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.