Efficient Phylogenetics on Large Trees

asr_empirical_probabilities | Empirical ancestral state probabilities. |

asr_independent_contrasts | Ancestral state reconstruction via phylogenetic independent... |

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 | 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... |

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... |

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... |

generate_tree_with_evolving_rates | Generate a random tree with evolving speciation/extinction... |

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... |

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... |

get_trait_stats_over_time | Calculate mean & standard deviation of a numeric trait on a... |

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... |

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_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)... |

reconstruct_past_diversification | Reconstruct past diversification dynamics from a diversity... |

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... |

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... |

simulate_rou_model | Simulate a reflected Ornstein-Uhlenbeck model for continuous... |

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. |

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