RRphylo: distNodes – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

distNodes

Finding distance between nodes and tips

Description

The function computes the distance between pairs of nodes, pairs of tips, or between nodes and tips. The distance is meant as both patristic distance and the number of nodes intervening between the pair.

Usage

distNodes(tree,node=NULL,clus=0.5)

Arguments

`tree`	a phylogenetic tree. The tree needs not to be ultrametric and fully dichotomous.
`node`	either a single node/tip or a pair of nodes/tips.
`clus`	the proportion of clusters to be used in parallel computing. To run the single-threaded version of `distNodes` set `clus` = 0.

Value

If node is specified, the function returns a data frame with distances between the focal node/tip and the other nodes/tips on the tree (or for the selected pair only). Otherwise, the function returns a matrix containing the number of nodes intervening between each pair of nodes and tips.

Author(s)

Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

Examples

data("DataApes")
DataApes$Tstage->Tstage

cc<- 2/parallel::detectCores()
distNodes(tree=Tstage,clus=cc)
distNodes(tree=Tstage,node=64,clus=cc)
distNodes(tree=Tstage,node="Tro_2",clus=cc)
distNodes(tree=Tstage,node=c(64,48),clus=cc)
distNodes(tree=Tstage,node=c(64,"Tro_2"),clus=cc)

RRphylo

Phylogenetic Ridge Regression Methods for Comparative Studies

v2.5.0

GPL-2

Authors