PaleobiologyDBDescendantFinder: Palaeobiology Database Descendant Finder

In graemetlloyd/metatree: Generating Meta-Analytical Phylogenies

Description

Given a Paleobiology Database taxon number returns basic information on all descendants.

Usage

PaleobiologyDBDescendantFinder(
  taxon_nos,
  taxon_names = NULL,
  original = TRUE,
  interval = NULL,
  extant = "include",
  validonly = TRUE,
  returnrank = NULL,
  breaker = 100
)

Arguments

taxon_nos	The Paleobiology database taxon number.
taxon_names	A taxon name to search for in the database (default left to NULL); overrides taxon_nos if used.
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).
validonly	Whether or not to only return valid taxa (TRUE) or all taxa (FALSE).
returnrank	Whether or not to only return taxa of a specific rank (e.g., "3" for species, "5" for genera). See Paleobiology Database API for more infomation.
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 a known taxon number (or name) and returns information on the validity, name, and rank of all its descendants. Intended for use in building dynamic taxonomic resolutions when building 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

A ten-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 this taxon, the taxon validity (if relevant; returns NA if already valid), the accepted taxon number (if relevant), the accepted taxon name (if relevant) of all descendants found, the attribution of the original name as currently entered in the database, and whether ("1") or not ("0") the species is extant.

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 Loxommatinae (asking for species only):
PaleobiologyDBDescendantFinder("339413", returnrank = "3")

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