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Create Blank Cohorts Load File

Source: R/manifest_cohorts.R
createBlankCohortsLoadFile.Rd

Creates a blank cohortsLoad.csv template file in the specified folder with proper column structure. Users can fill this file manually in Excel, Google Sheets, or any text editor, then place it in the inputs/cohorts folder.

Usage

createBlankCohortsLoadFile(cohortsFolderPath = here::here("inputs/cohorts"))

Arguments

cohortsFolderPath

Character. Path where the blank file will be created. Defaults to "inputs/cohorts". Creates the folder if it doesn't exist.

Value

Invisibly returns the file path. Prints informative messages with tips.

Details

Column Guide:

  • atlasId (numeric): The ATLAS cohort ID. Get this from ATLAS > Cohort Definitions

  • label (character): Display name for your cohort (e.g., "Type 2 Diabetes patients")

  • category (character): Broad grouping category (e.g., "Disease Populations", "Treatment Groups")

  • subCategory (character): Optional sub-grouping within category

  • file_name (character): Path to JSON file (e.g., "json/t2dm_patients.json"). Note this is a placeholder will be replaced when you import from ATLAS.

Tips for Filling Out:

  1. Each row represents one cohort

  2. Use forward slashes (/) in file paths

  3. Ensure file_name matches the JSON files you'll import from ATLAS

  4. Logical sub-grouping in category/subCategory helps with organization

  5. Save as UTF-8 CSV when exporting from Excel to avoid encoding issues

Workflow:

  1. Call this function to create blank template

  2. Open cohortsLoad.csv in your preferred spreadsheet application

  3. Fill in your cohort metadata

  4. Save the file

  5. Use importAtlasCohorts() to import the actual JSON definitions from ATLAS

  6. Use loadCohortManifest() to load into your study

Examples

if (FALSE) {
  # Create blank template in default location
  createBlankCohortsLoadFile()
  # File created at: inputs/cohorts/cohortsLoad.csv
}