mooresea/lassa-model

Estimate sub-national LASV infections and LF incidence rates in West Africa # lassa-model Estimate sub-national LASV infections and LF incidence rates in West Africa This repository contains the code to recreate the modeling analysis in the article "Estimation of Lassa fever incidence rates in West Africa: development of a modeling framework to inform vaccine trial design". This article is currently available as a preprint at: doi.org The analysis involves running the following R scripts from the 'code' directory: *Note: to successfully complete this analysis for the 2nd administrative level, the zip file containing population data, adm_2_pop_upd.z, will first need to be unzipped. 0. prior_iceberg.R Description: Estimate priors for proportion of infections that are asymptomatic/mild/unreported, a reported case, a reported death Input: data/iceberg_data.csv Output: results/prior_iceberg.RData 2. step1_analyze_sero_lassa.R Description: Estimate the FOI for each administrative unit with serology data using a catalytic model. Input: data/case_reports_Lassa_IGG.csv Output: results/foi_from_sero_adm_X_revrateXX.RData Command variables: 1. admin: 1 or 2 2. reversion rate: 0,3,6 (%) 3. step2_estimate_proportion_by_type_country_effects.R Description: Estimate case and death reporting fractions for each country based on FOI estimates from step 1 and case/death data. Input: data/case_reports_Lassa_CASES.csv results/foi_from_sero_admX_revrateXX.RData Output: results/proportion_by_type_admX_revrateXX_country_upd.RData Command variables: 1. admin: 1 or 2 2. reversion rate: 0,3,6 (%) 4. step3_project_infections_by_country.R Description: Estimate number of spillover infections for administrative units based on reporting fractions from step2. Input: data/case_reports_Lassa_CASES.csv results/proportion_by_type_admX_revrateXX_country_upd.RData Output: results/projected_infections_admX_revrateXX_country_upd.RData Command variables: 1. admin: 1 or 2 2. reversion rate: 0,3,6 (%) 5. step4_project_foi_by_country.R Descripti …