Package: nosoi
Type: Package
Title: A Forward Agent-Based Transmission Chain Simulator
Version: 1.1.2
Authors@R: c(person("Sebastian", "Lequime", email = "sebastian.lequime@gmail.com",
                  role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3140-0651")),
                  person("Paul", "Bastide", email = "paul.bastide@umontpellier.fr",
                  role = "aut", comment = c(ORCID = "0000-0002-8084-9893")),
                  person("Simon", "Dellicour", email = "simon.dellicour@kuleuven.be",
                  role = "aut", comment = c(ORCID = "0000-0001-9558-1052")),
                  person("Philippe", "Lemey", email = "philippe.lemey@kuleuven.be",
                  role = "aut", comment = c(ORCID = "0000-0003-2826-5353")),
                  person("Guy", "Baele", email = "guy.baele@kuleuven.be",
                  role = "aut", comment = c(ORCID = "0000-0002-1915-7732")),
                  person("Thijs", "Janzen", email = "t.janzen@rug.nl",
                  role = "ctb", comment = c(ORCID = "0000-0002-4162-1140")))
Description: The aim of 'nosoi' (pronounced no.si) is to provide a
        flexible agent-based stochastic transmission chain/epidemic
        simulator (Lequime et al. Methods in Ecology and Evolution
        11:1002-1007). It is named after the daimones of plague,
        sickness and disease that escaped Pandora's jar in the Greek
        mythology. 'nosoi' is able to take into account the influence
        of multiple variable on the transmission process (e.g.
        dual-host systems (such as arboviruses), within-host viral
        dynamics, transportation, population structure), alone or taken
        together, to create complex but relatively intuitive
        epidemiological simulations.
URL: https://github.com/slequime/nosoi,
        https://slequime.github.io/nosoi/
BugReports: https://github.com/slequime/nosoi/issues
Language: en-US
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
biocViews:
Depends: R (>= 3.5.0)
Imports: data.table (>= 1.12.0), stats (>= 3.5.2), methods (>= 3.5.2),
        raster (>= 2.8-19)
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, igraph, ggplot2,
        ggnetwork, intergraph, viridis, gifski, png, gganimate, ape (>=
        5.3), tidytree (>= 0.3.3), treeio (>= 1.14.0), ggtree (>=
        2.4.0), magrittr (>= 1.5), dplyr (>= 0.8.0), covr
VignetteBuilder: knitr
Config/pak/sysreqs: libgdal-dev gdal-bin libgeos-dev libproj-dev
        libsqlite3-dev
Repository: https://slequime.r-universe.dev
Date/Publication: 2025-08-06 11:06:22 UTC
RemoteUrl: https://github.com/slequime/nosoi
RemoteRef: HEAD
RemoteSha: 2e70670ea0c7cf7d04267e04564257ebaf9c02c5
NeedsCompilation: no
Packaged: 2026-07-02 06:28:06 UTC; root
Author: Sebastian Lequime [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3140-0651>),
  Paul Bastide [aut] (ORCID: <https://orcid.org/0000-0002-8084-9893>),
  Simon Dellicour [aut] (ORCID: <https://orcid.org/0000-0001-9558-1052>),
  Philippe Lemey [aut] (ORCID: <https://orcid.org/0000-0003-2826-5353>),
  Guy Baele [aut] (ORCID: <https://orcid.org/0000-0002-1915-7732>),
  Thijs Janzen [ctb] (ORCID: <https://orcid.org/0000-0002-4162-1140>)
Maintainer: Sebastian Lequime <sebastian.lequime@gmail.com>