calcDstMtrx: Calculate the distance matrix

In treeman: Phylogenetic Tree Manipulation Class and Methods

Description

Returns a distance matrix for specified ids of a tree.

Usage

calcDstMtrx(tree, ids, parallel = FALSE, progress = "none")

Arguments

tree	TreeMan object
ids	IDs of nodes/tips
parallel	logical, make parallel?
progress	name of the progress bar to use, see create_progress_bar

Details

The distance between every id in the tree is calculated by summing the lengths of the branches that connect them. This can be useful for testing the distances between trees, checking for evoltuionary isolated tips etc. Parallelizable.

See Also

calcDstBLD, calcDstRF, calcDstTrp https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

# checking the distance between two trees
library(treeman)
tree_1 <- randTree(10)
tree_2 <- randTree(10)
dmat1 <- calcDstMtrx(tree_1, tree_1['tips'])
dmat2 <- calcDstMtrx(tree_2, tree_2['tips'])
mdl <- cor.test(x=dmat1, y=dmat2)
as.numeric(1 - mdl$estimate)  # 1 - Pearson's r

Example output

[1] 0.4014857

treeman documentation built on July 8, 2020, 7:28 p.m.