Simulation-Based Inference Methods for Infectious Disease Models
Produces ABC reference table
Runs ABC-SMC algorithm
Compiles SimBIID_model object
Parse custom model using SimInf style markup
Plots ABCSMC objects
Plots PMCMC objects
Plots SimBIID_runs objects
Runs particle MCMC algorithm
Predicts future course of outbreak from PMCMC objects
Prints ABCSMC objects
Prints PMCMC objects
Prints SimBIID_model objects
Prints SimBIID_runs objects
Runs SimBIID_model object
Simulation-based inference for infectious disease models
Summarises ABCSMC objects
Summarises PMCMC objects
Time windows for PMCMC objects
Provides some code to run simulations of state-space models, and then use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC) algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle filter based particle Markov chain Monte Carlo (PMCMC) algorithm (Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>). Also provides functions to plot and summarise the outputs.