Date a tree with initial branch lengths with treePL.

Date a tree with initial branch lengths with treePL.

Usage

use_calibrations_treePL(phy, calibrations)

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().

Value

A phylo object

Details

This function uses treePL as described in Smith, S. A., & O’Meara, B. C. (2012). doi:10.1093/bioinformatics/bts492 , with the function treePL.phylo. It attempts to use the 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

Smith, S. A., & O’Meara, B. C. (2012). "treePL: divergence time estimation using penalized likelihood for large phylogenies". Bioinformatics, 28(20), 2689-2690, doi:10.1093/bioinformatics/bts492 .