CRAN/E | SimInf

SimInf

A Framework for Data-Driven Stochastic Disease Spread Simulations

Installation

About

Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) doi:10.18637/jss.v091.i12. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) doi:10.1098/rsif.2008.0172.

Citation SimInf citation info
github.com/stewid/SimInf
System requirements GNU Scientific Library (GSL)
Bug report File report

Key Metrics

Version 9.5.0
R ≥ 4.0
Published 2023-01-23 311 days ago
Needs compilation? yes
License GPL-3
CRAN checks SimInf results

Downloads

Last 24 hours 0 -100%
Last 7 days 38 -57%
Last 30 days 418 +5%
Last 90 days 1.241 -17%
Last 365 days 6.200 -19%

Maintainer

Maintainer

Stefan Widgren

stefan.widgren@gmail.com

Authors

Stefan Widgren

aut / cre

Robin Eriksson

aut

Stefan Engblom

aut

Pavol Bauer

aut

Thomas Rosendal

ctb

Ivana Rodriguez Ewerlöf

ctb

Attractive Chaos

cph

(Author of 'kvec.h'.)

Material

README
NEWS
Reference manual
Package source

In Views

Epidemiology

Vignettes

SimInf: An R Package for Data-Driven Stochastic Disease Spread Simulations
Scheduled events

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

SimInf archive

Depends

R ≥ 4.0

Imports

digest
graphics
grDevices
MASS
methods
stats
utils
Matrix ≥ 1.3-0

Suggests

knitr
rmarkdown