Other packages > Find by keyword >

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", "1.8.2")



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 1.8.2, https://cran.r-project.org/web/packages/castor. Accessed 21 Nov. 2024.
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), 1.8.0 (2024-01-09 13:10), 1.8.2 (2024-06-29 10:40)
Other packages that cited castor R package
View castor citation profile
Other R packages that castor depends, imports, suggests or enhances
Complete documentation for castor
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
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency  
RcppHNSW  
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R int ...
Download / Learn more Package Citations See dependency  
deductive  
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from vali ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
kgschart  
KGS Rank Graph Parser
Restore underlining numeric data from rating history graph of KGS (an online platform of the game o ...
Download / Learn more Package Citations See dependency  
SCBiclust  
Identifies Mean, Variance, and Hierarchically Clustered Biclusters
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA