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README.md

A flexible and efficient framework for data-driven stochastic disease spread simulations

Build Status Build status CRAN status CRAN RStudio mirror downloads Coverage Status

SimInf

The package 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.

Installation

To install the latest release on CRAN

install.packages("SimInf")

To install the development version of SimInf, it's easiest to use the devtools package:

# install.packages("devtools")
library(devtools)
install_github("stewid/SimInf"")

Another alternative is to use git and make

$ git clone https://github.com/stewid/SimInf.git
$ cd SimInf
$ make install

Dependencies

On a Debian based system

Before installing SimInf you need to install The GNU Scientific Library (GSL).

apt-get install libgsl0-dev

You may need to do:

sudo apt-get install libgsl0-dev

On a Windows machine

To install the development version of SimInf you first need to download and install Rtools

Authors

  • Pavol Bauer (Uppsala University, Sweden)
  • Robin Eriksson (Uppsala University, Sweden)
  • Stefan Engblom (Uppsala University, Sweden)
  • Stefan Widgren (National Veterinary Institute, Sweden) (Maintainer)

Acknowledgments

This work was financially supported by the Swedish Research Council within the UPMARC Linnaeus centre of Excellence (Pavol Bauer, Robin Eriksson and Stefan Engblom), the Swedish Research Council Formas (Stefan Engblom and Stefan Widgren), the Swedish Board of Agriculture (Stefan Widgren), and by the Swedish strategic research program eSSENCE (Stefan Widgren).

License

The SimInf package is licensed under the GPLv3.

Any suggestions, bug reports, forks and pull requests are appreciated. Get in touch.