Skip to contents

Use calibrations to date a topology with the BLADJ algorithm.

Source: R/use_calibrations_bladj.R
use_calibrations_bladj.Rd

The function use_calibrations_bladj prepares the input for BLADJ and calls make_bladj_tree().

Usage

use_calibrations_bladj(phy = NULL, calibrations, type = "median", root_age)

Arguments

phy

A phylo object with or without branch lengths.

calibrations

A data.frame of secondary calibrations for any pair of taxon names in phy, usually obtained with get_all_calibrations().

type

The type of age to use as calibration. Options are "median", "mean", "min", or "max".

root_age

Numeric specifying the age of the root. Only used if there are no ages for the root node in calibrations argument. If missing, NULL, or not numeric, the value of the oldest calibration plus one unit of the mean differences across calibrations, will be used as root calibration. If there is one single age point provided as calibrations, the root age will be set to 10% more than the age of the single calibration.

Value

A chronogram: a phylo object with branch lengths proportional to time.

Details

The BLADJ algorithm is part of the Phylocom software, presented in Webb et al. (2008) doi:10.1093/bioinformatics/btn358 .

References

Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). "Phylocom: software for the analysis of phylogenetic community structure and trait evolution". Bioinformatics, 24(18), doi:10.1093/bioinformatics/btn358 .