PaleobiologyDBTaxaQuerier: Palaeobiology Database Taxa Querier

In graemetlloyd/metatree: Generating Meta-Analytical Phylogenies

Description

Given a Paleobiology Database taxon name or number returns basic information on that taxon.

Usage

PaleobiologyDBTaxaQuerier(
  taxon_nos,
  taxon_names = NULL,
  original = TRUE,
  interval = NULL,
  extant = "include",
  stopfororphans = TRUE,
  breaker = 100
)

Arguments

taxon_nos	A vector of Paleobiology Database taxon numbers to retrieve from the database.
taxon_names	A vector of taxon names to search for in the database (default left to NULL).
original	Whether or not to return the original (TRUE) or resolved version (FALSE).
interval	The beginning and ending geologic intervals if only wanting taxa from a specified time window (default is NULL).
extant	What to do with extant taxa, one of: "only" (only return extant taxa), "exclude" (exclude extant taxa), or "include" (make no distinction, the default).
stopfororphans	Whether or not to stop with an Error message for taxa with no parent.
breaker	Size of breaker to use if querying a large number of taxa (reduces load on database of individual queries; default is 100).

Details

Uses the Paleobiology Database (paleobiodb.org) API (Peters and McLennen 2016) to query known taxon names or numbers and returns information on their validity, name, and rank. Intended for use in building dynamic taxonomic resolutions when constructing metatree matrices (see Lloyd et al. 2016).

Note that if using the interval option these must be terms used by the Paleobiology Database. Generally this means (for example) using Early/Late, not Lower/Upper.

Value

An eight-column matrix detailing the original taxon number (if relevant), the valid (resolved) taxon number, the taxon name, the taxon rank (Paleobiology Database rank number), the taxon number of the parent of each taxon, the taxon validity (if relevant; returns NA if already valid), the accepted taxon number (if relevant), and the accepted taxon name (if relevant).

Author(s)

Graeme T. Lloyd [e-mail]

References

Lloyd, G. T., Bapst, D. W., Friedman, M. and Davis, K. E., 2016. Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight, and crown birds. Biology Letters, 12, 20160609.

Peters, S. E. and McClennen, M., 2016. The Paleobiology Database application programming interface. Paleobiology, 42, 1-7.

Examples

# Taxon query for Allosaurus fragilis:
PaleobiologyDBTaxaQuerier(taxon_nos = "52962")

graemetlloyd/metatree documentation built on April 29, 2021, 2:32 a.m.