castor
Efficient Phylogenetics on Large Trees

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API for castor
Efficient Phylogenetics on Large Trees

Global functions
ABC_MCMC Source code
ACF_continuous_trait_CPP Source code
ACF_spherical_CPP Source code
ASR_binomial_CPP Source code
ASR_via_independent_contrasts_CPP Source code
ASR_via_squared_change_parsimony_CPP Source code
ASR_with_fixed_rates_Markov_model_CPP Source code
CDF_from_samples Source code
CR_HBD_model_loglikelihood_CPP Source code
HBD_PDR_loglikelihood_CPP Source code
HBD_PSR_loglikelihood_CPP Source code
HBD_model_loglikelihood_CPP Source code
Mk_loglikelihood_CPP Source code
SBM_LLs_of_sampled_transitions_CPP Source code
SBM_LLs_of_transitions_CPP Source code
SBM_get_SBM_PD_functor_CPP Source code
SBM_get_average_transition_angle_CPP Source code
TR_Mk_loglikelihood_ICs_CPP Source code
TSBM_LL_of_sampled_transitions_CPP Source code
TSBM_LL_of_transitions_CPP Source code
WMPR_ASR_CPP Source code
all_pairwise_geodesic_angles Source code
apply_BM_parsimony_to_missing_clades_CPP Source code
apply_attributes_to_descendants_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
asr_subtree_averaging Man page Source code
assign_clades_to_taxa Source code
assign_clades_to_taxa_CPP Source code
assign_points_to_tiles_on_sphere Source code
back Source code
bootstrap_Kolmogorov_Smirnov_test Source code
bootstraps_to_confidence_intervals Source code
calculate_equal_tailed_CIs_of_curves Source code
castor Man page
castor-package Man page
check_biom_json_validity Source code
clade_densities Man page Source code
collapse_monofurcations Man page Source code
collapse_tree_at_resolution Man page Source code
collapse_tree_at_resolution_CPP Source code
completement Source code
compress_musse_params Source code
congruent_divergence_times Man page Source code
congruent_hbds_model Man page Source code
congruify_trees Source code
congruify_trees_CPP Source code
consensus_taxonomies Man page Source code
consensus_taxonomies_CPP Source code
consentrait_depth Man page Source code
correlate_phylo_geodistances Man page Source code
count_clades_at_regular_times_CPP Source code
count_clades_at_times_CPP Source code
count_lineages_through_time Man page Source code
count_lineages_through_time_BD Source code
count_tips_per_node Man page Source code
count_transitions_between_clades Man page Source code
count_transitions_between_clades_CPP Source code
date_tree_red Man page Source code
date_tree_via_RED_CPP Source code
dbeta4 Source code
dense_binary_matrix_row2column_major_CPP Source code
derivatives_of_grid_curve_CPP Source code
discrete_trait_depth Man page Source code
draw_SBM_geodesic_angle_CPP Source code
eliminate_bifurcating_root Source code
eliminate_bifurcating_root_CPP Source code
ensure_uncompressed Source code
evaluate_spline Man page Source code
evaluate_spline_CPP Source code
evaluate_univariate_expression Source code
evaluate_univariate_expression_CPP Source code
expanded_tree_from_jplace Man page Source code
expected_SBM_distance Source code
expected_distances_sbm Man page 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
extract_HBDS_events_from_tree Source code
extract_deep_frame Man page Source code
extract_deep_frame_CPP Source code
extract_fasttree_constraints Man page Source code
extract_fasttree_constraints_CPP Source code
extract_independent_rates_from_transition_matrix Source code
extract_independent_rates_from_vector Source code
extract_tip_neighborhood Man page Source code
extract_tip_neighborhood_CPP Source code
extract_tip_radius Man page 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_tip_pair Man page Source code
find_farthest_tips Man page Source code
find_nearest_tips Man page Source code
find_non_zeros_float_CPP Source code
find_non_zeros_int_CPP 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_Wasserstein_distance Source code
first_Wasserstein_distance_CPP Source code
first_derivative Source code
fit_OU1_model Source code
fit_SBM_diffusivity_from_transitions_CPP Source code
fit_SBM_from_sampled_transitions_CPP Source code
fit_and_compare_bm_models Man page Source code
fit_and_compare_sbm_const Man page Source code
fit_bm_model Man page Source code
fit_exp_LeastLogSquares_moving_window_CPP Source code
fit_exp_Poisson_moving_window_CPP Source code
fit_hbd_model_on_best_grid_size Source code
fit_hbd_model_on_grid Man page Source code
fit_hbd_model_parametric Man page Source code
fit_hbd_pdr_on_best_grid_size Man page Source code
fit_hbd_pdr_on_grid Man page Source code
fit_hbd_pdr_parametric Man page Source code
fit_hbd_psr_on_best_grid_size Man page Source code
fit_hbd_psr_on_grid Man page Source code
fit_hbd_psr_parametric Man page Source code
fit_hbds_model_on_best_grid_size Source code
fit_hbds_model_on_grid Man page Source code
fit_hbds_model_parametric Man page Source code
fit_local_exponential_rate Source code
fit_mk Man page Source code
fit_musse Man page Source code
fit_sbm_const Man page Source code
fit_sbm_const_biased_sampling Source code
fit_sbm_geobiased_const Man page Source code
fit_sbm_linear Man page Source code
fit_sbm_on_best_grid_size Source code
fit_sbm_on_grid Man page Source code
fit_sbm_parametric Man page Source code
fit_sbm_trend Source code
fit_symmetric_mk Source code
fit_tree_model Man page Source code
flatten_list_first_level Source code
flatten_musse_params Source code
forest_distance Source code
gamma_statistic Man page Source code
generate_OU_time_series Source code
generate_bounded_BM_time_series Source code
generate_gene_tree_in_species_tree_MSC_CPP Source code
generate_gene_tree_in_species_tree_MSC_HGT_DL_CPP Source code
generate_gene_tree_msc Man page Source code
generate_gene_tree_msc_hgt_dl 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_random_tree_HBDS_CPP Source code
generate_random_tree_Mk_rates_CPP Source code
generate_random_tree_OU_rates_CPP Source code
generate_random_tree_tdSSE_CPP Source code
generate_tree_from_PSR_CPP Source code
generate_tree_hbd_reverse Man page Source code
generate_tree_hbds Man page Source code
generate_tree_with_evolving_rates Man page Source code
geodesic_angle Source code
geodesic_angles Source code
geodesic_angles_CPP Source code
geographic_acf Man page Source code
get_Colless_Imbalance_CPP Source code
get_HBDS_model_loglikelihood_CPP Source code
get_LTT_BD_CPP Source code
get_MuSSE_loglikelihood_CPP Source code
get_MuSSE_loglikelihood_classic_CPP Source code
get_Ornstein_Uhlenbeck_time_series_CPP Source code
get_PSR_from_PDR_HBD Source code
get_PSR_from_PDR_HBD_CPP Source code
get_PSR_of_CR_HBD_model_CPP Source code
get_PSR_of_HBD_model Source code
get_PSR_of_HBD_model_CPP Source code
get_Poisson_event_times_CPP Source code
get_Robinson_Foulds_distance_CPP Source code
get_SBM_ACF Source code
get_SBM_independent_contrasts Source code
get_adjacent_edges_per_edge Source code
get_adjacent_edges_per_edge_CPP Source code
get_all_branching_ages Source code
get_all_distances_to_root Man page Source code
get_all_distances_to_tip Man page Source code
get_all_distances_to_tip_CPP Source code
get_all_node_depths Man page Source code
get_all_pairwise_distances Man page Source code
get_all_pairwise_geodesic_angles_CPP Source code
get_ancestral_nodes Man page Source code
get_ancestral_nodes_CPP Source code
get_antiderivative_CPP Source code
get_antiderivative_of_splines_function Source code
get_bounded_BM_time_series_CPP Source code
get_branching_ages_from_LTT Source code
get_branching_ages_from_LTT_CPP Source code
get_child_count_per_node Source code
get_child_count_per_node_CPP Source code
get_clade_list Man page Source code
get_closest_tip_per_clade_CPP Source code
get_complement Source code
get_conditional_transition_probabilities Source code
get_congruent_HBDS_CPP Source code
get_connected_subgraphs Source code
get_derivative_CPP Source code
get_derivative_of_splines_function Source code
get_discrete_trait_depth_CPP 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_CPP Source code
get_expected_SBM_sinsquare Source code
get_farthest_tip_pair_CPP Source code
get_farthest_tip_per_clade_CPP Source code
get_farthest_tips_per_edge_CPP Source code
get_file_extension Source code
get_flat_musse_param_names Source code
get_gamma_statistic_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_independent_sister_tips Man page Source code
get_independent_sister_tips_CPP Source code
get_inhomogeneous_grid_1D Source code
get_inhomogeneous_grid_1D_CPP Source code
get_inhomogeneous_grid_1D_from_samples Source code
get_intersection Source code
get_mean_depth_per_node_CPP Source code
get_mean_state_per_node_CPP Source code
get_member_lists_from_group_assignments Source code
get_member_lists_from_group_assignments_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_name_series 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_phylogram_geometry Source code
get_phylogram_geometry_CPP Source code
get_random_diffusivity_matrix Man page Source code
get_random_mk_transition_matrix Man page Source code
get_random_params Source code
get_rate_index_vector Source code
get_reds Man page Source code
get_relative_evolutionary_divergences_CPP Source code
get_root_clade_CPP Source code
get_smallest_items Source code
get_speciation_extinction_events_CPP Source code
get_spline_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_clades 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_subtrees_at_nodes Man page Source code
get_subtrees_at_nodes_CPP Source code
get_sum_of_edge_lengths_per_clade_CPP 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_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 Man page Source code
get_transition_matrix_from_rate_vector Source code
get_tree_from_branching_ages_CPP Source code
get_tree_from_sampling_branching_ages_CPP 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
guesstimate_Mk_rate_via_independent_contrasts Source code
guesstimate_Mk_transition_rates_via_max_parsimony_ASR Source code
hsp_binomial Man page 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_nearest_neighbor Man page Source code
hsp_squared_change_parsimony Man page Source code
hsp_subtree_averaging Man page Source code
is_bifurcating Man page Source code
is_monophyletic Man page Source code
is_monophyletic_tip_set_CPP Source code
join_rooted_trees Man page Source code
join_rooted_trees_CPP Source code
keep_unique_tip_labels Source code
list_to_biom_string Source code
load_jplace Source code
loglikelihood_hbd Man page Source code
make_biom_table Source code
make_matrix_sparse Source code
map_tip_or_node_names_to_indices Source code
map_to_state_space Man page Source code
match_tree_nodes Source code
match_tree_nodes_CPP Source code
matrix_from_biom_table Source code
mean_abs_change_scalar_ou Man page Source code
merge_nodes_to_multifurcations Man page Source code
merge_nodes_to_multifurcations_CPP Source code
merge_short_edges Man page Source code
merge_short_edges_CPP Source code
metadata_from_biom_table Source code
model_adequacy_hbd Man page Source code
model_adequacy_hbds Man page Source code
monotonize_series_by_pruning Source code
monotonize_series_by_pruning_CPP Source code
monotonize_series_via_interpolation_CPP Source code
monotonize_time_series_via_interpolation Source code
move_points_on_sphere_CPP Source code
multifurcations_to_bifurcations Man page Source code
multifurcations_to_bifurcations_CPP Source code
open_file Source code
parent_nodes Source code
pick_random_tips Man page Source code
pick_random_tips_CPP Source code
place_sorted_values_into_bins_CPP Source code
place_tips_on_edges Source code
place_tips_on_nodes Source code
place_tips_taxonomically Man page Source code
place_tips_taxonomically_CPP Source code
propagate_max_ages_downstream_CPP Source code
propagate_min_ages_upstream_CPP Source code
random_semiboxed_left Source code
rbeta4 Source code
read_Newick_string_CPP Source code
read_biom_table Source code
read_distances_list Source code
read_distances_list_CPP Source code
read_fasta Source code
read_fasta_from_file_CPP Source code
read_tree Man page 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
refine_time_grid Source code
relative_to_absolute_node_ages_CPP Source code
remove_outliers 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
root_via_rtt Man page Source code
rowCovs Source code
rowVars Source code
sample_pairwise_tip_distances Source code
sanitize_parameters_for_fitting Source code
scale_params Source code
shift_clade_times Man page Source code
shift_clade_times_CPP Source code
simulate_Ornstein_Uhlenbeck_on_tree_CPP Source code
simulate_SBM_on_tree_CPP Source code
simulate_SBM_trajectory Source code
simulate_SBM_trajectory_CPP Source code
simulate_TSBM_on_tree_CPP Source code
simulate_bm_model Man page Source code
simulate_deterministic_HBDS_CPP Source code
simulate_deterministic_HBD_MSC_CPP Source code
simulate_deterministic_HBD_model_CPP Source code
simulate_deterministic_diversity_growth_CPP Source code
simulate_deterministic_hbd Man page Source code
simulate_deterministic_hbd_msc Source code
simulate_deterministic_hbds Man page Source code
simulate_diversification_model Man page Source code
simulate_dsse Man page Source code
simulate_fixed_rates_Markov_model_CPP Source code
simulate_geobiased_sbm Source code
simulate_mk_model Man page Source code
simulate_multivariate_Brownian_motion_model_CPP Source code
simulate_musse Man page 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_on_tree_CPP Source code
simulate_rou_model Man page Source code
simulate_sbm Man page Source code
simulate_scalar_Brownian_motion_model_CPP Source code
simulate_tdsse Man page Source code
sliding_window_average1D Source code
smoothenTimeSeriesSavitzkyGolay_CPP Source code
smoothen_time_series Source code
sort_tree_edges_root_to_tips_CPP Source code
spline_coefficients Man page Source code
split_sphere_into_equisized_tiles Source code
split_tree_at_height Man page Source code
split_tree_at_height_CPP Source code
split_undirected_graph_CPP Source code
sprint_tree_parameters Source code
tree_distance Man page Source code
tree_from_branching_ages Man page Source code
tree_from_placements_CPP Source code
tree_from_sampling_branching_ages Man page Source code
tree_from_taxa Man page Source code
tree_from_taxa_file Source code
tree_has_multifurcations_CPP Source code
tree_imbalance Man page Source code
tree_to_Newick_string_CPP Source code
tree_to_clade_list_CPP Source code
trim_tree_at_height Man page Source code
trim_tree_at_height_CPP Source code
uncompress_musse_params Source code
unflatten_hbds_params Source code
unflatten_musse_params Source code
unlist_with_nulls Source code
unscale_params Source code
variance Source code
weighted_graph_Laplacian_of_tree Source code
write_biom_table Source code
write_tree Man page Source code
castor documentation built on June 29, 2024, 9:08 a.m.

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