The epidemiological impact, costs, and cost-effectiveness of implementing household contact investigation with tuberculosis preventive treatment in Nepal: a model-based analysis

Data and Scripts This repository contains the data and code associated with the manuscript: The epidemiological impact, costs, and cost-effectiveness of implementing household contact investigation with tuberculosis preventive treatment in Nepal: a model-based analysis Rajan Paudel¹, Anchal Thapa¹, Suvesh Shrestha², Kunchok Dorjee³, Raghu Dhital¹, David Dowdy⁴, Maxine Caws¹'⁵, Sourya Shrestha⁴ ¹Birat Nepal Medical Trust, Kathmandu, Nepal. ²School of Epidemiology and Public Health, University of Ottawa, Ottawa, Canada. ³Johns Hopkins School of Medicine, Baltimore, US. ⁴Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, US. ⁵Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK. Data Description par_range: Range used to obtain distribution of each parameters for simulation. cascade_for_model: Intervention cascade for both districts developed based on the pilot implementation data. cal_targets_district.csv: Calibration targets for named district. costing_parms_district.csv: Parameters used for cost-effectiveness analysis for each district. Code Description 01_model_setup: Setting up model to simulate TB transmission as well as scale-up scenario. 02_parameters_sampling: Generating distribution of parameters using provided range. 03_calibration_setup: Setting up calibration and running until transience for 100 years and 22 years after transience (from 2000 to 2022). 04_selection_from_calibration: Selection of the simulations that fall within the calibration targets for each district. Also includes scripts to plot results. 05_intervention_sim: Simulating intervention scenarios including no intervention for comparison. Calculation of overall and yearwise cases and deaths averted and plots. 06_cost_effectiveness: Setup for and results from cost-effectiveness analysis. 07_scale_up: Simulating scale-up scenario described in the manuscript using the scale-up model setup up in 01_model_setup. 08_sensitivity_analysis: Sensitivity analysis, willingness to pay analysis and cases and deaths averted for the scale-up scenario including plots.