API for castor
Efficient Phylogenetics on Large Trees

Global functions
ASR_via_independent_contrasts_CPP Source code
ASR_via_squared_change_parsimony_CPP Source code
ASR_with_fixed_rates_Markov_model_CPP Source code
WMPR_ASR_CPP Source code
apply_BM_parsimony_to_missing_clades_CPP Source code
apply_MPR_to_missing_clades_CPP Source code
apply_fixed_rate_Markov_model_to_missing_clades_CPP Source code
asr_empirical_probabilities Man page Source code
asr_independent_contrasts Man page Source code
asr_max_parsimony Man page Source code
asr_mk_model Man page Source code
asr_squared_change_parsimony Man page Source code
autocorrelation_function_of_continuous_trait_CPP Source code
back Source code
castor Man page
castor-package Man page
collapse_monofurcations Man page Source code
collapse_tree_at_resolution Man page Source code
collapse_tree_at_resolution_CPP Source code
count_clades_at_regular_times_CPP Source code
count_clades_at_times_CPP Source code
count_clades_over_time Man page Source code
count_tips_per_node Man page Source code
date_tree_PL Source code
dense_binary_matrix_row2column_major_CPP Source code
exponentiate_matrix Man page Source code
exponentiate_matrix_for_multiple_scalings_CPP Source code
extend_tree_to_height Man page Source code
extend_tree_to_height_CPP Source code
fill_gaps_in_integer_state_list Source code
find_edge_splitting_tree Source code
find_edge_splitting_tree_CPP Source code
find_farthest_tips Man page Source code
find_nearest_tips Man page Source code
find_root Man page Source code
find_root_for_monophyletic_clade_CPP Source code
find_root_of_monophyletic_tips Man page Source code
first_derivative Source code
fit_bm_model Man page Source code
fit_tree_model Man page Source code
generate_random_tree Man page Source code
generate_random_tree_BM_rates_CPP Source code
generate_random_tree_CPP Source code
generate_tree_with_evolving_rates Man page Source code
get_adjacent_edges_per_edge Source code
get_adjacent_edges_per_edge_CPP Source code
get_all_distances_to_root Man page Source code
get_all_node_depths Man page Source code
get_closest_tip_per_clade_CPP Source code
get_conditional_transition_probabilities Source code
get_distance_matrix_between_clades_CPP Source code
get_distances_between_clades_CPP Source code
get_distances_from_root_CPP Source code
get_diversities_from_birth_and_death_events_CPP Source code
get_empirical_state_frequencies_per_node Source code
get_farthest_tip_per_clade_CPP Source code
get_incoming_edges_per_clade Source code
get_incoming_edges_per_clade_CPP Source code
get_independent_contrasts Man page Source code
get_mean_depth_per_node_CPP Source code
get_min_max_tip_distance_from_root_CPP Source code
get_most_recent_common_ancestor_CPP Source code
get_most_recent_common_ancestors_CPP Source code
get_mrca_defining_tips_CPP Source code
get_mrca_of_set Man page Source code
get_outgoing_edges_per_clade Source code
get_outgoing_edges_per_clade_CPP Source code
get_pairwise_ancestries_CPP Source code
get_pairwise_distances Man page Source code
get_pairwise_mrcas Man page Source code
get_paths_root_to_tips Source code
get_paths_root_to_tips_CPP Source code
get_phylogenetic_independent_contrasts_CPP Source code
get_random_diffusivity_matrix Man page Source code
get_random_mk_transition_matrix Man page Source code
get_root_clade_CPP Source code
get_speciation_extinction_events_CPP Source code
get_stationary_distribution Man page Source code
get_subtree_at_node Man page Source code
get_subtree_at_node_CPP Source code
get_subtree_with_specific_clades_CPP Source code
get_subtree_with_specific_tips_CPP Source code
get_subtree_with_tips Man page Source code
get_tips_for_mrcas Man page Source code
get_total_tip_count_per_node_CPP Source code
get_trait_acf Man page Source code
get_trait_depth Man page Source code
get_trait_depth_consenTRAIT_CPP Source code
get_trait_richness_collectors_curve_CPP Source code
get_trait_stats_at_times_CPP Source code
get_trait_stats_over_time Man page Source code
get_transition_index_matrix Source code
get_transition_matrix_from_rate_vector Source code
get_tree_span Man page Source code
get_tree_traversal_root_to_tips Man page Source code
get_tree_traversal_root_to_tips_CPP Source code
get_tree_with_collapsed_monofurcations_CPP Source code
hsp_empirical_probabilities Man page Source code
hsp_independent_contrasts Man page Source code
hsp_max_parsimony Man page Source code
hsp_mk_model Man page Source code
hsp_squared_change_parsimony Man page Source code
is_monophyletic Man page Source code
is_monophyletic_tip_set_CPP Source code
map_tip_or_node_names_to_indices Source code
map_to_state_space Man page Source code
merge_short_edges Man page Source code
merge_short_edges_CPP Source code
multifurcations_to_bifurcations Man page Source code
multifurcations_to_bifurcations_CPP Source code
pick_random_tips Man page Source code
pick_random_tips_CPP Source code
propagate_max_ages_downstream_CPP Source code
propagate_min_ages_upstream_CPP Source code
reconstruct_past_diversification Man page Source code
reconstruct_past_diversifications_CPP Source code
reconstruct_past_diversity_from_biased_coalescent_CPP Source code
reconstruct_past_diversity_from_coalescent_CPP Source code
relative_to_absolute_node_ages_CPP Source code
reorder_tree_edges Man page Source code
root_at_midpoint Man page Source code
root_at_node Man page Source code
root_in_edge Man page Source code
root_tree_at_node_CPP Source code
root_via_outgroup Man page Source code
simulate_Ornstein_Uhlenbeck_model_CPP Source code
simulate_bm_model Man page Source code
simulate_deterministic_diversity_growth_CPP Source code
simulate_diversification_model Man page Source code
simulate_fixed_rates_Markov_model_CPP Source code
simulate_mk_model Man page Source code
simulate_multivariate_Brownian_motion_model_CPP Source code
simulate_neutral_gene_evolution Source code
simulate_neutral_gene_evolution_CPP Source code
simulate_ou_model Man page Source code
simulate_reflected_Ornstein_Uhlenbeck_model_CPP Source code
simulate_rou_model Man page Source code
simulate_scalar_Brownian_motion_model_CPP Source code
sliding_window_average1D Source code
smoothenTimeSeriesSavitzkyGolay_CPP Source code
sort_tree_edges_root_to_tips_CPP Source code
sprint_tree_parameters Source code
tree_to_Newick_string_CPP Source code
trim_tree_at_height Man page Source code
trim_tree_at_height_CPP Source code
variance Source code
write_tree Man page Source code
castor documentation built on Nov. 29, 2017, 5:01 p.m.