defined.multi.profile: A function to plot phylogenetic informativeness profiles...
In carolinafishes/PhyInformR: Rapid Calculation of Phylogenetic Information Content

Description Usage Arguments Value Author(s) References Examples

A function to plot phylogenetic informativeness profiles based on site rate cutoffs (e.g., loci)

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

`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

Graphical display of phylogenetic informativeness

A. Dornburg

Townsend, J. P. “Profiling Phylogenetic Informativeness” Systematic biology 56, no. 2 (2007): 222–231. Dornburg, A., Townsend, J. P., Friedman, M., and Near, T. J. “Phylogenetic Informativeness Reconciles Ray-Finned Fish Molecular Divergence Times” BMC evolutionary biology 14, (2014): 169. Prum, R. O., Berv, J. S., Alex, D., Field, D. J., Townsend, J. P., Lemmon, E. M., and Lemmon, A. R. “A Comprehensive Phylogeny of Birds (Aves) Using Targeted next-Generation DNA Sequencing” Nature 526, no. 7574 (2015): 569–573.

library("ape")
library("splines")
read.tree(system.file("extdata","Prumetal_timetree.phy",package="PhyInformR"))->tree
prumetalrates->Prates
as.matrix(Prates)->rates
lower<-c(0, 1594)
upper<-c(1595,2787)
breaks<-cbind(lower,upper)
defined.multi.profile(rates, tree, breaks, values = "off")