get_all_pairwise_distances {castor} | R Documentation |

Calculate phylogenetic ("patristic") distances between all pairs of tips or nodes in the tree, or among a subset of tips/nodes requested.

get_all_pairwise_distances( tree, only_clades = NULL, as_edge_counts = FALSE, check_input = TRUE)

`tree` |
A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge. |

`only_clades` |
Optional integer vector or character vector, listing tips and/or nodes to which to restrict pairwise distance calculations. If an integer vector, it must list indices of tips (from 1 to Ntips) and/or nodes (from Ntips+1 to Ntips+Nnodes). If a character vector, it must list tip and/or node names. For example, if |

`check_input` |
Logical, whether to perform basic validations of the input data. If you know for certain that your input is valid, you can set this to |

`as_edge_counts` |
Logical, specifying whether distances should be calculated in terms of edge counts, rather than cumulative edge lengths. This is the same as if all edges had length 1. |

The "patristic distance" between two tips and/or nodes is the shortest cumulative branch length that must be traversed along the tree in order to reach one tip/node from the other.This function returns a square distance matrix, containing the patristic distance between all possible pairs of tips/nodes in the tree (or among the ones provided in `only_clades`

).

If `tree$edge.length`

is missing, then each edge is assumed to be of length 1; this is the same as setting `as_edge_counts=TRUE`

. The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child). The input tree must be rooted at some node for technical reasons (see function `root_at_node`

), but the choice of the root node does not influence the result. If `only_clades`

is a character vector, then `tree$tip.label`

must exist. If node names are included in `only_clades`

, then `tree$node.label`

must also exist.

The asymptotic average time complexity of this function for a balanced binary tree is O(NC*NC*Nanc + Ntips), where NC is the number of tips/nodes considered (e.g., the length of `only_clades`

) and Nanc is the average number of ancestors per tip.

A 2D numeric matrix of size NC x NC, where NC is the number of tips/nodes considered, and with the entry in row r and column c listing the distance between the r-th and the c-th clade considered (e.g., between clades `only_clades[r]`

and `only_clades[c]`

). Note that if `only_clades`

was specified, then the rows and columns in the returned distance matrix correspond to the entries in `only_clades`

(i.e., in the same order). If `only_clades`

was `NULL`

, then the rows and columns in the returned distance matrix correspond to tips (1,..,Ntips) and nodes (Ntips+1,..,Ntips+Nnodes)

Stilianos Louca

`get_all_distances_to_root`

,
`get_pairwise_distances`

# generate a random tree Ntips = 100 tree = generate_random_tree(list(birth_rate_intercept=1),Ntips)$tree # calculate distances between all internal nodes only_clades = c((Ntips+1):(Ntips+tree$Nnode)) distances = get_all_pairwise_distances(tree, only_clades) # reroot at some other node tree = root_at_node(tree, new_root_node=20, update_indices=FALSE) new_distances = get_all_pairwise_distances(tree, only_clades) # verify that distances remained unchanged plot(distances,new_distances,type='p')

[Package *castor* version 1.6.8 Index]