slendr: A Simulation Framework for Spatiotemporal Population Genetics

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.

Version: 1.0.0
Depends: R (≥ 3.6.0)
Imports: ggplot2, dplyr, purrr, readr, magrittr, reticulate, tidyr, png, ijtiff, ape, shinyWidgets, shiny, scales, digest
Suggests: testthat (≥ 3.0.0), sf, stars, rnaturalearth, gganimate, knitr, rmarkdown, admixr, units, magick, cowplot, forcats, rsvg
Published: 2024-11-22
DOI: 10.32614/CRAN.package.slendr
Author: Martin Petr ORCID iD [aut, cre]
Maintainer: Martin Petr <contact at bodkan.net>
BugReports: https://github.com/bodkan/slendr/issues
License: MIT + file LICENSE
URL: https://github.com/bodkan/slendr
NeedsCompilation: no
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/>.
Materials: README NEWS
CRAN checks: slendr results

Documentation:

Reference manual: slendr.pdf
Vignettes: Installation instructions (source)
Introduction and basic tutorial (source, R code)
Demes on a regular spatial grid (source, R code)
Programming dispersion dynamics (source, R code)
Traditional, non-spatial models (source, R code)
Tree-sequence processing and statistics (source, R code)
Spatially annotated tree sequences (source, R code)
Simulations using SLiM and msprime engines (source, R code)
Analyzing non-slendr tree sequences (source, R code)
Extracting true ancestry tracts (source, R code)
Extending models with custom SLiM code (source, R code)

Downloads:

Package source: slendr_1.0.0.tar.gz
Windows binaries: r-devel: slendr_0.9.1.zip, r-release: slendr_0.9.1.zip, r-oldrel: slendr_0.9.1.zip
macOS binaries: r-release (arm64): slendr_0.9.1.tgz, r-oldrel (arm64): slendr_0.9.1.tgz, r-release (x86_64): slendr_1.0.0.tgz, r-oldrel (x86_64): slendr_0.9.1.tgz
Old sources: slendr archive

Linking:

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