Files in castor
Efficient Phylogenetics on Large Trees
MD5
NAMESPACE
DESCRIPTION
R/simulate_neutral_gene_evolution.R
R/RcppExports.R
R/hsp_empirical_probabilities.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/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/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/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/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
src/registerDynamicSymbol.c
src/phylogenetics_cpp_routines.cpp
src/RcppExports.cpp
src/STMathExpression.cpp
src/STMathExpression.h
inst/CITATION
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/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/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/fit_sbm_parametric.Rd
man/expected_distances_sbm.Rd
man/find_root.Rd
man/hsp_independent_contrasts.Rd
man/get_pairwise_mrcas.Rd
man/get_ancestral_nodes.Rd
man/hsp_nearest_neighbor.Rd
man/discrete_trait_depth.Rd
man/spline_coefficients.Rd
