cdb_check_species {Rcompadre}

Check whether a COM(P)ADRE database contains one or more species of interest

Description

Takes a vector of species names and checks whether those species are represented within a CompadreDB object. It outputs either a data frame depicting the species of interest and whether they occur in the database (TRUE/FALSE), or, if return_db == TRUE, a CompadreDB object subset to the species of interest.

Usage

cdb_check_species(cdb, species, return_db = FALSE)

Arguments

cdb

A CompadreDB object

species

Character vector of binomial species names, with the genus and specific epithet separated by either an underscore or a space (e.g. c("Acipenser_fulvescens", "Borrelia_burgdorferi"))

return_db

Logical argument indicating whether a database should be returned

Value

If return_db == FALSE, returns a data frame with a column of species names and a column indicating whether a species occurs in the database. If return_db == TRUE, returns a subset of cdb containing only those species within argument species.

Author(s)

Danny Buss <[e-mail]>

Owen R. Jones <[e-mail]>

Rob Salguero-Gómez <[e-mail]>

Patrick Barks <[e-mail]>

See Also

Other data checking: cdb_collapse(), cdb_compare(), cdb_flag(), mpm_methods

Examples

species <- c("Primula vulgaris", "Trillium ovatum", "Homo sapiens")
cdb_check_species(Compadre, species)
CompadreSubset <- cdb_check_species(Compadre, species, return_db = TRUE)