Package: SimInf
Title: A Framework for Data-Driven Stochastic Disease Spread
        Simulations
Version: 7.0.1
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("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>.
Acknowledgements: This work was financially supported by 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),
        and by the Swedish strategic research program eSSENCE (Stefan
        Widgren).
License: GPL-3
URL: https://github.com/stewid/SimInf
BugReports: https://github.com/stewid/SimInf/issues
Type: Package
LazyData: true
Biarch: true
NeedsCompilation: yes
SystemRequirements: GNU Scientific Library (GSL)
Depends: R(>= 3.3)
Imports: digest, graphics, grDevices, methods, stats, utils, Matrix
Collate: 'C-generator.R' 'check_arguments.R' 'init.R' 'valid.R'
        'SimInf_events.R' 'SimInf_model.R' 'SEIR.R' 'SIR.R' 'SISe.R'
        'SISe3.R' 'SISe3_sp.R' 'SISe_sp.R' 'SimInf.R' 'degree.R'
        'distance.R' 'formula.R' 'mparse.R' 'openmp.R'
        'package_skeleton.R' 'plot.R' 'prevalence.R' 'print.R'
        'priors.R' 'punchcard.R' 'run.R' 'trajectory.R'
Encoding: UTF-8
RoxygenNote: 7.1.0
Packaged: 2020-06-18 16:21:43 UTC; stefan
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>),
  Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>),
  Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>),
  Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>),
  Thomas Rosendal [ctb] (<https://orcid.org/0000-0002-6576-9668>),
  Attractive Chaos [cph] (Author of 'kvec.h'.)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Repository: CRAN
Date/Publication: 2020-06-18 17:20:02 UTC
Built: R 3.6.3; x86_64-w64-mingw32; 2020-08-05 02:06:46 UTC; windows
Archs: i386, x64
