date_with_pbdb: Date with Paleobiology Database and paleotree

Description Usage Arguments Value Examples

View source: R/tree_from_taxonomy.R

Description

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

Usage

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

Arguments

phy

Phylogeny of taxa

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

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

phylotastic/datelife documentation built on Jan. 22, 2019, 12:29 a.m.