├── .Rbuildignore ├── .github ├── CONTRIBUTING.md ├── issue_template.md ├── pull_request_template.md └── workflows │ └── R-check.yml ├── .gitignore ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── aot.R ├── bladj.R ├── comdist.R ├── comstruct.R ├── comtrait.R ├── ecovolve.R ├── executables.R ├── pd.R ├── phylocomr-inputs.R ├── phylocomr-package.R ├── phylomatic.R ├── rao.R ├── write_tree_.R └── zzz.R ├── README.Rmd ├── README.md ├── codemeta.json ├── cran-comments.md ├── inst ├── AUTHORS ├── COPYRIGHT ├── WORDLIST └── examples │ ├── ages │ ├── phylo │ ├── phylo_aot │ ├── phylo_bladj │ ├── phylo_comstruct │ ├── sample_comstruct │ ├── taxa │ ├── traits_aot │ └── traits_aot_df ├── man-roxygen ├── com_args.R ├── com_null_models.R └── phylo.R ├── man ├── executables.Rd ├── figures │ └── unnamed-chunk-9-1.png ├── ph_aot.Rd ├── ph_bladj.Rd ├── ph_comdist.Rd ├── ph_comstruct.Rd ├── ph_comtrait.Rd ├── ph_ecovolve.Rd ├── ph_pd.Rd ├── ph_phylomatic.Rd ├── ph_rao.Rd ├── phylocomr-inputs.Rd └── phylocomr-package.Rd ├── phylocomr.Rproj ├── revdep ├── data.sqlite └── library.noindex │ └── phylocomr │ └── old │ └── phylocomr │ ├── AUTHORS │ ├── COPYRIGHT │ ├── DESCRIPTION │ ├── INDEX │ ├── LICENSE │ ├── Meta │ ├── Rd.rds │ ├── features.rds │ ├── hsearch.rds │ ├── links.rds │ ├── nsInfo.rds │ ├── package.rds │ └── vignette.rds │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ ├── phylocomr │ ├── phylocomr.rdb │ └── phylocomr.rdx │ ├── bin │ ├── ecovolve │ ├── phylocom │ └── phylomatic │ ├── doc │ ├── index.html │ ├── phylocomr.R │ ├── phylocomr.Rmd │ └── phylocomr.html │ ├── examples │ ├── ages │ ├── phylo │ ├── phylo_aot │ ├── phylo_bladj │ ├── phylo_comstruct │ ├── sample_comstruct │ ├── taxa │ ├── traits_aot │ └── traits_aot_df │ ├── help │ ├── AnIndex │ ├── aliases.rds │ ├── figures │ │ └── unnamed-chunk-9-1.png │ ├── paths.rds │ ├── phylocomr.rdb │ └── phylocomr.rdx │ ├── html │ ├── 00Index.html │ └── R.css │ └── libs │ └── 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