generateDrugUtilisationCohortSet {DrugUtilisation} | R Documentation |
Generate a set of drug cohorts based on given concepts
Description
Adds a new cohort table to the cdm reference with individuals who have drug exposure records with the specified concepts. Cohort start and end dates will be based on drug record start and end dates, respectively. Records that overlap or have fewer days between them than the specified gap era will be concatenated into a single cohort entry.
Usage
generateDrugUtilisationCohortSet(
cdm,
name,
conceptSet,
gapEra = 1,
subsetCohort = NULL,
subsetCohortId = NULL,
numberExposures = FALSE,
daysPrescribed = FALSE
)
Arguments
cdm |
A |
name |
Name of the new cohort table, it must be a length 1 character vector. |
conceptSet |
List of concepts to be included. |
gapEra |
Number of days between two continuous exposures to be considered in the same era. |
subsetCohort |
Cohort table to subset. |
subsetCohortId |
Cohort id to subset. |
numberExposures |
Whether to include 'number_exposures' (number of drug exposure records between indexDate and censorDate). |
daysPrescribed |
Whether to include 'days_prescribed' (number of days prescribed used to create each era). |
Value
The function returns the cdm reference provided with the addition of the new cohort table.
Examples
library(DrugUtilisation)
library(CodelistGenerator)
library(dplyr, warn.conflicts = FALSE)
cdm <- mockDrugUtilisation()
druglist <- getDrugIngredientCodes(cdm = cdm,
name = c("acetaminophen", "metformin"),
nameStyle = "{concept_name}")
cdm <- generateDrugUtilisationCohortSet(cdm = cdm,
name = "drug_cohorts",
conceptSet = druglist,
gapEra = 30,
numberExposures = TRUE,
daysPrescribed = TRUE)
cdm$drug_cohorts |>
glimpse()