Files in bodkan/slendr
A Simulation Framework for Spatiotemporal Population Genetics

.Rbuildignore
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DESCRIPTION
LICENSE
LICENSE.md
Makefile
NAMESPACE
NEWS.md R/compilation.R R/extensions.R R/extract_parameters.R R/geometry.R R/interface.R R/msprime.R R/print.R R/shiny.R R/slendr-package.R R/slim.R R/tree-sequences.R R/tspop.R R/utils.R R/visualization.R R/zzz.R README.Rmd README.md
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generate_examples.R
inst/extdata/extension_introgression.txt
inst/extdata/extension_purifying.txt
inst/extdata/extension_sweep.txt
inst/extdata/extension_trajectory.txt
inst/extdata/extension_trajectory_params.txt
inst/extdata/models/introgression/checksums.tsv
inst/extdata/models/introgression/description.txt
inst/extdata/models/introgression/direction.txt
inst/extdata/models/introgression/geneflow.tsv
inst/extdata/models/introgression/generation_time.txt
inst/extdata/models/introgression/length.txt
inst/extdata/models/introgression/orig_length.txt
inst/extdata/models/introgression/populations.tsv
inst/extdata/models/introgression/ranges.rds
inst/extdata/models/introgression/script.py
inst/extdata/models/introgression/script.slim
inst/extdata/models/introgression/time_units.txt
inst/extdata/models/introgression_msprime.trees
inst/extdata/models/introgression_slim.trees
inst/extdata/models/msprime.trees
inst/naturalearth/ne_110m_land.zip
inst/pylib/pylib.py
inst/scripts/script.py
inst/scripts/script.slim
logo.R man/animate_model.Rd man/area.Rd man/as.phylo.slendr_phylo.Rd man/check_dependencies.Rd man/check_env.Rd man/clear_env.Rd man/compile_model.Rd man/distance.Rd man/examples/model_definition.R man/examples/spatial_functions.R man/expand_range.Rd man/explore_model.Rd man/extract_parameters.Rd
man/figures/README-plot_gif-1.gif
man/figures/README-plot_gif-1.png
man/figures/README-plot_popmaps-1.png
man/figures/README-plot_regions-1.png
man/figures/README-plot_world-1.png
man/figures/logo.png
man/figures/shiny_graph.jpg
man/figures/shiny_maps.jpg
man/gene_flow.Rd man/get_env.Rd man/init_env.Rd man/join.Rd man/move.Rd man/msprime.Rd man/overlap.Rd man/pipe.Rd man/plot_map.Rd man/plot_model.Rd man/population.Rd man/print.slendr_pop.Rd man/print.slendr_ts.Rd man/read_model.Rd man/region.Rd man/reproject.Rd man/resize.Rd man/schedule_sampling.Rd man/set_dispersal.Rd man/set_range.Rd man/setup_env.Rd man/shrink_range.Rd man/slendr.Rd man/slim.Rd man/substitute_values.Rd man/subtract.Rd man/summary.slendr_nodes.Rd man/ts_afs.Rd man/ts_ancestors.Rd man/ts_coalesced.Rd man/ts_descendants.Rd man/ts_divergence.Rd man/ts_diversity.Rd man/ts_draw.Rd man/ts_edges.Rd man/ts_eigenstrat.Rd man/ts_f4ratio.Rd man/ts_fst.Rd man/ts_genotypes.Rd man/ts_ibd.Rd man/ts_load.Rd man/ts_metadata.Rd man/ts_mutate.Rd man/ts_names.Rd man/ts_nodes.Rd man/ts_phylo.Rd man/ts_read.Rd man/ts_recapitate.Rd man/ts_samples.Rd man/ts_save.Rd man/ts_segregating.Rd man/ts_simplify.Rd man/ts_table.Rd man/ts_tajima.Rd man/ts_tracts.Rd man/ts_tree.Rd man/ts_vcf.Rd man/ts_write.Rd man/world.Rd
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pkgdown/favicon/favicon-16x16.png
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pkgdown/favicon/favicon.ico
slendr.Rproj
tests/testthat.R
tests/testthat/afs_Darwin.png
tests/testthat/afs_Darwin.tsv.gz
tests/testthat/afs_Linux.png
tests/testthat/afs_Linux.tsv.gz
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tests/testthat/f4ratio_Windows.tsv.gz
tests/testthat/helper-functions.R
tests/testthat/manual_ts_nodes+edges+inds+pops+muts.py
tests/testthat/manual_ts_nodes+edges+inds+pops.py
tests/testthat/manual_ts_nodes+edges+inds.py
tests/testthat/manual_ts_nodes+edges.py
tests/testthat/map.rds
tests/testthat/test-abstract-vs-real-landscapes.R tests/testthat/test-compilation.R tests/testthat/test-coordinate-conversions.R tests/testthat/test-dynamics.R tests/testthat/test-engines.R tests/testthat/test-extensions.R tests/testthat/test-future.R tests/testthat/test-geneflow.R tests/testthat/test-geometrical-operations.R tests/testthat/test-ibd-squashing.R tests/testthat/test-ibd.R tests/testthat/test-interaction-changes.R tests/testthat/test-interactive-elements.R tests/testthat/test-manual-ts.R tests/testthat/test-msprime-geneflow.R tests/testthat/test-msprime-metadata.R tests/testthat/test-msprime.R tests/testthat/test-naturalearth.R tests/testthat/test-nonserialized.R tests/testthat/test-population.R tests/testthat/test-pure-msprime-vs-slendr.R tests/testthat/test-pure-slim-vs-slendr.R tests/testthat/test-resizes-locked.R tests/testthat/test-resizes.R tests/testthat/test-runners.R tests/testthat/test-sampling.R tests/testthat/test-serialization.R tests/testthat/test-simulation-runs.R tests/testthat/test-time-direction.R tests/testthat/test-trees.R tests/testthat/test-ts-ancestors-descendants.R tests/testthat/test-ts-pure-nonspatial.R tests/testthat/test-ts-pure-spatial.R tests/testthat/test-ts.R tests/testthat/test-tspop.R tests/testthat/test-utililites.R
ubuntu_deps.txt
vignettes/.gitignore
vignettes/images/demographic_models.jpg
vignettes/images/f4_tree.jpg
vignettes/images/geneflow_graph.jpg
vignettes/images/haak_map.jpg
vignettes/images/original_ex4.png
vignettes/images/shiny_graph.jpg
vignettes/images/shiny_maps.jpg
vignettes/vignette-00-installation.Rmd vignettes/vignette-01-tutorial.Rmd vignettes/vignette-02-grid-model.Rmd vignettes/vignette-03-interactions.Rmd vignettes/vignette-04-nonspatial-models.Rmd vignettes/vignette-05-tree-sequences.Rmd vignettes/vignette-06-locations.Rmd vignettes/vignette-07-engines.Rmd vignettes/vignette-08-nonslendr-tskit.Rmd vignettes/vignette-09-paper.Rmd vignettes/vignette-10-tracts.Rmd vignettes/vignette-11-extensions.Rmd
bodkan/slendr documentation built on Dec. 19, 2024, 11:41 p.m.