Files in castor

Efficient Phylogenetics on Large Trees

R/simulate_neutral_gene_evolution.R R/RcppExports.R R/hsp_empirical_probabilities.R R/expanded_tree_from_jplace.r R/generate_tree_hbds.R R/extract_tip_radius.R R/tree_distance.R R/evaluate_spline.R R/loglikelihood_hbd.R R/model_adequacy_hbds.R R/hsp_max_parsimony.R R/get_pairwise_mrcas.R R/tree_from_sampling_branching_ages.R R/get_clade_list.R R/get_all_distances_to_root.R R/get_transition_index_matrix.R R/clade_densities.R R/get_independent_contrasts.R R/reorder_tree_edges.R R/fit_hbds_model_on_grid.R R/asr_subtree_averaging.R R/asr_max_parsimony.R R/geographic_acf.R R/fit_hbd_psr_parametric.R R/discrete_trait_depth.R R/consensus_taxonomies.R R/get_transition_matrix_from_rate_vector.R R/fit_hbd_pdr_on_best_grid_size.R R/simulate_dsse.R R/map_to_state_space.R R/asr_squared_change_parsimony.R R/fit_sbm_trend.R R/asr_independent_contrasts.R R/get_independent_sister_tips.R R/hsp_mk_model.R R/hsp_nearest_neighbor.R R/fit_hbd_model_on_grid.R R/hsp_binomial.R R/asr_mk_model.R R/fit_sbm_const.R R/fit_sbm_geobiased_const.R R/model_adequacy_hbd.R R/get_stationary_distribution.R R/fit_hbds_model_parametric.R R/get_random_mk_transition_matrix.R R/simulate_deterministic_hbd.R R/reconstruct_past_diversification.R R/fit_and_compare_sbm_const.R R/get_all_node_depths.R R/get_mrca_of_set.R R/fit_sbm_on_grid.R R/get_all_pairwise_distances.R R/simulate_musse.R R/get_all_distances_to_tip.R R/extract_fasttree_constraints.R R/spline_coefficients.R R/root_via_rtt.R R/get_tree_traversal_root_to_tips.R R/simulate_deterministic_hbds.R R/root_via_outgroup.R R/fit_sbm_linear.R R/fit_symmetric_mk.R R/fit_hbd_pdr_parametric.R R/consentrait_depth.R R/fit_hbd_pdr_on_grid.R R/tree_imbalance.R R/split_tree_at_height.R R/hsp_subtree_averaging.R R/simulate_ou_model.R R/count_transitions_between_clades.R R/simulate_mk_model.R R/extend_tree_to_height.R R/fit_musse.R R/extract_deep_frame.R R/generate_gene_tree_msc_hgt_dl.R R/fit_tree_model.R R/count_tips_per_node.R R/generate_random_tree.R R/correlate_phylo_geodistances.R R/get_tips_for_mrcas.R R/asr_empirical_probabilities.R R/read_tree.R R/root_at_midpoint.R R/simulate_diversification_model.R R/auxiliary_routines.R R/generate_tree_with_evolving_rates.R R/write_tree.R R/gamma_statistic.R R/forest_distance.R R/exponentiate_matrix.R R/root_in_edge.R R/fit_hbd_model_parametric.R R/trim_tree_at_height.R R/fit_bm_model.R R/is_monophyletic.R R/fit_sbm_parametric.R R/is_bifurcating.R R/collapse_tree_at_resolution.R R/tree_from_branching_ages.R R/fit_and_compare_bm_models.R R/find_root_of_monophyletic_tips.R R/find_nearest_tips.R R/get_subtree_at_node.R R/shift_clade_times.R R/join_rooted_trees.R R/fit_hbd_psr_on_best_grid_size.R R/simulate_rou_model.R R/pick_random_tips.R R/find_farthest_tips.R R/fit_mk.R R/simulate_tdsse.R R/date_tree_red.R R/find_root.R R/collapse_monofurcations.R R/get_ancestral_nodes.R R/mean_abs_change_scalar_ou.R R/extract_tip_neighborhood.R R/get_random_diffusivity_matrix.R R/get_tree_span.R R/multifurcations_to_bifurcations.R R/tree_from_taxa.R R/get_subtrees_at_nodes.R R/expected_distances_sbm.R R/fit_hbd_psr_on_grid.R R/get_reds.R R/fit_sbm_const_biased_sampling_unfinished.R R/get_trait_acf.R R/simulate_sbm.R R/biom.R R/root_at_node.R R/count_lineages_through_time.R R/get_subtree_with_tips.R R/get_pairwise_distances.R R/hsp_independent_contrasts.R R/merge_nodes_to_multifurcations.R R/simulate_bm_model.R R/congruent_divergence_times.R R/get_trait_stats_over_time.R R/generate_tree_hbd_reverse.R R/place_tips_taxonomically.R R/hsp_squared_change_parsimony.R R/merge_short_edges.R R/simulate_deterministic_hbd_msc.R R/generate_gene_tree_msc.R R/find_farthest_tip_pair.R R/congruent_hbds_model.R man/asr_max_parsimony.Rd man/fit_hbds_model_parametric.Rd man/fit_sbm_const.Rd man/get_trait_stats_over_time.Rd man/fit_sbm_linear.Rd man/consensus_taxonomies.Rd man/simulate_bm_model.Rd man/simulate_rou_model.Rd man/fit_hbd_psr_on_grid.Rd man/generate_gene_tree_msc_hgt_dl.Rd man/get_transition_index_matrix.Rd man/generate_tree_with_evolving_rates.Rd man/asr_mk_model.Rd man/mean_abs_change_scalar_ou.Rd man/get_all_distances_to_tip.Rd man/fit_hbd_psr_parametric.Rd man/get_tree_traversal_root_to_tips.Rd man/fit_sbm_geobiased_const.Rd man/geographic_acf.Rd man/root_in_edge.Rd man/find_root_of_monophyletic_tips.Rd man/consentrait_depth.Rd man/get_independent_sister_tips.Rd man/get_reds.Rd man/get_all_distances_to_root.Rd man/simulate_deterministic_hbds.Rd man/count_transitions_between_clades.Rd man/reorder_tree_edges.Rd man/asr_squared_change_parsimony.Rd man/merge_short_edges.Rd man/tree_from_sampling_branching_ages.Rd man/extract_deep_frame.Rd man/fit_hbd_pdr_parametric.Rd man/simulate_tdsse.Rd man/find_farthest_tip_pair.Rd man/generate_random_tree.Rd man/extract_tip_neighborhood.Rd man/generate_tree_hbd_reverse.Rd man/is_bifurcating.Rd man/get_tree_span.Rd man/get_random_diffusivity_matrix.Rd man/get_subtree_with_tips.Rd man/simulate_dsse.Rd man/simulate_mk_model.Rd man/fit_hbd_psr_on_best_grid_size.Rd man/loglikelihood_hbd.Rd man/fit_and_compare_bm_models.Rd man/count_lineages_through_time.Rd man/hsp_squared_change_parsimony.Rd man/count_tips_per_node.Rd man/join_rooted_trees.Rd man/get_subtrees_at_nodes.Rd man/generate_gene_tree_msc.Rd man/simulate_diversification_model.Rd man/map_to_state_space.Rd man/clade_densities.Rd man/extract_fasttree_constraints.Rd man/root_via_rtt.Rd man/fit_and_compare_sbm_const.Rd man/date_tree_red.Rd man/hsp_binomial.Rd man/find_farthest_tips.Rd man/shift_clade_times.Rd man/fit_bm_model.Rd man/find_nearest_tips.Rd man/tree_from_branching_ages.Rd man/merge_nodes_to_multifurcations.Rd man/reconstruct_past_diversification.Rd man/read_tree.Rd man/fit_hbds_model_on_grid.Rd man/get_independent_contrasts.Rd man/correlate_phylo_geodistances.Rd man/root_at_midpoint.Rd man/simulate_ou_model.Rd man/model_adequacy_hbds.Rd man/root_at_node.Rd man/split_tree_at_height.Rd man/is_monophyletic.Rd man/evaluate_spline.Rd man/fit_hbd_pdr_on_best_grid_size.Rd man/congruent_divergence_times.Rd man/castor.Rd man/hsp_empirical_probabilities.Rd man/hsp_mk_model.Rd man/collapse_tree_at_resolution.Rd man/exponentiate_matrix.Rd man/extract_tip_radius.Rd man/tree_imbalance.Rd man/asr_independent_contrasts.Rd man/hsp_subtree_averaging.Rd man/fit_musse.Rd man/expanded_tree_from_jplace.Rd man/get_mrca_of_set.Rd man/gamma_statistic.Rd man/hsp_max_parsimony.Rd man/get_all_node_depths.Rd man/generate_tree_hbds.Rd man/extend_tree_to_height.Rd man/asr_empirical_probabilities.Rd man/get_all_pairwise_distances.Rd man/simulate_sbm.Rd man/get_subtree_at_node.Rd man/get_trait_acf.Rd man/get_clade_list.Rd man/write_tree.Rd man/get_tips_for_mrcas.Rd man/get_random_mk_transition_matrix.Rd man/fit_hbd_pdr_on_grid.Rd man/fit_hbd_model_on_grid.Rd man/trim_tree_at_height.Rd man/simulate_deterministic_hbd.Rd man/fit_hbd_model_parametric.Rd man/model_adequacy_hbd.Rd man/asr_subtree_averaging.Rd man/collapse_monofurcations.Rd man/multifurcations_to_bifurcations.Rd man/pick_random_tips.Rd man/get_stationary_distribution.Rd man/fit_sbm_on_grid.Rd man/get_pairwise_distances.Rd man/fit_mk.Rd man/fit_tree_model.Rd man/congruent_hbds_model.Rd man/tree_distance.Rd man/root_via_outgroup.Rd man/tree_from_taxa.Rd man/fit_sbm_parametric.Rd man/expected_distances_sbm.Rd man/find_root.Rd man/hsp_independent_contrasts.Rd man/get_pairwise_mrcas.Rd man/place_tips_taxonomically.Rd man/get_ancestral_nodes.Rd man/hsp_nearest_neighbor.Rd man/discrete_trait_depth.Rd man/spline_coefficients.Rd