Skip to contents

Date a tree with secondary calibrations using PATHd8

Source: R/use_calibrations_pathd8.R
use_calibrations_pathd8.Rd

use_calibrations_pathd8 uses secondary calibrations to date a tree with initial branch lengths using PATHd8.

Usage

use_calibrations_pathd8(
  phy = NULL,
  calibrations = NULL,
  expand = 0.1,
  giveup = 100
)

Arguments

phy

A phylo object with branch lengths.

calibrations

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

expand

How much to expand by each step to get consistent calibrations. Should be between 0 and 1.

giveup

How many expansions to try before giving up

Value

A phylo object with branch lengths proportional to time.

Details

This function implements the PATHd8 algorithm described in Britton et al. (2007) doi:10.1080/10635150701613783 , with geiger::PATHd8.phylo(). The function first attempts to use the given calibrations as fixed ages. If that fails (often due to conflict between calibrations), it will expand the range of the minimum age and maximum age and try again. And repeat. If expand = 0, it uses the summarized calibrations. In some cases, it returns edge lengths in relative time (with maximum tree depth = 1) instead of absolute time, as given by calibrations. In this case, the function returns NA. This is an issue from PATHd8.

References

Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S., & Bremer, K. (2007). "Estimating divergence times in large phylogenetic trees". Systematic biology, 56(5), 741-752. doi:10.1080/10635150701613783 .