Bbar: Given a tree, return the average root to tip distance between...

In Euphrasiologist/VCVglmm: Manipulating model outputs from MCMCglmm and lme4 objects, usually involving variance-covariance matrices

Description

Given a tree, return the average root to tip distance between a random pair of taxa. For calculating ICC the phylogenetic variance should always be multiplied by the average root-to-tip branch length if you want the average ICC. If the tree is ultrametric and scaled then the root-to-tip branch length is one and there is no need.

Usage

Bbar(phylo, type = c("All", "Genus", "Species"))

Arguments

phylo	object of class phylo
type	at what level calculation should be at, between all species, at the level of genus or any combination within genus

Examples

# requires ape
library(ape)
tree <- rtree(100, rooted = TRUE)
Bbar(tree, type = "Genus")

Euphrasiologist/VCVglmm documentation built on June 4, 2020, 7:08 p.m.