/dengue_foi

Example code to estimate force of infection from age-stratified incidence data, as described in "Opportunities for improved surveillance and control of infectious diseases from age-specific case data: insight from dengue".

Primary LanguageRMIT LicenseMIT

This repository includes example code to estimate forces of infection for dengue as described in "Opportunities for improved surveillance and control of infectious diseases from age-specific case data: insight from dengue
"
The data folder contains example data from Brazil.
"dhf_brazil_2002_2015.Rdata": Age-specific counts for Brazil 2002:2015
"census_brazil_2002_2015.Rdata" Census projections for Braizl 2002:2015

The code folder contains example code and functions required to fit the model
"Example_code.R": Code to run an example and estimate forces of infection from the data
"ll.1_pois.R": Likelihood function to produce estimates (maximum likelihood optimization"
"stan_code1.stan" Stan code
"figure_plot_stan_output.R" Function to plot stan model outputs