date_with_pbdb: Date with Paleobiology Database and paleotree.

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

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

## Not run:  # This is a flag for package development. You are welcome to run the example.

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

## End(Not run) # end dontrun

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