tree.to.vector {TML} | R Documentation |
Phylogenetic tree to vector
Description
A tree is converted to a vector of pairwise distances between leaves. Distance between leaves is defined as the cophenetic distance between them. Normalization is applied so that the maximum distance in the vector output is 1.
Usage
tree.to.vector(tree, normalization = TRUE)
Arguments
tree |
phylogenetic tree |
normalization |
logical; normalize the tree if TRUE |
Value
vector of pairwise distances in R^(m choose 2), where m is the number of leaves
Author(s)
Georgios Aliatimis g.aliatimis@lancaster.ac.uk
References
Aliatimis, Georgios, Ruriko Yoshida, Burak Boyaci, James A. Grant (2023). Tropical Logistic Regression on Space of Phylogenetic Trees
Examples
tree <- ape::read.tree(text='((A:1, B:1):2, (C:1.5, D:1.5):1.5);')
tree.to.vector(tree)
[Package TML version 2.3.0 Index]