R Packages that start with:
A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .
Functions
- asr_empirical_probabilities()
- asr_independent_contrasts()
- asr_max_parsimony()
- asr_mk_model()
- asr_squared_change_parsimony()
- asr_subtree_averaging()
- castor()
- clade_densities()
- collapse_monofurcations()
- collapse_tree_at_resolution()
- congruent_divergence_times()
- congruent_hbds_model()
- consensus_taxonomies()
- consentrait_depth()
- correlate_phylo_geodistances()
- count_lineages_through_time()
- count_tips_per_node()
- count_transitions_between_clades()
- date_tree_red()
- discrete_trait_depth()
- evaluate_spline()
- expanded_tree_from_jplace()
- expected_distances_sbm()
- exponentiate_matrix()
- extend_tree_to_height()
- extract_deep_frame()
- extract_fasttree_constraints()
- extract_tip_neighborhood()
- extract_tip_radius()
- find_farthest_tips()
- find_farthest_tip_pair()
- find_nearest_tips()
- find_root()
- find_root_of_monophyletic_tips()
- fit_and_compare_bm_models()
- fit_and_compare_sbm_const()
- fit_bm_model()
- fit_hbds_model_on_grid()
- fit_hbds_model_parametric()
- fit_hbd_model_on_grid()
- fit_hbd_model_parametric()
- fit_hbd_pdr_on_best_grid_size()
- fit_hbd_pdr_on_grid()
- fit_hbd_pdr_parametric()
- fit_hbd_psr_on_best_grid_size()
- fit_hbd_psr_on_grid()
- fit_hbd_psr_parametric()
- fit_mk()
- fit_musse()
- fit_sbm_const()
- fit_sbm_geobiased_const()
- fit_sbm_linear()
- fit_sbm_on_grid()
- fit_sbm_parametric()
- fit_tree_model()
- gamma_statistic()
- generate_gene_tree_msc()
- generate_gene_tree_msc_hgt_dl()
- generate_random_tree()
- generate_tree_hbds()
- generate_tree_hbd_reverse()
- generate_tree_with_evolving_rates()
- geographic_acf()
- get_all_distances_to_root()
- get_all_distances_to_tip()
- get_all_node_depths()
- get_all_pairwise_distances()
- get_ancestral_nodes()
- get_clade_list()
- get_independent_contrasts()
- get_independent_sister_tips()
- get_mrca_of_set()
- get_pairwise_distances()
- get_pairwise_mrcas()
- get_random_diffusivity_matrix()
- get_random_mk_transition_matrix()
- get_reds()
- get_stationary_distribution()
- get_subtrees_at_nodes()
- get_subtree_at_node()
- get_subtree_with_tips()
- get_tips_for_mrcas()
- get_trait_acf()
- get_trait_stats_over_time()
- get_transition_index_matrix()
- get_tree_span()
- get_tree_traversal_root_to_tips()
- hsp_binomial()
- hsp_empirical_probabilities()
- hsp_independent_contrasts()
- hsp_max_parsimony()
- hsp_mk_model()
- hsp_nearest_neighbor()
- hsp_squared_change_parsimony()
- hsp_subtree_averaging()
- is_bifurcating()
- is_monophyletic()
- join_rooted_trees()
- loglikelihood_hbd()
- map_to_state_space()
- mean_abs_change_scalar_ou()
- merge_nodes_to_multifurcations()
- merge_short_edges()
- model_adequacy_hbd()
- model_adequacy_hbds()
- multifurcations_to_bifurcations()
- pick_random_tips()
- place_tips_taxonomically()
- read_tree()
- reconstruct_past_diversification()
- reorder_tree_edges()
- root_at_midpoint()
- root_at_node()
- root_in_edge()
- root_via_outgroup()
- root_via_rtt()
- shift_clade_times()
- simulate_bm_model()
- simulate_deterministic_hbd()
- simulate_deterministic_hbds()
- simulate_diversification_model()
- simulate_dsse()
- simulate_mk_model()
- simulate_ou_model()
- simulate_rou_model()
- simulate_sbm()
- simulate_tdsse()
- spline_coefficients()
- split_tree_at_height()
- tree_distance()
- tree_from_branching_ages()
- tree_from_sampling_branching_ages()
- tree_imbalance()
- trim_tree_at_height()
- write_tree()
R Codes
- asr_empirical_probabilities.R
- asr_independent_contrasts.R
- asr_max_parsimony.R
- asr_mk_model.R
- asr_squared_change_parsimony.R
- asr_subtree_averaging.R
- auxiliary_routines.R
- biom.R
- clade_densities.R
- collapse_monofurcations.R
- collapse_tree_at_resolution.R
- congruent_divergence_times.R
- congruent_hbds_model.R
- consensus_taxonomies.R
- consentrait_depth.R
- correlate_phylo_geodistances.R
- count_lineages_through_time.R
- count_tips_per_node.R
- count_transitions_between_clades.R
- date_tree_red.R
- discrete_trait_depth.R
- evaluate_spline.R
- expected_distances_sbm.R
- exponentiate_matrix.R
- extend_tree_to_height.R
- extract_deep_frame.R
- extract_fasttree_constraints.R
- extract_tip_neighborhood.R
- extract_tip_radius.R
- find_farthest_tips.R
- find_farthest_tip_pair.R
- find_nearest_tips.R
- find_root.R
- find_root_of_monophyletic_tips.R
- fit_and_compare_bm_models.R
- fit_and_compare_sbm_const.R
- fit_bm_model.R
- fit_hbds_model_on_grid.R
- fit_hbds_model_parametric.R
- fit_hbd_model_on_grid.R
- fit_hbd_model_parametric.R
- fit_hbd_pdr_on_best_grid_size.R
- fit_hbd_pdr_on_grid.R
- fit_hbd_pdr_parametric.R
- fit_hbd_psr_on_best_grid_size.R
- fit_hbd_psr_on_grid.R
- fit_hbd_psr_parametric.R
- fit_mk.R
- fit_musse.R
- fit_sbm_const.R
- fit_sbm_const_biased_sampling_unfinished.R
- fit_sbm_geobiased_const.R
- fit_sbm_linear.R
- fit_sbm_on_grid.R
- fit_sbm_parametric.R
- fit_sbm_trend.R
- fit_symmetric_mk.R
- fit_tree_model.R
- forest_distance.R
- gamma_statistic.R
- generate_gene_tree_msc.R
- generate_gene_tree_msc_hgt_dl.R
- generate_random_tree.R
- generate_tree_hbds.R
- generate_tree_hbd_reverse.R
- generate_tree_with_evolving_rates.R
- geographic_acf.R
- get_all_distances_to_root.R
- get_all_distances_to_tip.R
- get_all_node_depths.R
- get_all_pairwise_distances.R
- get_ancestral_nodes.R
- get_clade_list.R
- get_independent_contrasts.R
- get_independent_sister_tips.R
- get_mrca_of_set.R
- get_pairwise_distances.R
- get_pairwise_mrcas.R
- get_random_diffusivity_matrix.R
- get_random_mk_transition_matrix.R
- get_reds.R
- get_stationary_distribution.R
- get_subtrees_at_nodes.R
- get_subtree_at_node.R
- get_subtree_with_tips.R
- get_tips_for_mrcas.R
- get_trait_acf.R
- get_trait_stats_over_time.R
- get_transition_index_matrix.R
- get_transition_matrix_from_rate_vector.R
- get_tree_span.R
- get_tree_traversal_root_to_tips.R
- hsp_binomial.R
- hsp_empirical_probabilities.R
- hsp_independent_contrasts.R
- hsp_max_parsimony.R
- hsp_mk_model.R
- hsp_nearest_neighbor.R
- hsp_squared_change_parsimony.R
- hsp_subtree_averaging.R
- is_bifurcating.R
- is_monophyletic.R
- join_rooted_trees.R
- loglikelihood_hbd.R
- map_to_state_space.R
- mean_abs_change_scalar_ou.R
- merge_nodes_to_multifurcations.R
- merge_short_edges.R
- model_adequacy_hbd.R
- model_adequacy_hbds.R
- multifurcations_to_bifurcations.R
- pick_random_tips.R
- place_tips_taxonomically.R
- RcppExports.R
- read_tree.R
- reconstruct_past_diversification.R
- reorder_tree_edges.R
- root_at_midpoint.R
- root_at_node.R
- root_in_edge.R
- root_via_outgroup.R
- root_via_rtt.R
- shift_clade_times.R
- simulate_bm_model.R
- simulate_deterministic_hbd.R
- simulate_deterministic_hbds.R
- simulate_deterministic_hbd_msc.R
- simulate_diversification_model.R
- simulate_dsse.R
- simulate_mk_model.R
- simulate_musse.R
- simulate_neutral_gene_evolution.R
- simulate_ou_model.R
- simulate_rou_model.R
- simulate_sbm.R
- simulate_tdsse.R
- spline_coefficients.R
- split_tree_at_height.R
- tree_distance.R
- tree_from_branching_ages.R
- tree_from_sampling_branching_ages.R
- tree_imbalance.R
- trim_tree_at_height.R
- write_tree.R
Selected R package: castor
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