rfishbase (version 2.1.1)

synonyms: synonyms

Description

Check for alternate versions of a scientific name

Usage

synonyms(species_list, limit = 50, server = getOption("FISHBASE_API", FISHBASE_API), fields = c("SynGenus", "SynSpecies", "Valid", "Misspelling", "Status", "Synonymy", "Combination", "SpecCode", "SynCode", "CoL_ID", "TSN", "WoRMS_ID"))

Arguments

species_list

A vector of scientific names (each element as "genus species"). If empty, the table will be loaded up to the limit. This makes it possible to load an entire table without knowledge of the species in the table, thus avoiding uneccesary API calls.

limit

The maximum number of matches from a single API call (e.g. per species). Function will warn if this needs to be increased, otherwise can be left as is.

server

base URL to the FishBase API (by default). For SeaLifeBase, use http://fishbase.ropensci.org/sealifebase

fields

a character vector specifying which fields (columns) should be returned. By default, all available columns recognized by the parser are returned. This option can be used to limit the amount of data transfered over the network if only certain columns are needed.

Value

A table with information about the synonym. Will generally be only a single row if a species name is given. If a FishBase SpecCode is given, all synonyms matching that SpecCode are shown, and the table indicates which one is Valid for FishBase. This may or may not match the valid name for Catalog of Life (Col), also shown in the table. See examples for details.

Details

For further information on fields returned, see: http://www.fishbase.org/manual/english/fishbasethe_synonyms_table.htm

Examples

## Not run: 
# # Query using a synonym:
# synonyms("Callyodon muricatus")
#  
#  # Check for misspellings or alternate names
#  x <- synonyms("Labroides dimidatus") # Species name misspelled
#  species_list(SpecCode = x$SpecCode)  # correct: "Labroides dimidiatus"
# 
#  # See all synonyms using the SpecCode
#  species("Bolbometopon muricatum", fields="SpecCode")[[1]]
#  synonyms(5537)
#  ## End(Not run)