AsymTB

Bayesian empirical models for considering asymptomatic TB

Theoretical models

Scripts for model fitting

• 2_Fit_ANP.R: Asymptomatic->Smr-/Smr+ model
• 2_Fit_ASC.R: Asymptomatic->Symptomatic with/without care-seeking model
• 2_Fit_Full_BLT.R: For Blantyre data with strata of age, sex, HIV
• 2_Fit_Full_KEN.R: For Kenya data with strata of age, sex, HIV

Model inference

• 3_Inference.R: inference with the posterior distribution

Sensitivity analyses

• 2_Fit_Sens_Sym.R: definitions of TB-like symptoms
• 2_Fit_Sens_Mor.R: assumptions for TB-related deaths
• 2_Fit_Sens_HIV.R: assumptions for TB-related deaths of PLHIV

Table outputs

• 4_Tab_basic.R Data summary
• 4_Tab_posterior.R Posterior distributions by country
• 4_Tab_HIV.R Summary of the HIV inference
• 4_Tab_covariates.R Regression analysis for the asymptomatic duration

Data visualisation

• 4_Vis_gof.R Goodness of fit figures
• 4_Vis_duration.R Time to event distributions
• 4_Vis_conversion.R Smear-type conversion
• 4_Vis_burden.R Figures for burden estimates
• 4_Vis_cascade.R Health-care cascade