bdvis (version 0.2.9)

gettaxo: Get higher taxonomy data

Description

Retrieve higher taxonomy information (like Family and Order) for each record from the "Encyclopedia of Life" web API.

Usage

gettaxo(indf, genus = FALSE, verbose = FALSE)

Arguments

indf
input data frame containing biodiversity data set
genus
If TRUE, use only genus level data to get taxanomy
verbose
If TRUE, displays each name string for which the higher taxonomy is sought

Value

indf with added / updated columns
  • "Kingdom"Kingdom of the Scientific name
  • "Phylum"Phylum of the Scientific name
  • "Order_"Order of the Scientific name
  • "Family"Family of the Scientific name
  • "Genus"Genus of the Scientific name
and also saves a local copy of taxanomy downloaded for future use in taxo.bd sqlite file

Details

This function makes use of certain functions in the taxize package. It scans and retrieves the taxonomic hierarchy for each scientific name (or just genus name) in the data set. When new data are retrieved, they are stored in a local sqlite database, taxo.db, for faster further access.

See Also

Other Data preparation functions: bdsummary, fixstr, getcellid

Examples

Run this code
## Not run: 
# inat=gettaxo(inat)
# ## End(Not run)

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