chronos_calib: Make calibration table

In naturalis/nbaR: R Package Client for the Netherlands Biodiversity API

Make calibration table

Description

Make calibration table compatible with ape's 'chronos'

Usage

chronos_calib(specimens, tree, level = "genus")

Arguments

specimens	list of objects of class Specimen, must have chronostratigraphy information
tree	object of class 'phylo'
level	character giving taxonomic level

Details

Given a list of specimen objects, and a phylogenetic tree, makes a calibration table that is compatible with the 'chronos' function from the 'ape' package. This can be done for various taxonomic levels

See Also

Other utils: geo_age

Examples

# get specimen with chronostratigraphic data
sc <- SpecimenClient$new()
sp <- sc$find_by_unit_id("RGM.156532")$content
# load tree
library('ape')
data(shark_tree)
# make calibration table
chronos_calib(sp, shark_tree, "genus")

naturalis/nbaR documentation built on Nov. 12, 2023, 4:47 p.m.