library("rstanmed")

# Assumes SEER data is stored as txt in Data/Raw/ subfolder
# Assumed CanCORS colorectal cohort is as CSV in Data/Raw/ subfolder
dir <- paste0(getwd(), "/")

# Main --------------------------------------------------------------------

options(mc.cores = 4)
bayes_res <- run_data_app(seer_file_path = paste0(dir, "Data/Raw/data_SEER_for_BSA_summer_project.txt"), 
                          cancors_file_path = paste0(dir, "Data/Raw/selected_cancors_data_2016_3_14.csv"),
                          samples_file_path = paste0(dir, "data_app_samples_", format(Sys.Date(), "%Y%m%d"), ".csv"),
                          am_intx = 1, 
                          inf_fact = 1, 
                          chains = 4, 
                          iter = 2000, 
                          seed = 20200219,
                          init_r = 0.05, 
                          control = list(adapt_delta = 0.97, max_treedepth = 20),
                          auto_write = TRUE, 
                          mc.cores = 4)

rstan::summary(bayes_res, par = "meffects[1]")$summary[,"n_eff"]
rstan::summary(bayes_res, par = "meffects[1]")$summary[,"Rhat"]


# Inflation factor --------------------------------------------------------

dainf_res <- run_data_app(seer_file_path = paste0(dir, "Data/Raw/data_SEER_for_BSA_summer_project.txt"), 
                          cancors_file_path = paste0(dir, "Data/Raw/selected_cancors_data_2016_3_14.csv"),
                          samples_file_path = paste0(dir, "data_app_samples_", format(Sys.Date(), "%Y%m%d"), ".csv"),
                          am_intx = 1, 
                          inf_fact = 10, 
                          chains = 4, iter = 2000, 
                          seed = 20201101,
                          init_r = 0.05, 
                          control = list(adapt_delta = 0.95, max_treedepth = 15),
                          auto_write = TRUE, 
                          mc.cores = 4)


rstan::summary(dainf_res, par = "meffects[1]")$summary[,"n_eff"]
rstan::summary(dainf_res, par = "meffects[1]")$summary[,"Rhat"]