{ "_id": "6a12a54bacfb0bcc41d136cb", "Package": "slendr", "Title": "A Simulation Framework for Spatiotemporal Population Genetics", "Version": "1.4.0.9000", "Authors@R": "person(given = \"Martin\",\nfamily = \"Petr\",\nrole = c(\"aut\", \"cre\"),\nemail = \"contact@bodkan.net\",\ncomment = c(ORCID = \"0000-0003-4879-8421\"))", "Description": "A framework for simulating spatially explicit genomic data\nwhich leverages real cartographic information for programmatic\nand visual encoding of spatiotemporal population dynamics on\nreal geographic landscapes. Population genetic models are then\nautomatically executed by the 'SLiM' software by Haller et al.\n(2019) behind the scenes, using a\ncustom built-in simulation 'SLiM' script. Additionally, fully\nabstract spatial models not tied to a specific geographic\nlocation are supported, and users can also simulate data from\nstandard, non-spatial, random-mating models. These can be\nsimulated either with the 'SLiM' built-in back-end script, or\nusing an efficient coalescent population genetics simulator\n'msprime' by Baumdicker et al. (2022)\n with a custom-built 'Python'\nscript bundled with the R package. Simulated genomic data is\nsaved in a tree-sequence format and can be loaded, manipulated,\nand summarised using tree-sequence functionality via an R\ninterface to the 'Python' module 'tskit' by Kelleher et al.\n(2019) . Complete model\nconfiguration, simulation and analysis pipelines can be\ntherefore constructed without a need to leave the R\nenvironment, eliminating friction between disparate tools for\npopulation genetic simulations and data analysis.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "SystemRequirements": "'SLiM' is a forward simulation software for\npopulation genetics and evolutionary biology. See\n for installation instructions and\nfurther information. The 'Python' coalescent framework\n'msprime' and the 'tskit' module can by installed by following\nthe instructions at .", "VignetteBuilder": "knitr", "URL": "https://github.com/bodkan/slendr", "BugReports": "https://github.com/bodkan/slendr/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake libfftw3-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libtiff-dev libuv1-dev\nlibwebp-dev libzstd-dev python3 libx11-dev zlib1g-dev", "Repository": "https://bodkan.r-universe.dev", "Date/Publication": "2026-04-24 20:40:33 UTC", "RemoteUrl": "https://github.com/bodkan/slendr", "RemoteRef": "HEAD", "RemoteSha": "9955e6c4599fdbbc53a11f7c3796b54c9b7fef28", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 07:05:21 UTC", "User": "root" }, "Author": "Martin Petr [aut, cre] (ORCID: )", "Maintainer": "Martin Petr ", "MD5sum": "af29496c2faf5999b1cebbf16d44ff76", "_user": "bodkan", "_type": "src", "_file": "slendr_1.4.0.9000.tar.gz", "_fileid": 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"vignette-06-locations.html", "title": "Spatially annotated tree sequences", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Model specification", "Scheduling sampling events and simulation", "Extracting spatial tree sequence information", "Using the simple features interface", "Plotting locations of simulated sampled individuals", "Extracting spatio-temporal ancestral relationships", "Calculating distances and other statistics using the sf package" ], "created": "2021-08-03 22:58:57", "modified": "2026-01-15 09:36:40", "commits": 57 }, { "source": "vignette-08-nonslendr-tskit.Rmd", "filename": "vignette-08-nonslendr-tskit.html", "title": "Standard SLiM and msprime tree sequences", "engine": "knitr::rmarkdown", "headings": [ "SLiM tree sequences", "msprime tree sequences", "Spatial SLiM tree sequences", "Conclusion" ], "created": "2022-06-22 14:55:51", "modified": "2026-01-15 21:32:07", "commits": 35 }, { "source": "vignette-04-nonspatial-models.Rmd", "filename": "vignette-04-nonspatial-models.html", "title": "Traditional, non-spatial models", "engine": "knitr::rmarkdown", "headings": [ "Extracting parameters from a model or tree sequences", "Named samples" ], "created": "2021-07-16 18:57:58", "modified": "2026-01-15 21:32:07", "commits": 45 }, { "source": "vignette-05-tree-sequences.Rmd", "filename": "vignette-05-tree-sequences.html", "title": "Tree-sequence processing and statistics", "engine": "knitr::rmarkdown", "headings": [ "Setting up Python environment", "Model of Neanderthal introgression into Eurasians", "Scheduling of sampling events", "Named samples", "R interface for tskit and pyslim", "Loading and processing tree-sequence output files", "Visualisation of trees and tree-sequences", "Accessing tskit functionality directly", "Calculating f-statistics", "Estimating Neanderthal ancestry proportions", "ADMIXTOOLS analyses", "VCF output", "Other statistics", "$F_{st}$", "Tajima's $D$", "Diversity", "Divergence", "More information" ], 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