Efficient Phylogenetics on Large Trees

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Documentation for package ‘castor’ version 1.8.2

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A C D E F G H I J L M P R S T W

castor-package Efficient computations on large phylogenetic trees.

-- A --

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.

-- C --

castor Efficient computations on large phylogenetic trees.
clade_densities Estimate the density of tips & nodes in a timetree.
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
congruent_hbds_model Generate a congruent homogenous-birth-death-sampling model.
consensus_taxonomies Compute consensus taxonomies across a tree.
consentrait_depth Calculate phylogenetic depth of a binary trait using the consenTRAIT metric.
correlate_phylo_geodistances Correlations between phylogenetic & geographic distances.
count_lineages_through_time Count number of lineages through time (LTT).
count_tips_per_node Count descending tips.
count_transitions_between_clades Count the number of state transitions between tips or nodes.

-- D --

date_tree_red Date a tree based on relative evolutionary divergences.
discrete_trait_depth Calculate phylogenetic depth of a discrete trait.

-- E --

evaluate_spline Evaluate a scalar spline at arbitrary locations.
expanded_tree_from_jplace Place queries on a tree from a jplace file.
expected_distances_sbm Expected distances traversed by a Spherical Brownian Motion.
exponentiate_matrix Exponentiate a matrix.
extend_tree_to_height Extend a rooted tree up to a specific height.
extract_deep_frame Extract tips representing a tree's deep splits.
extract_fasttree_constraints Extract tree constraints in FastTree alignment format.
extract_tip_neighborhood Extract a subtree spanning tips within a certain neighborhood.
extract_tip_radius Extract a subtree spanning tips within a certain radius.

-- F --

find_farthest_tips Find farthest tip to each tip & node of a tree.
find_farthest_tip_pair Find the two most distant tips in 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_and_compare_bm_models Fit and compare Brownian Motion models for multivariate trait evolution between two data sets.
fit_and_compare_sbm_const Fit and compare Spherical Brownian Motion models for diffusive geographic dispersal between two data sets.
fit_bm_model Fit a Brownian Motion model for multivariate trait evolution.
fit_hbds_model_on_grid Fit a homogenous birth-death-sampling model on a discrete time grid.
fit_hbds_model_parametric Fit a parametric homogenous birth-death-sampling model to a timetree.
fit_hbd_model_on_grid Fit a homogenous birth-death model on a discrete time grid.
fit_hbd_model_parametric Fit a parametric homogenous birth-death model to a timetree.
fit_hbd_pdr_on_best_grid_size Fit pulled diversification rates of birth-death models on a time grid with optimal size.
fit_hbd_pdr_on_grid Fit pulled diversification rates of birth-death models on a time grid.
fit_hbd_pdr_parametric Fit parameterized pulled diversification rates of birth-death models.
fit_hbd_psr_on_best_grid_size Fit pulled speciation rates of birth-death models on a time grid with optimal size.
fit_hbd_psr_on_grid Fit pulled speciation rates of birth-death models on a time grid.
fit_hbd_psr_parametric Fit parameterized pulled speciation rates of birth-death models.
fit_mk Fit a Markov (Mk) model for discrete trait evolution.
fit_musse Fit a discrete-state-dependent diversification model via maximum-likelihood.
fit_sbm_const Fit a phylogeographic Spherical Brownian Motion model.
fit_sbm_geobiased_const Fit a phylogeographic Spherical Brownian Motion model with geographic sampling bias.
fit_sbm_linear Fit a phylogeographic Spherical Brownian Motion model with linearly varying diffusivity.
fit_sbm_on_grid Fit a phylogeographic Spherical Brownian Motion model with piecewise-linear diffusivity.
fit_sbm_parametric Fit a time-dependent phylogeographic Spherical Brownian Motion model.
fit_tree_model Fit a cladogenic model to an existing tree.

-- G --

gamma_statistic Calculate the gamma-statistic of a tree.
generate_gene_tree_msc Generate a gene tree based on the multi-species coalescent model.
generate_gene_tree_msc_hgt_dl Generate gene trees based on the multi-species coalescent, horizontal gene transfers and duplications/losses.
generate_random_tree Generate a tree using a Poissonian speciation/extinction model.
generate_tree_hbds Generate a tree from a birth-death-sampling model in forward time.
generate_tree_hbd_reverse Generate a tree from a birth-death model in reverse time.
generate_tree_with_evolving_rates Generate a random tree with evolving speciation/extinction rates.
geographic_acf Phylogenetic autocorrelation function of geographic locations.
get_all_distances_to_root Get distances of all tips and nodes to the root.
get_all_distances_to_tip Get distances of all tips/nodes to a focal tip.
get_all_node_depths Get the phylogenetic depth of each node in a tree.
get_all_pairwise_distances Get distances between all pairs of tips and/or nodes.
get_ancestral_nodes Compute ancestral nodes.
get_clade_list Get a representation of a tree as a table listing tips/nodes.
get_independent_contrasts Phylogenetic independent contrasts for continuous traits.
get_independent_sister_tips Extract disjoint tip pairs with independent relationships.
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_subtrees_at_nodes Extract subtrees descending from specific nodes.
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_stats_over_time Calculate mean & standard deviation of a numeric trait on a dated tree over time.
get_transition_index_matrix Create an index matrix for a Markov transition model.
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.

-- H --

hsp_binomial Hidden state prediction for a binary trait based on the binomial distribution.
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_nearest_neighbor Hidden state prediction based on nearest neighbor.
hsp_squared_change_parsimony Hidden state prediction via squared-change parsimony.
hsp_subtree_averaging Hidden state prediction via subtree averaging.

-- I --

is_bifurcating Determine if a tree is bifurcating.
is_monophyletic Determine if a set of tips is monophyletic.

-- J --

join_rooted_trees Join two rooted trees.

-- L --

loglikelihood_hbd Galculate the log-likelihood of a homogenous birth-death model.

-- M --

map_to_state_space Map states of a discrete trait to integers.
mean_abs_change_scalar_ou Compute the expected absolute change of an Ornstein-Uhlenbeck process.
merge_nodes_to_multifurcations Merge specific nodes into multifurcations.
merge_short_edges Eliminate short edges in a tree by merging nodes into multifurcations.
model_adequacy_hbd Check if a birth-death model adequately explains a timetree.
model_adequacy_hbds Check if a birth-death-sampling model adequately explains a timetree.
multifurcations_to_bifurcations Expand multifurcations to bifurcations.

-- P --

pick_random_tips Pick random subsets of tips on a tree.
place_tips_taxonomically Place queries on a tree based on taxonomic identities.

-- R --

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 a tree at the midpoint node.
root_at_node Root a tree at a specific node.
root_in_edge Root a tree in the middle of an edge.
root_via_outgroup Root a tree based on an outgroup tip.
root_via_rtt Root a tree via root-to-tip regression.

-- S --

shift_clade_times Shift the time of specific nodes & tips.
simulate_bm_model Simulate a Brownian motion model for multivariate trait co-evolution.
simulate_deterministic_hbd Simulate a deterministic homogenous birth-death model.
simulate_deterministic_hbds Simulate a deterministic homogenous birth-death-sampling model.
simulate_diversification_model Simulate a deterministic uniform speciation/extinction model.
simulate_dsse Simulate a Discrete-State Speciation and Extinction (dSSE) model.
simulate_mk_model Simulate an Mk model for discrete trait evolution.
simulate_musse Simulate a Discrete-State Speciation and Extinction (dSSE) model.
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.
simulate_sbm Simulate Spherical Brownian Motion on a tree.
simulate_tdsse Simulate a time-dependent Discrete-State Speciation and Extinction (tdSSE) model.
spline_coefficients Get the polynomial coefficients of a spline.
split_tree_at_height Split a tree into subtrees at a specific height.

-- T --

tree_distance Calculate the distance between two trees.
tree_from_branching_ages Generate a random timetree with specific branching ages.
tree_from_sampling_branching_ages Generate a random timetree with specific tip/sampling and node/branching ages.
tree_from_taxa Construct a rooted tree from lists of taxa.
tree_imbalance Calculate various imbalance statistics for a tree.
trim_tree_at_height Trim a rooted tree down to a specific height.

-- W --

write_tree Write a tree in Newick (parenthetic) format.