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Generate a cohort set on a CDM object (optimized, no Java dependency)

Source: R/optimizer.R
generateCohortSet2.Rd

Generates cohort sets using an optimized DAG-based SQL pipeline that does not require Java or CirceR. This is a faster alternative to generateCohortSet that produces equivalent results.

A "cohort_table" object consists of four components:

  • A remote table reference to an OHDSI cohort table with columns: cohort_definition_id, subject_id, cohort_start_date, cohort_end_date.

  • A settings attribute containing cohort settings including names.

  • An attrition attribute 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 containing cohort counts.

Usage

generateCohortSet2(
  cdm,
  cohortSet,
  name,
  computeAttrition = TRUE,
  overwrite = TRUE,
  cache = FALSE
)

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. 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

cache

Logical; if TRUE, enable incremental DAG caching. Previously computed intermediate tables are reused, and only changed portions of the DAG are recomputed. Default FALSE.

Value

A cdm reference with the generated cohort table added.

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 <- generateCohortSet2(cdm, cohortSet, name = "cohort")

print(cdm$cohort)

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