readMCMCTree: Read MCMCtree output tree into R

In PuttickMacroevolution/MCMCTreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees

Description

Read MCMCtree output tree into R to produce time-scaled tree in APE format, and a table of the mean and 95

Usage

readMCMCtree(inputPhy, forceUltrametric = TRUE, from.file = TRUE)

Arguments

inputPhy	file directory of 'Figtree' output from MCMCtree
forceUltrametric	alters branch lengths at tips so tree is fully ultrametric (default = TRUE)
from.file	Logical. Read a tree from file or locally from within R?

Value

apePhy time-scaled output tree from MCMCtree in APE format

nodeAges mean and 95

Author(s)

Mark Puttick

Examples

data(MCMCtree.output)
attach(MCMCtree.output)
# tree and node ages
readMCMCtree(MCMCtree.phy, from.file=FALSE)

PuttickMacroevolution/MCMCTreeR documentation built on Nov. 23, 2019, 10:24 a.m.