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: | 0.9.1 |
| 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: | 2024-02-21 |
| DOI: | 10.32614/CRAN.package.slendr |
| Author: | Martin Petr  [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:
Downloads:
| Package source: | slendr_0.9.1.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_0.9.1.tgz, r-oldrel (x86_64): slendr_0.9.1.tgz |
| Old sources: | slendr archive |
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