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

In iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

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.

Details

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

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.

Note

Version 1: 2016.2.14

Author(s)

Daliang Ning

See Also

taxa.binphy.big,tree.droot

Examples

data("example.data")
tree=example.data$tree
nworker=2 # parallel computing thread number
treepath=tree.path(tree=tree, nworker=nworker)

iCAMP documentation built on June 1, 2022, 9:08 a.m.