README.md

epiABC

This repository collects code to perform ABC inference of infectious disease epidemics, used in the paper "A tutorial introduction to Bayesian inference for stochastic epidemic models using Approximate Bayesian Computation" by Kypraios, Neal and Prangle.

The code is presented as an R package for solely for convenience. It is not our intention to develop or support this as a fully featured package.

Organisation

The package contains functions to run various ABC analyses. These functions fall into several groups, indicated by a prefix. More details of some groups in given in sections below.

Several scripts are available to run analyses as in the paper. These are contained within the package as demos.

"coupled" prefix: homogeneous SIR epidemics

Vanilla/SMC ABC

Demo

Function files

Coupled ABC

Demo

Function files

"house" prefix: household SIR epidemics

Note that priors for lambda_G and lambda_L have been semi-hard coded to be Exp (1).

Seattle and Tecumseh datasets are included in the package.

Partially coupled ABC

Demo

Function files

Vanilla ABC

Demo

Function files

SMC-ABC

Demo

Function files

Partially coupled ABC

Demo

Function files



kypraios/epiABC documentation built on May 21, 2017, 7:34 a.m.