Generate Print-Friendly Cohort Documentation from JSON

Converts CIRCE-based JSON cohort definitions to human-readable R Markdown files using CirceR print-friendly formatting. Preserves category subdirectories (e.g., target/, comparator/) in output structure.

Usage

makePrintFriendlyFile(
  cohorts_dir = "inputs/cohorts",
  output_base = "AI_translation",
  verbose = TRUE
)

Arguments

cohorts_dir

Character. Path to cohorts folder containing json/ subdirectory. Default: "inputs/cohorts" (Ulysses standard structure)

output_base

Character. Path to base output directory where printFriendly/ subdirectory will be created. Default: "AI_translation" (created at repo root, separate from inputs/)

verbose

Logical. Print progress messages. Default: TRUE

Value

Invisibly returns character vector of generated file paths

Details

Input folder structure expected:

inputs/cohorts/

  └── json/

      ├── target/

      │   ├── cohort1.json

      │   └── cohort2.json

      └── comparator/

          └── cohort3.json

Output folder structure created:

AI_translation/

  └── printFriendly/

      ├── target/

      │   ├── cohort1 - cohort_print_friendly.Rmd

      │   └── cohort2 - cohort_print_friendly.Rmd

      └── comparator/

          └── cohort3 - cohort_print_friendly.Rmd

Each generated Rmd file contains a human-readable specification of the cohort definition suitable for publication or documentation. CirceR must be installed.

Examples

if (FALSE) {
  # Generate print-friendly files with defaults
  makePrintFriendlyFile()

  # Custom locations
  makePrintFriendlyFile(
    cohorts_dir = "path/to/cohorts",
    output_base = "path/to/output"
  )
}