Estimates the rate of in-situ speciation events per lineage per unit time

For each tip, counts the number of in-situ speciation events on the path from the root to the tip and divides that by the total branch length of the path. When the tree was prepared with prep_phylo and a sampling_fraction less than 1 was set, branch lengths are scaled upward by dividing by the sampling fraction before computing rates. This approach corrects for the fact that incomplete sampling shortens the total branch length of the observed tree relative to the true underlying tree.

Usage

insitu_speciation_rate(phy, events)

Arguments

phy

The matched phylogenetic tree prepared with prep_phylo

events

The data frame returned by map_insitu_events.

Value

A data frame with one row per tip and columns:

species

Tip label.

n_insitu

Number of in-situ speciation events on the path from root to tip.

path_length

Total branch length from root to tip.

insitu_rate

In-situ speciation events per unit time.