GitHub - sarahkada/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".

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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".

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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