rcatfish_collections: Accesses the Eschmeyer's Catalog of Fishes Guide to Fish...

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

Accesses the Eschmeyer's Catalog of Fishes Guide to Fish Collections

Description

Accesses the Eschmeyer's Catalog of Fishes Guide to Fish Collections

Usage

rcatfish_collections(
  query = NULL,
  abbreviation = NULL,
  country = NULL,
  phrase = FALSE,
  sleep.time = 10,
  verbose = TRUE
)

Arguments

query	Character Vector of search terms to search for. Default is NULL.
abbreviation	Character vector containing the musuem collection code(s). Default is NULL.
country	Character vector of country names to search for. Default is NULL.
phrase	Logical. Should query be passed as a quoted phrase (e.g. "Museum of Zoology"). Default is FALSE.
sleep.time	Numeric. Time in seconds to sleep between query calls to the California Academy of Sciences page. This is set by default to 10 seconds, which is in their robots.txt. Adjust at your own risk.
verbose	Logical. Should query progress be messaged to the screen? Default is TRUE.

Details

This function retrieves and parses natural history collection data from the Eschmeyer's Catalog of Fishes. Returned information includes the collection abbreviation, country, alternate abbreviations, old and new collection names, websites and databases associated with the collection, remarks, and publications associated with the collection.

It is important that search criteria match exactly how they are on the Catalog of Fishes, otherwise data will not be found (case must match, spelling, etc.). Users wishing to query more than one query mixed with either a country or abbreviation should note that all parameters must be of equal length, so if searching two queries both in U.S.A., the country should be supplied twice (see the final example in the examples below).

Value

Data frame, in which each row is a natural history collection and each column the corresponding collection information (see itemized list below).

• Code - Character. Natural history collection abbreviation code.

• Name - Character. Full name of the natural history collection.

• Country - Character. Country of the natural history collection.

• OtherAbbr - Character. Other and previous abbreviation(s) used for that natural history collection.

• OldName - Character. Previous name(s) used by the natural history.

• NewName - Character. New name(s) of the natural history collection.

• WebPage - Character. URL for the webpage of the natural history collection if one exists.

• CollectionDB - Character. URL for accessing the collection database of the natural history collection if one exists.

• TypesDB - Character. URL for accessing the type database of the natural history collection if one exists.

• Remarks - Character. Additional information about the natural history collection (e.g. includes specimens from other collections, closed, etc.).

• Publications - Character. Comma separated character vector of Eschmeyer's Catalog of Fishes reference numbers citing the natural history collection.

Author(s)

Samuel R. Borstein

References

Fricke, R. & Eschmeyer, W.N. (Year Accessed). Eschmeyer's Catalog of Fishes: Guide to Fish Collections. https://researcharchive.calacademy.org/research/ichthyology/catalog/collections.asp.

Examples

#Search Museum Code For UMMZ (University of Michigan Museum of Zoology)
my.collections <- rcatfish_collections(abbreviation = "UMMZ", country = NULL, 
query = NULL, verbose = TRUE)

#Search For Collections in France
my.collections <- rcatfish_collections(abbreviation = NULL, country = "France", query = NULL)
#Search For Collections in The United States that are in Illinois
my.collections <- rcatfish_collections(abbreviation = NULL, country = "U.S.A.", query = "Illinois")
#Search For Collections in the United States that are in California & Alaska.
my.collections <- rcatfish_collections(abbreviation = NULL, country = rep("U.S.A.",2), 
query = c("California","Alaska"), sleep.time = 10)
#Search for Collections with Museum of Zoology in the name
my.collections <- rcatfish_collections(query = "Museum of Zoology", phrase = TRUE)

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