Preferential Sampling in Disease Surveillance

This repository contains simulations and a case study to estimate disease risk from preferentially sampled disease surveillance data monitoring plague in sciurid rodents.

Organization

case_study

Fits and evaluates various models to a surveillance dataset monitoring the incidence of plague in sciurid rodents throughout the state of California.

• fit_poisson.R: fits a Poisson regression model.
• fit_spatial_poisson.R: fits a spatial Poisson regression model with Gausssian process residuals.
• fit_slp.R: fits a shared latent process model attempting to correct for preferential sampling.
• cdph_results.R: summarizes results from model fitting.
• data/
  • plague_data_simulated.rds: R data file of data for case study.
  • sim_from_fitted.R: simulates data from the fitted SLP model.
  • data_dictionary.md: describes plague_data_simulated.rds.

simulation

• sim_datasets.R: simulates preferentially sampled disease surveillance datasets.
• sim_results.R: evaluates model performance on simulated data.

stan

• poisson.stan: STAN file defining the Poisson model.
• spatial_poisson.stan: STAN file defining the spatial Poisson model.
• slp.stan: STAN file defining the shared latent process model.