Simulation-Based Inference Methods for Infectious Disease Models

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) and a bootstrap particle filter based particle Markov chain Monte Carlo (PMCMC) algorithm (Andrieu et al., 2010 ). Also provides functions to plot and summarise the outputs.


Reference manual

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0.2.1 by Trevelyan J. McKinley, a year ago

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Authors: Trevelyan J. McKinley [aut, cre] , Stefan Widgren [aut] (Author of 'R/mparse.R') , Pavol Bauer [cph] (R/mparse.R) , Robin Eriksson [cph] (R/mparse.R) , Stefan Engblom [cph] (R/mparse.R)

Documentation:   PDF Manual  

GPL (>= 3) license

Imports stats, dplyr, purrr, tibble, ggplot2, tidyr, mvtnorm, grDevices, RColorBrewer, Rcpp, RcppXPtrUtils, coda

Suggests parallel, GGally, testthat

Linking to Rcpp, RcppArmadillo

See at CRAN