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castor  

Efficient Phylogenetics on Large Trees
View on CRAN: Click here


Download and install castor package within the R console
Install from CRAN:
install.packages("castor")

Install from Github:
library("remotes")
install_github("cran/castor")

Install by package version:
library("remotes")
install_version("castor", "1.8.0")



Attach the package and use:
library("castor")
Maintained by
Stilianos Louca
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-05-20
Latest Update: 2024-01-09
Description:
Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) .
How to cite:
Stilianos Louca (2017). castor: Efficient Phylogenetics on Large Trees. R package version 1.8.0, https://cran.r-project.org/web/packages/castor
Previous versions and publish date:
1.0 (2017-05-20 09:13), 1.1 (2017-06-02 07:39), 1.2.1 (2017-09-24 12:59), 1.2.2 (2017-09-27 23:49), 1.2 (2017-09-23 06:27), 1.3.2 (2018-01-20 23:03), 1.3.3 (2018-04-11 20:32), 1.3.4 (2018-08-16 20:10), 1.3.5 (2019-02-15 15:30), 1.3.6 (2019-05-06 09:20), 1.3 (2017-11-29 17:35), 1.4.0 (2019-06-14 09:10), 1.4.1 (2019-06-16 00:30), 1.4.2 (2019-07-30 00:40), 1.4.3 (2019-09-20 09:20), 1.5.0 (2019-11-01 23:20), 1.5.3 (2019-12-20 13:20), 1.5.4 (2020-01-08 14:00), 1.5.5 (2020-01-10 11:40), 1.5.7 (2020-04-12 08:00), 1.6.1 (2020-06-29 06:50), 1.6.2 (2020-07-19 06:50), 1.6.3 (2020-08-27 15:50), 1.6.4 (2020-10-26 23:20), 1.6.5 (2021-01-06 17:01), 1.6.6 (2021-02-20 07:40), 1.6.7 (2021-03-11 07:20), 1.6.8 (2021-06-20 23:40), 1.6.9 (2021-08-16 09:30), 1.7.0 (2021-10-25 09:40), 1.7.1 (2022-01-05 04:30), 1.7.2 (2022-01-08 12:23), 1.7.3 (2022-09-02 01:10), 1.7.4 (2022-10-23 04:45), 1.7.5 (2022-11-10 11:10), 1.7.6 (2022-12-14 20:40), 1.7.8 (2023-03-01 10:20), 1.7.9 (2023-04-18 07:40), 1.7.10 (2023-05-19 10:00), 1.7.11 (2023-08-17 23:22)
Other packages that cited castor R package
View castor citation profile
Other R packages that castor depends, imports, suggests or enhances
Functions, R codes and Examples using the castor R package
Some associated 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_tip_pair . find_farthest_tips . find_nearest_tips . find_root . find_root_of_monophyletic_tips . fit_and_compare_bm_models . fit_and_compare_sbm_const . fit_bm_model . 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_hbds_model_on_grid . fit_hbds_model_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_hbd_reverse . generate_tree_hbds . 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_subtree_at_node . get_subtree_with_tips . get_subtrees_at_nodes . 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 . 
Some associated R codes: RcppExports.R . 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_tip_pair.R . find_farthest_tips.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_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_hbds_model_on_grid.R . fit_hbds_model_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_hbd_reverse.R . generate_tree_hbds.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_subtree_at_node.R . get_subtree_with_tips.R . get_subtrees_at_nodes.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 . 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_hbd_msc.R . simulate_deterministic_hbds.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 .  Full castor package functions and examples
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