tree.droot {iCAMP}

Distance from root to tip(s) and node(s) on phylogenetic tree

Description

To calculate the distance from root to tip(s) and node(s) on phylogenetic tree

Usage

tree.droot(tree, range = NA, nworker = 4, output.path = FALSE)

Arguments

tree

Phylogenetic tree, an object of class "phylo".

range

NA or a vector of integer, to specify the numbering of the tips/nodes of which the distances to root will be calculated. The numbering corresponds to those in the element "edge" of the tree. Default is NA, means to calculate all tips and nodes.

nworker

integer, 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, means 4 threads will be run.

output.path

logic, this function will call the function tree.path, if output.path is TRUE, the result of tree.path will be included in the output. Default is FALSE.

Details

A tool to get distances to root, used in phylogenetic binning.

Value

If output.path is FALSE, output is a matrix where the first column indicates the numbering of nodes/tips and the second column has the distance to root. If output.path is TRUE, output is a list with two elements.

droot

matrix, the first column indicates the numbering of nodes/tips and the second column has the distance to root.

path

result of tree.path, list of nodes and edge lengthes from root to each tip and/or node.

Note

Version 2: 2020.8.19, add example. Version 1: 2015.8.19

Author(s)

Daliang Ning

See Also

tree.path

Examples

tree=ape::rtree(4)
nworker=2 # parallel computing thread number
droot=tree.droot(tree = tree, nworker = nworker)