rcatfish_species_by: Find number of available fish names, number of valid species,...

In rcatfish: An R Interface to the California Academy of Sciences Eschmeyer's Catalog of Fishes

Find number of available fish names, number of valid species, and number of descriptions in the last 10 years by family or subfamily

Description

This function retrieves and parses data on the number of genera and species per family from the Eschmeyer's Catalog of Fishes. It returns a table containing the number of genera and species that are available, valid, and described in the last 10 years in its columns. Each row represents either a class, order, family, or subfamily, so some columns for higher taxonomic groups may have NA for lower taxonomic groups (e.g. if you Search for Cypriniformes, the row containing Cypriniformes will have NA for family and subfamily as it is above those taxonomic levels).

Given the function reads in the page containing the table, for speed, it is highly recommended that if a user wishes to obtain information on numerous orders, families, or subfamilies that they pass them in as a single query. To do this, see the last example.

Usage

rcatfish_species_by(query, verbose = TRUE)

Arguments

query	A character vector of taxa to search for. For users wishing to obtain the information for all fishes please query "Totals".
verbose	Logical. Should query progress be messaged to the screen? Default is TRUE.

Value

A list with each element containing a data frame for each query. List elements are named by the queried taxa. The list contains information on the number of genera and species available, valid, and described in the last 10 years. An itemized list describing the contents in the columns of the data frame(s) returned is described below. #'

• Class - Character. Taxonomic class.

• Order - Character. Taxonomic order.

• Family - Character. Taxonomic family

• Subfamily - Character. Taxonomic subfamily.

• Available.Genera - Integer. Number of available genera for the taxonomic rank.

• Valid.Genera - Integer. Number of valid genera for the taxonomic rank.

• Genera.Last.Ten.Years - Integer. Number of genera described over the past ten years for the taxonomic rank.

• Available.Species - Integer. Number of available species for the taxonomic rank.

• Valid.Species - Integer. Number of valid species for the taxonomic rank.

• Species.Last.Ten.Years - Integer. Number of species described over the past ten years for the taxonomic rank.

Author(s)

Samuel R. Borstein

References

Fricke, R., Eschmeyer, W.N. & Fong J.D. (Year Accessed). Eschmeyer’s Catalog of Fishes: Species by family/subfamily in the Catalog of Fishes. https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp.

Examples

#Search for the number of described Cypriniformes
MySearch <- rcatfish_species_by(query = "Cypriniformes") 
#Obtain the total number of genera and species available, valid, and described in the last 10 years
CofF_totals <- rcatfish_species_by(query = "Totals")
#Search for more than one family
MySearch <- rcatfish_species_by(query = c("Cichlidae","Embiotocidae"))

rcatfish documentation built on Feb. 3, 2026, 5:07 p.m.