set(
      cdm[[name]],
      cohort_set_ref = cohort_set_ref,
      cohort_attrition_ref = cohort_attrition_ref,
      cohort_count_ref = cohort_count_ref)

   return(cdm)
 }

## End(Not run)

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