match_all_calibrations: Match calibrations to nodes of a given tree

In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Match calibrations to nodes of a given tree

Description

match_all_calibrations searches a given tree for the most recent common ancestor (mrca) of all taxon name pairs in a datelifeCalibration. It uses phytools::findMRCA().

Usage

match_all_calibrations(phy, calibrations)

Arguments

phy	A phylo object.
calibrations	A calibrations object, an output of extract_calibrations_phylo().

Details

The function takes pairs of taxon names in a secondary calibrations data frame, and looks for them in the vector of tip labels of the tree. If both are present, then it gets the node that represents the most recent common ancestor (mrca) for that pair of taxa in the tree. Nodes of input phy can be named or not.

Value

A list of two elements:

phy

A phylo object with nodes renamed with tree_add_nodelabels().

matched_calibrations

A matchedCalibrations object, which is the input calibrations object with two additional columns storing results from the mrca search with phytools::findMRCA(): ⁠$mrca_node_number⁠ and ⁠$mrca_node_name⁠.

datelife documentation built on July 10, 2023, 2:02 a.m.