extend_tips_to_ultrametricize: Take a tree, extend all tips (including fossils) up to 0.0 my...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/BioGeoBEARS_generics_v1.R

Makes tree precisely ultrametric by extending the terminal branches up to the highest tip (which is treated as 0 my before present).

1 2	extend_tips_to_ultrametricize(obj, age_of_root = 0, tips_end_at_this_date = NA)

`obj`	An `ape` `phylo` object.
`age_of_root`	The length of the branch below the root. Default 0.
`tips_end_at_this_date`	The tips can be set to something other than 0, if desired. (This could produce negative branclengths, however.)

This function ADDS the time_before_present to everything, including fossils. You have been warned.

obj The corrected phylogeny

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster

Matzke_2012_IBS

read.tree, prt, average_tr_tips

test=1

Loading required package: rexpokit
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: Rcpp
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges