Package: slendr 0.9.1.9000

Martin Petr

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.

Authors:Martin Petr [aut, cre]

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Bug tracker:https://github.com/bodkan/slendr/issues

On CRAN:

popgenpopulation-geneticssimulationsspatial-statistics

67 exports 54 stars 3.71 score 82 dependencies 88 scripts 308 downloads

Last updated 8 days agofrom:4ac600cfa7. Checks:OK: 1 ERROR: 6. Indexed: yes.

Exports:%>%animate_modelareaas.phylo.slendr_phylocheck_dependenciescheck_envclear_envcompile_modeldistanceexpand_rangeexplore_modelextract_parametersgene_flowinit_envjoinmovemsprimeoverlapplot_mapplot_modelpopulationprint.slendr_tsread_modelregionreprojectresizeschedule_samplingset_dispersalset_rangesetup_envshrink_rangeslimsubstitute_valuessubtractts_afsts_ancestorsts_coalescedts_descendantsts_divergencets_diversityts_drawts_edgests_eigenstratts_f2ts_f3ts_f4ts_f4ratiots_fstts_genotypests_ibdts_loadts_metadatats_mutatets_namests_nodests_phylots_recapitatets_samplests_savets_segregatingts_simplifyts_tablets_tajimats_tractsts_treets_vcfworld

Dependencies:anytimeapebackportsbase64encBHbitbit64bslibcachemcheckmateclicliprcolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtableherehmshtmltoolshttpuvijtiffisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpngprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppTOMLreadrreticulaterlangrprojrootsassscalesshinyshinyWidgetssourcetoolsstrexstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxtablezeallot