├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── admix_label_cols.R ├── admix_reorder_cols.R ├── avg_kinship_subpops.R ├── fst.R ├── get_mem_lim.R ├── hgdp_subset.R ├── inbr.R ├── inbr_diag.R ├── mean_kinship.R ├── n_eff.R ├── n_eff_max_gradient.R ├── n_eff_max_heuristic.R ├── n_eff_max_newton.R ├── phylo_max_edge.R ├── plot_admix.R ├── plot_phylo.R ├── plot_popkin.R ├── popkin-package.R ├── popkin.R ├── popkin_A.R ├── popkin_A_min_subpops.R ├── popkin_af.R ├── pwfst.R ├── rescale_popkin.R ├── solve_m_mem_lim.R ├── validate_kinship.R └── weights_subpops.R ├── README.md ├── cran-comments.md ├── data └── hgdp_subset.rda ├── inst └── CITATION ├── man ├── admix_label_cols.Rd ├── admix_order_cols.Rd ├── avg_kinship_subpops.Rd ├── figures │ └── logo.png ├── fst.Rd ├── hgdp_subset.Rd ├── inbr.Rd ├── inbr_diag.Rd ├── mean_kinship.Rd ├── n_eff.Rd ├── plot_admix.Rd ├── plot_phylo.Rd ├── plot_popkin.Rd ├── popkin-package.Rd ├── popkin.Rd ├── popkin_A.Rd ├── popkin_A_min_subpops.Rd ├── popkin_af.Rd ├── pwfst.Rd ├── rescale_popkin.Rd ├── validate_kinship.Rd └── weights_subpops.Rd ├── tests ├── testthat.R └── testthat │ ├── Xs.RData │ ├── Xs.bed │ ├── Xs.bim │ ├── Xs.fam │ ├── make_data.R │ ├── test_popkin_BEDMatrix.R │ ├── test_popkin_af.R │ ├── test_popkin_fn.R │ ├── test_popkin_plot.R │ ├── test_popkin_precalc.R │ └── test_popkin_random.R └── vignettes ├── popkin.Rmd └── popkin.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/StoreyLab/popkin/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/StoreyLab/popkin/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: 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