Package: slendr
Title: A Simulation Framework for Spatiotemporal Population Genetics
Version: 1.5.0.9000
Authors@R: 
    person(given = "Martin",
           family = "Petr",
           role = c("aut", "cre"),
           email = "contact@bodkan.net",
           comment = c(ORCID = "0000-0003-4879-8421"))
Description: A framework for simulating spatially explicit genomic data
        which leverages real cartographic information for programmatic
        and visual encoding of spatiotemporal population dynamics on
        real geographic landscapes. Population genetic models are then
        automatically executed by the 'SLiM' software by Haller et al.
        (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a
        custom built-in simulation 'SLiM' script. Additionally, fully
        abstract spatial models not tied to a specific geographic
        location are supported, and users can also simulate data from
        standard, non-spatial, random-mating models. These can be
        simulated either with the 'SLiM' built-in back-end script, or
        using an efficient coalescent population genetics simulator
        'msprime' by Baumdicker et al. (2022)
        <doi:10.1093/genetics/iyab229> with a custom-built 'Python'
        script bundled with the R package. Simulated genomic data is
        saved in a tree-sequence format and can be loaded, manipulated,
        and summarised using tree-sequence functionality via an R
        interface to the 'Python' module 'tskit' by Kelleher et al.
        (2019) <doi:10.1038/s41588-019-0483-y>. Complete model
        configuration, simulation and analysis pipelines can be
        therefore constructed without a need to leave the R
        environment, eliminating friction between disparate tools for
        population genetic simulations and data analysis.
Depends: R (>= 3.6.0)
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
SystemRequirements: 'SLiM' is a forward simulation software for
        population genetics and evolutionary biology. See
        <https://messerlab.org/slim/> for installation instructions and
        further information. The 'Python' coalescent framework
        'msprime' and the 'tskit' module can by installed by following
        the instructions at <https://tskit.dev/>.
Imports: ggplot2, dplyr, purrr, readr, magrittr, reticulate, tidyr,
        png, ijtiff, ape, scales, digest, ggrepel
Suggests: testthat (>= 3.0.0), sf, stars, lwgeom, rnaturalearth,
        gganimate, knitr, rmarkdown, admixr, units, magick, cowplot,
        forcats, shinyWidgets, shiny, rsvg
VignetteBuilder: knitr
URL: https://github.com/bodkan/slendr
BugReports: https://github.com/bodkan/slendr/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libfftw3-dev make libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libtiff-dev libuv1-dev
        libwebp-dev libzstd-dev python3 libx11-dev zlib1g-dev
Repository: https://bodkan.r-universe.dev
Date/Publication: 2026-07-03 13:23:00 UTC
RemoteUrl: https://github.com/bodkan/slendr
RemoteRef: HEAD
RemoteSha: 91915ea414b2ac6ab7395205c1595e83abb3490f
NeedsCompilation: no
Packaged: 2026-07-03 13:36:34 UTC; root
Author: Martin Petr [aut, cre] (ORCID: <https://orcid.org/0000-0003-4879-8421>)
Maintainer: Martin Petr <contact@bodkan.net>