Subset a cdm to the individuals in one or more cohorts

cdmSubset will return a new cdm object that contains lazy queries pointing to each of the cdm tables but subset to individuals in a generated cohort. Since the cdm tables are lazy queries, the subset operation will only be done when the tables are used. computeQuery can be used to run the SQL used to subset a cdm table and store it as a new table in the database.

Usage

cdmSubsetCohort(cdm, cohortTable = "cohort", cohortId = NULL, verbose = FALSE)

Arguments

cdm

A cdm_reference object

cohortTable

The name of a cohort table in the cdm reference

cohortId

IDs of the cohorts that we want to subset from the cohort table. If NULL (default) all cohorts in cohort table are considered.

verbose

Should subset messages be printed? TRUE or FALSE (default)

Value

A modified cdm_reference with all clinical tables subset to just the persons in the selected cohorts.

Examples

if (FALSE) { # \dontrun{
library(CDMConnector)
library(dplyr, warn.conflicts = FALSE)

con <- DBI::dbConnect(duckdb::duckdb(), eunomiaDir())

cdm <- cdmFromCon(con, cdmSchema = "main", writeSchema = "main")

# generate a cohort
path <- system.file("cohorts2", mustWork = TRUE, package = "CDMConnector")

cohortSet <- readCohortSet(path) %>%
  filter(cohort_name == "GIBleed_male")

# subset cdm to persons in the generated cohort
cdm <- generateCohortSet(cdm, cohortSet = cohortSet, name = "gibleed")

cdmGiBleed <- cdmSubsetCohort(cdm, cohortTable = "gibleed")

cdmGiBleed$person %>%
  tally()
#> # Source:   SQL [1 x 1]
#> # Database: DuckDB 0.6.1
#>       n
#>   <dbl>
#> 1   237

cdm$person %>%
  tally()
#> # Source:   SQL [1 x 1]
#> # Database: DuckDB 0.6.1
#>       n
#>   <dbl>
#> 1  2694


DBI::dbDisconnect(con, shutdown = TRUE)
} # }