multi.profile: A function to plot phylogenetic informativeness profiles...

In carolinafishes/PhyInformR: Rapid Calculation of Phylogenetic Information Content

Description

A function to plot phylogenetic informativeness profiles based on site rate breaks

Usage

multi.profile(rate.vector, tree, breaks, values = "display")

Arguments

rate.vector	site rate vector, converted to class 'matrix'
tree	A phylogenetic tree
breaks	bounds for each profile
values	'display' or 'off': whether to return PI values for each time

Author(s)

Alex Dornburg

References

Townsend, J. P. “Profiling Phylogenetic Informativeness” Systematic biology 56, no. 2 (2007): 222–231.

Examples

library("ape")
library("splines")
read.tree(system.file("extdata","polypterus_trees.phy",package="PhyInformR"))->trees
trees[[1]]->tree
as.matrix(rag1)->rates
lower<-c(0.,0.003)
upper<-c(0.003000000001,10)
breaks<-cbind(lower,upper)
multi.profile(rates, tree, breaks, values = "off")

carolinafishes/PhyInformR documentation built on May 13, 2019, 12:50 p.m.