Package: SimInf
Title: A Framework for Data-Driven Stochastic Disease Spread
        Simulations
Version: 10.1.0.9000
Authors@R: c(person("Stefan", "Widgren", role = c("aut", "cre"),
                    email = "stefan.widgren@gmail.com",
                    comment = c(ORCID = "0000-0001-5745-2284")),
             person("Robin", "Eriksson", role = "aut",
                    comment = c(ORCID = "0000-0002-4291-712X")),
             person("Stefan", "Engblom", role = "aut",
                    comment = c(ORCID = "0000-0002-3614-1732")),
             person("Pavol", "Bauer", role = "aut",
                    comment = c(ORCID = "0000-0003-4328-7171")),
             person("Thomas", "Rosendal", role = "ctb",
                    comment = c(ORCID = "0000-0002-6576-9668")),
             person("Ivana", "Rodriguez Ewerlöf", role = "ctb",
                    comment = c(ORCID = "0000-0002-9678-9813")),
             person("Attractive Chaos", role = "cph",
                    comment = "Author of 'kvec.h'."))
Description: 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> or the Particle Markov
        Chain Monte Carlo ('PMCMC') algorithm of 'Andrieu' and others
        (2010) <doi:10.1111/j.1467-9868.2009.00736.x>.
Acknowledgements: This software has been made possible by support from
        the Swedish Research Council within the UPMARC Linnaeus center
        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), the Swedish strategic research program eSSENCE
        (Stefan Widgren), and in the framework of the Full Force
        project, supported by funding from the European Union’s Horizon
        2020 Research and Innovation programme under grant agreement No
        773830: One Health European Joint Programme (Stefan Widgren).
License: GPL-3
URL: https://github.com/stewid/SimInf, https://stewid.github.io/SimInf/
BugReports: https://github.com/stewid/SimInf/issues
Type: Package
LazyData: true
Biarch: true
NeedsCompilation: yes
SystemRequirements: GNU Scientific Library (GSL)
Depends: R (>= 4.0)
Imports: digest, graphics, grDevices, MASS, methods, stats, utils,
        Matrix (>= 1.3-0)
Suggests: knitr, rmarkdown
Collate: 'C-generator.R' 'check_arguments.R' 'init.R' 'valid.R'
        'classes.R' 'SimInf_model.R' 'SEIR.R' 'SIR.R' 'SIS.R' 'SISe.R'
        'SISe3.R' 'SISe3_sp.R' 'SISe_sp.R' 'SimInf-package.R'
        'SimInf.R' 'SimInf_events.R' 'SimInf_individual_events.R'
        'run.R' 'density_ratio.R' 'abc.R' 'degree.R' 'distance.R'
        'distributions.R' 'edge_properties.R' 'lambert.R'
        'match_compartments.R' 'mparse.R' 'pmcmc.R' 'pfilter.R' 'n.R'
        'openmp.R' 'package_skeleton.R' 'plot.R' 'prevalence.R'
        'print.R' 'punchcard.R' 'trajectory.R' 'u0.R' 'v0.R'
Encoding: UTF-8
VignetteBuilder: utils, knitr
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libgsl0-dev
Repository: https://stewid.r-universe.dev
Date/Publication: 2026-06-20 10:03:02 UTC
RemoteUrl: https://github.com/stewid/siminf
RemoteRef: HEAD
RemoteSha: 749e39464004e2ad3ff77dbe5d58c670ff1bf544
Packaged: 2026-06-20 11:25:15 UTC; root
Author: Stefan Widgren [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5745-2284>),
  Robin Eriksson [aut] (ORCID: <https://orcid.org/0000-0002-4291-712X>),
  Stefan Engblom [aut] (ORCID: <https://orcid.org/0000-0002-3614-1732>),
  Pavol Bauer [aut] (ORCID: <https://orcid.org/0000-0003-4328-7171>),
  Thomas Rosendal [ctb] (ORCID: <https://orcid.org/0000-0002-6576-9668>),
  Ivana Rodriguez Ewerlöf [ctb] (ORCID:
    <https://orcid.org/0000-0002-9678-9813>),
  Attractive Chaos [cph] (Author of 'kvec.h'.)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>