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Generate Cohorts for Pipeline Execution

Source: R/execute.R
generateCohorts.Rd

Loads the cohort manifest, displays the cohorts to be generated, optionally prompts for user confirmation, and then generates the cohorts and retrieves their counts. This function serves as the foundational step for all subsequent analytical tasks in the pipeline.

Usage

generateCohorts(executionSettings, pipelineVersion, override = FALSE)

Arguments

executionSettings

An ExecutionSettings object containing database configuration for cohort generation.

pipelineVersion

Character. The pipeline version used to organize the output folder structure. Output will be saved to exec/results/databaseName/pipelineVersion/00_buildCohorts/

override

Logical. If TRUE, skips the user confirmation prompt and proceeds directly with cohort generation. Defaults to FALSE.

Value

Invisibly returns the cohort counts data frame (id, label, tags, cohort_entries, cohort_subjects). Also saves counts to cohortCounts.csv in the output folder.