Files in TheoPannetier/comrad
R implementation of a Competitive Radiation model
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/test-coverage.yaml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/RcppExports.R
R/apply_mutations.R
R/apply_speciation.R
R/build_spp_tbl.R
R/check_dd_model_is_avail.R
R/dd_loglik_func.R
R/dd_model_lc.R
R/dd_model_ll.R
R/dd_model_lp.R
R/dd_model_lx.R
R/dd_model_pc.R
R/dd_model_pl.R
R/dd_model_pp.R
R/dd_model_px.R
R/dd_model_xc.R
R/dd_model_xl.R
R/dd_model_xp.R
R/dd_model_xx.R
R/dd_models.R
R/ddd_imports.R
R/default_params_doc.R
R/default_pars.R
R/draw_comm_next_gen.R
R/draw_init_params_dd_ml.R
R/exclude_ephemeral_spp.R
R/fit_dd_model_with_fossil.R
R/fit_dd_model_without_fossil.R
R/fitness_functions.R
R/get_carrying_cap.R
R/get_comp_coeff_comm.R
R/get_dnltt.R
R/get_edge_tbl.R
R/get_fitness.R
R/get_fitness_landscape.R
R/get_ltt_tbl.R
R/get_root_age.R
R/has_brute_force_opt.R
R/interpolate_ltt.R
R/ltt_tbl_to_func.R
R/plot_aicw_pie.R
R/plot_comm_bubbles.R
R/plot_comm_size.R
R/plot_comm_trait_evolution.R
R/plot_comm_traits.R
R/plot_comm_traits_anim.R
R/plot_compare_dd_functions.R
R/plot_fitness_landscape.R
R/plot_fitness_landscape_evolution.R
R/plot_trait_disparity.R
R/rand_comm.R
R/rates_from_dd_model.R
R/rates_from_exp_dist.R
R/read_comrad_tbl.R
R/run_simulation.R
R/set_sampling_freq.R
R/sim_to_phylo.R
R/simulate_dd_phylo.R
R/stem_or_crown.R
R/summarise_aicw_over_trees.R
R/summarise_waiting_times.R
R/utils-pipe.R
R/utils-rcpp_dummy.R
R/utils-testargs.R
R/waiting_times.R
R/write_newick_str.R
README.md
codecov.yml
comrad.Rproj
man/apply_mutations.Rd
man/apply_speciation.Rd
man/build_spp_tbl.Rd
man/check_dd_model_is_avail.Rd
man/dd_func_colours.Rd
man/dd_func_names.Rd
man/dd_loglik_func.Rd
man/dd_model_colours.Rd
man/dd_model_comrad_to_ddd.Rd
man/dd_model_lc.Rd
man/dd_model_ll.Rd
man/dd_model_lp.Rd
man/dd_model_lx.Rd
man/dd_model_names.Rd
man/dd_model_pc.Rd
man/dd_model_pl.Rd
man/dd_model_pp.Rd
man/dd_model_px.Rd
man/dd_model_to_extinction_func.Rd
man/dd_model_to_speciation_func.Rd
man/dd_model_xc.Rd
man/dd_model_xl.Rd
man/dd_model_xp.Rd
man/dd_model_xx.Rd
man/dd_models.Rd
man/ddd_optimizer.Rd
man/default_params_doc.Rd
man/default_pars.Rd
man/draw_comm_next_gen.Rd
man/draw_init_params_dd_ml.Rd
man/draw_nb_offspring.Rd
man/exclude_ephemeral_spp.Rd
man/find_trait_gaps.Rd
man/fit_dd_model_with_fossil.Rd
man/fit_dd_model_without_fossil.Rd
man/fitness_func.Rd
man/get_carrying_cap.Rd
man/get_comp_coeff_comm.Rd
man/get_dnltt.Rd
man/get_edge_tbl.Rd
man/get_fitness.Rd
man/get_fitness_landscape.Rd
man/get_ltt_tbl.Rd
man/get_n_eff.Rd
man/get_root_age.Rd
man/has_brute_force_opt.Rd
man/interpolate_ltt.Rd
man/ltt_tbl_to_func.Rd
man/pipe.Rd
man/plot_aicw_pie.Rd
man/plot_comm_bubbles.Rd
man/plot_comm_size.Rd
man/plot_comm_trait_evolution.Rd
man/plot_comm_traits.Rd
man/plot_comm_traits_anim.Rd
man/plot_compare_dd_functions.Rd
man/plot_dd_func_colours.Rd
man/plot_dd_model_colours.Rd
man/plot_fitness_landscape.Rd
man/plot_fitness_landscape_evol.Rd
man/plot_trait_disparity.Rd
man/rand_comm.Rd
man/rates_from_dd_model.Rd
man/rates_from_exp_dist.Rd
man/read_comrad_tbl.Rd
man/run_simulation.Rd
man/set_sampling_freq.Rd
man/sim_to_phylo.Rd
man/simulate_dd_phylo.Rd
man/sort_by_ref.Rd
man/stem_or_crown.Rd
man/summarise_aicw_over_trees.Rd
man/summarise_waiting_times.Rd
man/testargs.Rd
man/transform_pars.Rd
man/untransform_pars.Rd
man/waiting_times.Rd
man/write_newick_str.Rd
pics/Codecov.png
pics/fig_readme_01.png
pics/github_actions_logo.png
src/.gitignore
src/RcppExports.cpp
src/draw_nb_offspring.cpp
src/find_trait_gaps.cpp
src/get_n_eff.cpp
tests/testthat.R
tests/testthat/test-apply_speciation.R
tests/testthat/test-find_traits_gap.R
tests/testthat/test-fit_dd_model.R
tests/testthat/test-get-comp_coeff_comm.R
tests/testthat/test-get_carr_cap.R
tests/testthat/test-get_fitness.R
tests/testthat/test-get_n_eff.R
tests/testthat/test-phylo_builds.R
tests/testthat/test-run_simulation.R
tests/testthat/test-run_simulation_output.R
tests/testthat/test-utils_plots.R
vignettes/demo.R
vignettes/demo.Rmd
vignettes/demo.html
vignettes/demo_data/comrad_output_example.csv
