jessmhoehner / cdc_multicountry_trachoma_seroproject Goto Github PK

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)