Generate a cohort set on a cdm object — generateCohortSet • CDMConnector

A "cohort_table" object consists of four components

A remote table reference to an OHDSI cohort table with at least the columns: cohort_definition_id, subject_id, cohort_start_date, cohort_end_date. Additional columns are optional and some analytic packages define additional columns specific to certain analytic cohorts.
A settings attribute which points to a remote table containing cohort settings including the names of the cohorts.
An attrition attribute which points to a remote table with attrition information recorded during generation. This attribute is optional. Since calculating attrition takes additional compute it can be skipped resulting in a NULL attrition attribute.
A cohortCounts attribute which points to a remote table containing cohort counts

Usage

generateCohortSet(
  cdm,
  cohortSet,
  name,
  computeAttrition = TRUE,
  overwrite = TRUE
)

Arguments

cdm: A cdm reference created by CDMConnector. write_schema must be specified.
cohortSet: A cohortSet dataframe created with readCohortSet()
name: Name of the cohort table to be created. This will also be used as a prefix for the cohort attribute tables. This must be a lowercase character string that starts with a letter and only contains letters, numbers, and underscores.
computeAttrition: Should attrition be computed? TRUE (default) or FALSE
overwrite: Should the cohort table be overwritten if it already exists? TRUE (default) or FALSE

Examples

if (FALSE) { # \dontrun{
library(CDMConnector)
con <- DBI::dbConnect(duckdb::duckdb(), eunomiaDir())
cdm <- cdmFromCon(con,
                  cdmSchema = "main",
                  writeSchema = "main")

cohortSet <- readCohortSet(system.file("cohorts2", package = "CDMConnector"))
cdm <- generateCohortSet(cdm, cohortSet, name = "cohort")

print(cdm$cohort)

attrition(cdm$cohort)
settings(cdm$cohort)
cohortCount(cdm$cohort)
} # }