Create Blank Concept Sets Load File

Creates a blank conceptSetsLoad.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/conceptSets folder.

Usage

createBlankConceptSetsLoadFile(
  conceptSetsFolderPath = here::here("inputs/conceptSets")
)

Arguments

conceptSetsFolderPath

Character. Path where the blank file will be created. Defaults to "inputs/conceptSets". 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 concept set ID. Get this from ATLAS > Concept Sets

• label (character): Display name for your concept set (e.g., "Hypertension diagnoses")

• category (character): Broad grouping category (e.g., "Cardiovascular", "Medications")

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

• sourceCode (TRUE/FALSE): Whether this represents source codes (rarely TRUE for concept sets)

• domain (character): OMOP domain - must be one of:

  • drug_exposure - medication concept sets

  • condition_occurrence - diagnosis concept sets

  • measurement - lab/measurement concept sets

  • procedure - procedure concept sets

  • observation - observation concept sets

  • visit_occurrence - visit type concept sets

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

Tips for Filling Out:

1. Each row represents one concept set

2. Use forward slashes (/) in file paths

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

4. domain field is critical for vocabulary suggestions in extractSourceCodes()

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 conceptSetsLoad.csv in your preferred spreadsheet application

3. Fill in your concept set metadata

4. Save the file

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

6. Use loadConceptSetManifest() to load into your study

Examples

if (FALSE) {
  # Create blank template in default location
  createBlankConceptSetsLoadFile()
  # File created at: inputs/conceptSets/conceptSetsLoad.csv
}