Infer the divergence time of one node based on the TimeTree information.
Arguments
- node_pairs
A matrix with two columns (
leaf_1andleaf_2) computed with the functiongetTimeTreePairs. Each row in the matrix corresponds to a pair of informative leaves, identified by their node ID.- timelines
A named list mapping each node to its timeline from TimeTree. Each timeline contains all ancestors of the node up to the root of the Tree of Life. A timeline is represented as a dataframe with one row per ancestor.
Value
A data frame with one row per informative pair of leaves.
Each row is derived from the timelines object and contains the node IDs of the paired leaves,
along with information about their most recent common ancestor (MRCA), including its divergence time.
Details
This method estimates the divergence time of a node given "informative" pairs of descendant leaves.
An informative pair of leaves consists of two leaves, each belonging to a different direct descendant of the node, for which TimeTree data are available.
For each pair, the method identifies the most recent common ancestor (MRCA) and retrieves its estimated divergence time. Ideally, all pairs should have the same MRCA (i.e., the given node) and yield the same divergence time estimate. If they do not, this indicates that the topology of the phylogeny from TimeTree differs from that inferred by the ScrambledTreeBuilder package.