species: species

In rfishbase: R Interface to 'FishBase'

species

Description

Provide wrapper to work with species lists.

Usage

species(
  species_list = NULL,
  fields = NULL,
  server = getOption("FISHBASE_API", "fishbase"),
  version = get_latest_release(),
  db = default_db(server, version),
  ...
)

Arguments

species_list	A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
fields	a character vector specifying which fields (columns) should be returned. By default, all available columns recognized by the parser are returned. Mostly for backwards compatibility as users can subset by column later
server	can be set to either "fishbase" or "sealifebase" to switch between databases. NOTE: it is usually easier to leave this as NULL and set the source instead using the environmental variable 'FISHBASE_API', e.g. 'Sys.setenv(FISHBASE_API="sealifebase")'.
version	a version string for the database, will default to the latest release. see [get_releases()] for details.
db	the
...	unused; for backwards compatibility only

Details

The Species table is the heart of FishBase. This function provides a convenient way to query, tidy, and assemble data from that table given an entire list of species. For details, see: http://www.fishbase.org/manual/english/fishbasethe_species_table.htm

Species scientific names are defined according to fishbase taxonomy and nomenclature.

Value

a data.frame with rows for species and columns for the fields returned by the query (FishBase 'species' table)

Examples

## Not run: 

species(c("Labroides bicolor", "Bolbometopon muricatum")) 
species(c("Labroides bicolor", "Bolbometopon muricatum"), fields = species_fields$habitat) 


## End(Not run)

rfishbase documentation built on June 7, 2023, 6:14 p.m.