Clearance of untreated C. trachomatis infection in men

This repository contains code and other supplementary information for evidence synthesis of the clearance rate of untreated genital C. trachomatis infection in men.

• The directory named search_strategy contains details of the search strategy used for updating reviews of the evidence, and a supplementary table (data.pdf) summarising all the data used, from men and women.

• The directory named analysis contains:

  • Various STAN model specification files;
  • Various datasets, saved as RData objects;
  • Jupyter notebooks for running the STAN models and interpreting output, and
  • A directory named results containing saved output from the Jupyter notebooks.

Three notebooks are provided in the analysis directory:

• results_2comp.ipynb runs a model in which durations of chlamydia infection have a two-component mixture-of-exponentials distribution.
• model_comparison.ipynb compares the fit of the two-component mixture model with the fits of various alternative models.
• sensitivity_analysis.ipynb investigates the sensitivity of the model to the chlamydia diagnosis method used, and to the exclusion of each of the studies in turn.