get_all_pairwise_distances: Get distances between all pairs of tips and/or nodes.

Description

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

Usage

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

Arguments

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 only_clades=c('apple','lemon','pear'), then only the distance between `apple' and `lemon', between `apple' and 'pear', and between `lemon' and `pear' are calculated. If only_clades==NULL, then this is equivalent to only_clades=c(1:(Ntips+Nnodes)).

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 FALSE to reduce computation time.

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.

Value

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)

Details

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.

Examples

Run this code

# NOT RUN {
# 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')
# }