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.
asr_subtree_averaging   Ancestral state reconstruction via subtree
                        averaging.
castor-package          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.
congruent_divergence_times
                        Extract dating anchors for a target tree, using
                        a dated reference tree
count_clades_over_time
                        Count number of clades over time.
count_tips_per_node     Count descending tips.
date_tree_red           Date a tree based on relative evolutionary
                        divergences.
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 evolving
                        speciation/extinction rates.
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_reds                Calculate relative evolutionary divergences in
                        a tree.
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.
hsp_subtree_averaging   Hidden state prediction via subtree averaging.
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.
read_tree               Load a tree from a string or file in Newick
                        (parenthetic) format.
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.
tree_distance           Calculate the distance between two trees.
trim_tree_at_height     Trim a rooted tree down to a specific height.
write_tree              Write a tree in Newick (parenthetic) format.
