Efficient Phylogenetics on Large Trees

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Documentation for package ‘castor’ version 1.3

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castor-package Efficient computations on large phylogenetic trees.
asr_empirical_probabilities Empirical ancestral state probabilities.
asr_independent_contrasts Ancestral state reconstruction via phylogenetic independent contrasts.
asr_max_parsimony Maximum-parsimony ancestral state reconstruction.
asr_mk_model Ancestral state reconstruction with Mk models and rerooting
asr_squared_change_parsimony Squared-change parsimony ancestral state reconstruction.
castor Efficient computations on large phylogenetic trees.
collapse_monofurcations Remove monofurcations from a tree.
collapse_tree_at_resolution Collapse nodes of a tree at a phylogenetic resolution.
count_clades_over_time Count number of clades over time.
count_tips_per_node Count descending tips.
exponentiate_matrix Exponentiate a matrix.
extend_tree_to_height Extend a rooted tree up to a specific height.
find_farthest_tips Find farthest tip to each tip & node of a tree.
find_nearest_tips Find nearest tip to each tip & node of a tree.
find_root Find the root of a tree.
find_root_of_monophyletic_tips Find the node or tip that, as root, would make a set of target tips monophyletic.
fit_bm_model Fit a Brownian motion model for multivariate trait evolution.
fit_tree_model Fit a cladogenic model to an existing tree.
generate_random_tree Generate a tree using a Poissonian speciation/extinction model.
generate_tree_with_evolving_rates Generate a random tree with birth/death rates evolving under Brownian motion.
get_all_distances_to_root Get distances of all tips and nodes to the root.
get_all_node_depths Get the phylogenetic depth of each node in a tree.
get_independent_contrasts Phylogenetic independent contrasts for continuous traits.
get_mrca_of_set Most recent common ancestor of a set of tips/nodes.
get_pairwise_distances Get distances between pairs of tips or nodes.
get_pairwise_mrcas Get most recent common ancestors of tip/node pairs.
get_random_diffusivity_matrix Create a random diffusivity matrix for a Brownian motion model.
get_random_mk_transition_matrix Create a random transition matrix for an Mk model.
get_stationary_distribution Stationary distribution of Markov transition matrix.
get_subtree_at_node Extract a subtree descending from a specific node.
get_subtree_with_tips Extract a subtree spanning a specific subset of tips.
get_tips_for_mrcas Find tips with specific most recent common ancestors.
get_trait_acf Phylogenetic autocorrelation function of a numeric trait.
get_trait_depth Calculate depth of phylogenetic conservatism for a binary trait.
get_trait_stats_over_time Calculate mean & standard deviation of a numeric trait on a dated tree over time.
get_tree_span Get min and max distance of any tip to the root.
get_tree_traversal_root_to_tips Traverse tree from root to tips.
hsp_empirical_probabilities Hidden state prediction via empirical probabilities.
hsp_independent_contrasts Hidden state prediction via phylogenetic independent contrasts.
hsp_max_parsimony Hidden state prediction via maximum parsimony.
hsp_mk_model Hidden state prediction with Mk models and rerooting
hsp_squared_change_parsimony Hidden state prediction via squared-change parsimony.
is_monophyletic Determine if a set of tips is monophyletic.
map_to_state_space Map states of a discrete trait to integers.
merge_short_edges Eliminate short edges in a tree by merging nodes into multifurcations.
multifurcations_to_bifurcations Expand multifurcations to bifurcations.
pick_random_tips Pick random subsets of tips on a tree.
reconstruct_past_diversification Reconstruct past diversification dynamics from a diversity time series.
reorder_tree_edges Reorder tree edges in preorder or postorder.
root_at_midpoint Root or re-root a tree at the midpoint node.
root_at_node Root or re-root a tree at a specific node.
root_in_edge Root or re-root a tree in the middle of an edge.
root_via_outgroup Root or re-root a tree based on an outgroup tip.
simulate_bm_model Simulate a Brownian motion model for multivariate trait co-evolution.
simulate_diversification_model Simulate a speciation/extinction model.
simulate_mk_model Simulate an Mk model for discrete trait evolution.
simulate_ou_model Simulate an Ornstein-Uhlenbeck model for continuous trait evolution.
simulate_rou_model Simulate a reflected Ornstein-Uhlenbeck model for continuous trait evolution.
trim_tree_at_height Trim a rooted tree down to a specific height.
write_tree Write a tree in Newick (parenthetic) format.