├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── branch_length_calculations.R ├── general_utils.R ├── name_balances.R ├── philr.R ├── phylo2sbp.R ├── plot_utils.R └── weighted_ILR.R ├── README.md ├── docs ├── images │ ├── bg_hr.png │ ├── blacktocat.png │ ├── icon_download.png │ └── sprite_download.png ├── index.html ├── javascripts │ └── main.js ├── params.json └── stylesheets │ ├── github-light.css │ └── stylesheet.css ├── inst ├── CITATION └── NEWS ├── man ├── annotate_balance.Rd ├── buildilrBasep.Rd ├── calculate.blw.Rd ├── convert_to_long.Rd ├── g.colMeans.Rd ├── g.rowMeans.Rd ├── mean_dist_to_tips.Rd ├── miniclo.Rd ├── name.balance.Rd ├── name_nodenumber_conversion.Rd ├── named_rtree.Rd ├── philr.Rd ├── philrInv.Rd ├── phylo2sbp.Rd ├── shift.Rd ├── weighted_clr.Rd └── weighted_ilr.Rd ├── philr.Rproj ├── tests ├── testthat.R └── testthat │ ├── test-BLcalcs.R │ ├── test-general_utils.R │ ├── test-philr.R │ └── test-wilr.R └── vignettes ├── philr-intro.Rmd └── 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