mrca_calibrations: Identify nodes of a tree topology that are most recent common...

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

Identify nodes of a tree topology that are most recent common ancestor (mrca) of taxon pairs from a calibrations object

Description

mrca_calibrations get nodes of a tree topology given in phy that correspond to the most recent common ancestor (mrca) of taxon pairs given in calibrations. It uses phytools::findMRCA() to get mrca nodes.

Usage

mrca_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 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. They will be renamed.

Value

A list of two elements:

matched_phy

A phylo object with nodes renamed to match results of the mrca search. Nodes are renamed using 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.

phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.