A programmatic interface to fishbase.org.
Accessing data from FishBase using R
rfishbase is a package for interfacing with the fishbase.org database. It provides code to download and parse a local copy of fishbase, which can be used for rapid access for a variety of analysis functions.
rfishbase is available on CRAN and can be installed through the R package manager (see
install.packages). The latest (development) version is hosted here on github, and can be installed using the devtools package:
library(devtools) install_github("rfishbase", "ropensci")
rfishbase is developed by Carl Boettiger in collaboration with Duncan Temple Lang and Peter Wainwright, and is part of the rOpenSci project. This software, examples, and documentation are freely provided under the CC0 license.
Froese, R. and D. Pauly. Editors. 2011. FishBase.
World Wide Web electronic publication.
www.fishbase.org, version (08/2011).
clean_data: clean the fish.base data into pure ASCII
drop_nonascii: remove non-ASCII characters
familySearch: A function to find all fish that are members of a scientific Family
findSpecies: Returns the matching indices in the data given a list of species names
fish.data: A cached copy of extracted FishBase data, 03/2012.
fish_names: Return the scientific names, families, classes, or orders of the input data
fishbase: Query the XML page of fishbase given a fishbase id and return the XML R object
getData: Description: a general function to loop over all fish ids to get data also drops the missing entries
getDepth: Returns available depth range data
getQuantTraits: Returns all quantitative trait values found in the morphology data
getRefs: Returns the FishBase reference id numbers matching a query.
getSize: Returns available size data of specified type (length, weight, or age)
habitatSearch: A function to search for the occurances of any keyword in habitat description
labridtree: An example phylogeny of labrid fish
loadCache: Load an updated cache
updateCache: Update the cached copy of fishbase data
which_fish: which_fish is the the generic search function for fishbase a variety of description types