tree.path: List nodes and edge lengthes from root to each tip and/or node

Description

To list all the nodes and edge lengthes from root to every tip and/or node.

Usage

tree.path(tree, nworker = 4, range = NA, cum = c("no", "from.root", "from.tip", "both"))

Arguments

tree

Phylogenetic tree, an object of class "phylo".

nworker

for parallel computing. Either a character vector of host names on which to run the worker copies of R, or a positive integer (in which case that number of copies is run on localhost). default is 4.

range

a numeric vector, to specify nodes and/or tips to which the path from root will be calculated. default is NA, means all tips.

cum

method to calculate cumulative banch length. "no" means not to calculate cumulative lenght; "from.root" means to cumulate from root to tip; "from.tip" means to cumulate from tip to root; "both" means to calculate in both ways and return both results.

Value

A list result will be returned. 1st layer (the names of the list) is the end of the path, usually the names of tips and/or nodes In 2nd layer, [[1]] is the orders of nodes between root and the tip/node specified in 1st layer; [[2]] is the edge lengthes. if cum="both", [[3]] is cumulative length from root, and [[4]] is cumulative length from tip, otherwise, [[3]] is the cumulative length specified by cum.

Details

This function can be useful in phylogenetic diversity analysis, for example, phylogenetic distance, phylogenetic Hill number, phylogenetic binning, etc.

Examples

Run this code

# NOT RUN {
data("example.data")
tree=example.data$tree
nworker=2 # parallel computing thread number
treepath=tree.path(tree=tree, nworker=nworker)
# }