MOSAIC Data Clean

This set of scripts allows ongoing monitoring and cleaning of prospective data collection for the MOSAIC prospective cohort study (clinicaltrials.gov listing).

This is a work in progress. A full example of the process can be found in Jennifer Thompson's data cleaning & monitoring tutorial.

Configuration

All REDCap API tokens for an individual user are assumed to be stored in the user's .Renviron file within this working directory, in the following format:

MOSAIC_IH=ABCDEFGHIJKLMNOPQRSTUVWXYZ

R will use these tokens in combination with the httr package to programmatically access the appropriate REDCap databases.

File Structure

• Main directory
  • ih_dataclean.R: Primary script; sources additional scripts from /R
  • .Renviron: Contains API tokens used to access REDCap projects
• /R
  • old_queries.R: Exports previously noted queries in order to remove those which cannot or need not be corrected. NOT CURRENTLY AVAILABLE
  • dataclean_helpers.R: Helper functions used in primary data cleaning scripts
• /output: Destination for CSV files containing queries from each run of ih_dataclean.R. One file per site per date.