├── .Rbuildignore ├── .gitignore ├── .lintr ├── .travis.yml ├── Codecov.png ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── annotatedTreeReader.R ├── calc_act.R ├── calc_ess.R ├── calc_esses.R ├── drop_tip_write_annot_tree.R ├── is_posterior.R ├── is_trees_posterior.R ├── newCode.R ├── parse_beast_log.R ├── parse_beast_posterior.R ├── parse_beast_state.R ├── parse_beast_trees.R ├── plotStackedAreas.R ├── plot_glm.R ├── read_beast2_trees.R ├── remove_burn_in.R └── remove_burn_ins.R ├── RBeast.Rproj ├── README.md ├── TravisCI.png ├── inst ├── extdata │ ├── beast2_example_output.log │ ├── beast2_example_output.trees │ ├── beast2_example_output.xml │ ├── beast2_example_output.xml.state │ ├── beast_glm_example.log │ └── read_beast2_trees_example.trees └── java │ └── beast.jar ├── man ├── calc_act.Rd ├── calc_act_r.Rd ├── calc_ess.Rd ├── calc_esses.Rd ├── is_posterior.Rd ├── is_trees_posterior.Rd ├── parse_beast_log.Rd ├── parse_beast_posterior.Rd ├── parse_beast_state_operators.Rd ├── parse_beast_trees.Rd ├── plot_glm.Rd ├── plot_simple_glm.Rd ├── read_beast2_trees.Rd ├── remove_burn_in.Rd ├── remove_burn_ins.Rd └── runBeast.Rd ├── tests ├── testthat.R └── testthat │ ├── test-calc_act.R │ ├── test-calc_ess.R │ ├── test-calc_esses.R │ ├── test-is_posterior.R │ ├── test-is_trees_posterior.R │ ├── test-parse_beast_log.R │ ├── test-parse_beast_state_operators.R │ ├── test-parse_beast_trees.R │ ├── test-read_beast2_trees.R │ ├── test-remove_burn_in.R │ └── test-remove_burn_ins.R └── vignettes ├── GLM_plot.Rmd ├── demo_estimate_effective_sample_size.R ├── demo_estimate_effective_sample_size.Rmd ├── demo_estimate_effective_sample_size.html ├── profile_calc_act.R ├── profile_calc_act.Rmd ├── profile_calc_act.html ├── profile_calc_esses.R ├── profile_calc_esses.Rmd ├── profile_calc_esses.html ├── read_beast2_trees.R ├── read_beast2_trees.Rmd └── read_beast2_trees.html /.Rbuildignore: -------------------------------------------------------------------------------- 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