getTaxonomy: Extract taxonID(s) corresponding to the taxonomic description

In mchevalier2/crestr: A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets

Extract taxonID(s) corresponding to the taxonomic description

Description

Extract all possible TaxonIDs corresponding to the provided taxonomical description, which can be at the family, the genus or the species levels.

Usage

getTaxonomy(
  family = "",
  genus = "",
  species = "",
  taxaType = 1,
  depth.out = 8,
  dbname = "gbif4crest_02",
  crest = NA
)

Arguments

family	The name of the family.
genus	The name of the genus.
species	The name of the species.
taxaType	A numerical index (between 1 and 5) to define the type of palaeoproxy used: 1 for plants, 2 for beetles, 3 for chironomids, 4 for foraminifers, 5 for diatoms and 6 for rodents.
depth.out	The taxonomic resolution of the output table. 1 for Kingdom, 2 for phylum, 3 for class_name, 4 for order_name, 5 for family, 6 for genus, 7 for species and 8 to also include the taxonID.
dbname	The name of the data source database.
crest	A crestObj to be used to refine the selection to a specific study area. Set to NA by default (global search).

Value

A vector of unique taxonIDs.

Examples

## Not run: 
  getTaxonomy("Zamiaceae    ")
  getTaxonomy(genus="Ceratozamia", depth.out=6)
  ## \code{taxaType = 2} searches for beetles and not plants, so the next line returns nothing.
  getTaxonomy("Zamiaceae", "Ceratozamia", taxaType = 2)

## End(Not run)

mchevalier2/crestr documentation built on Feb. 14, 2025, 6:31 p.m.