Package: SimInf
Title: A Framework for Data-Driven Stochastic Disease Spread
        Simulations
Version: 10.1.0
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, http://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
RoxygenNote: 7.3.3
VignetteBuilder: utils, knitr
Packaged: 2025-11-16 16:02:53 UTC; stefan
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>
Repository: CRAN
Date/Publication: 2025-11-17 21:51:33 UTC
Built: R 4.6.0; x86_64-w64-mingw32; 2026-06-22 10:21:58 UTC; windows
Archs: x64
