tree.ages function

Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.

tree.ages(phylo0 = NULL, data = NULL, taxa = NULL)

Arguments

• phylo0: Either an object of class phylo, or a character vector containing taxon names for building the matrix
• data: Optional list()-object containing either taxon-range tables or occurrence datasets for all taxa. If NULL, data will be automatically downloaded via the pdb()-function
• taxa: Deprecated argument; vector containing taxa to include in calibration matrix (can now be provided directly as phylo0)

Returns

A two-column matrix containing earliest and latest occurrences for each taxon in taxa, with taxon names as row names

Details

tree.ages works best for getting occurrence dates for higher-level taxa (genus-level and up) that can be used as a base_name in a call to the paleobiology database and will return NAs for species names (or any other taxon that cannot be found in the paleobiology database or the provided list object). For a function optimized to recover taxon ranges for genera and species, see tree.ages.spp(). It is highly recommended to manually inspect the resulting table for accuracy.

Examples

data(archosauria)
data(tree_archosauria)
tree.ages(tree_archosauria,data=archosauria)->ages