Different files perform a different role in estimating cures and informing new extrapolations on different endpoints. The file Pola_cure_endpoint_direct.R performs a fit on the selected endpoints (typically OS, PFSINV - investigator PFS, PFSIRC - IRC assessed PFS) and returns a set of parameters in the files whose names start with:
Parms_mixed_direct_HE_friendly -- parameter estimates Variance_mixed_direct_HE_friendly -- variance on parameter estimates
The file Pola_informed_cure_endpoints.R uses inputs from the estimations obtained with the direct files.
Thes files depend on other files that contain functions that construct background hazard values for the subjects included in the trial.
One of such files is the haz_countries.R file, which reads a series of mortality tables (extracted from mortality.org) and builds the background hazard rates (annualized and subject specific).