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README.md

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Code for the manuscript:

"Comparison of platforms for testing antibodies to Chlamydia trachomatis antigens in the Democratic Republic of the Congo and Togo. Sci Rep 11, 7225 (2021). https://doi.org/10.1038/s41598-021-86639-8

Project structure

  1. clean
    • input (raw spreadsheets of age, titre, and sero_pos data)
    • src (script to clean the data in the input folder)
  2. observed
    • input (files for each sheet from the clean task)
    • src (script to calculate age seroprevalence)
  3. adjust
    • input (files for each sheet from the clean task)
    • output (age adjusted data)
    • src (script to adjust data by age weights)
  4. model
    • input (files for each sheet from the clean task)
    • src (script to run model)
  5. plot
    • input (cleaned and prepared files from the observed and model tasks)
    • output ( all original figures generated from analysis)
    • src (script to make figures)