date_with_pbdb: Date with Paleobiology Database and paleotree.

In OpenTreeChronograms: Open Tree of Life Chronograms

Date with Paleobiology Database and paleotree.

Description

This will take a topology, look up information about fossils for taxa on the tree, and use paleotree::timePaleoPhy() to compute branch lengths.

Usage

date_with_pbdb(phy, recent = FALSE, assume_recent_if_missing = TRUE)

Arguments

phy	A phylo object.
recent	If TRUE, forces the minimum age to be zero for any taxon
assume_recent_if_missing	If TRUE, any taxon missing from PBDB is assumed to be recent.

Value

A dated tree.

Examples

taxa <- c(
  "Archaeopteryx", "Pinus", "Quetzalcoatlus", "Homo sapiens",
  "Tyrannosaurus rex", "Megatheriidae", "Metasequoia", "Aedes", "Panthera"
)
phy <- tree_from_taxonomy(taxa, sources = "The Paleobiology Database")$phy
 # end donttest

OpenTreeChronograms documentation built on June 22, 2022, 9:08 a.m.