Code for MDR-LTBI burden estimates (Knight et al.)
cohort_ltbi_mdr.R: Main cohort model
Run_cohort_ltbi_mdr_final.R: Run the cohort model
Fit_model_for_prop_mdr.R: Runs Stan model
model_trend.stan: Stan code for model fit
Output_production.R: Code for gathering the data and plotting figures for the paper
{fit_model_for_prop_mdr_sa3.R output_production_sa3.R run_cohort_ltbi_mdr_final_sa3.R}: Equivalent code for running sensitivity analysis 3 (flexible spline function for India, China and the USA)
138_final_list_included_countries.csv: the final 138 included countries
all0_p_ds_mdr.Rdata: the 200 posterior estimates of MDR and DS ARI over time for each country
POP2014.Rdata / POP2035.Rdata / POP2050.Rdata: UN population estimates of population size
whokey.Rdata: WHO key for translating iso3 to country names and grouping by regions
results_sensitivity_analysis_3.xlsx: country level results for sensitivity analysis 3