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SimBIID (version 0.2.2)

Simulation-Based Inference Methods for Infectious Disease Models

Description

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.

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Version

Install

install.packages('SimBIID')

Monthly Downloads

358

Version

0.2.2

License

GPL (>= 3)

Issues

3

Pull Requests

0

Stars

2

Forks

1

Maintainer

Trevelyan J. McKinley

Last Published

April 3rd, 2025

Functions in SimBIID (0.2.2)

window.PMCMC

Time windows for PMCMC objects
print.SimBIID_model

Prints SimBIID_model objects
summary.PMCMC

Summarises PMCMC objects
print.PMCMC

Prints PMCMC objects
predict.PMCMC

Predicts future course of outbreak from PMCMC objects
print.ABCSMC

Prints ABCSMC objects
SimBIID

Simulation-based inference for infectious disease models
PMCMC

Runs particle MCMC algorithm
smallpox

Time series counts of smallpox cases
summary.ABCSMC

Summarises ABCSMC objects
run

Runs SimBIID_model object
print.SimBIID_runs

Prints SimBIID_runs objects
compileRcpp

Compiles SimBIID_model object
ABCRef

Produces ABC reference table
ebola

Time series counts of ebola cases
ABCSMC

Runs ABC-SMC algorithm
mparseRcpp

Parse custom model using SimInf style markup
plot.PMCMC

Plots PMCMC objects
plot.ABCSMC

Plots ABCSMC objects
plot.SimBIID_runs

Plots SimBIID_runs objects