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.

cdb_check_species(cdb, species, return_db = FALSE)



A CompadreDB object


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"))


Logical argument indicating whether a database should be returned


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.

See also

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


Danny Buss <dlb50@cam.ac.uk>

Owen R. Jones <jones@biology.sdu.dk>

Rob Salguero-Gómez <rob.salguero@zoo.ox.ac.uk>

Patrick Barks <patrick.barks@gmail.com>


species <- c("Primula vulgaris", "Trillium ovatum", "Homo sapiens")
cdb_check_species(Compadre, species)
#>            species in_db
#> 1 Primula vulgaris  TRUE
#> 2  Trillium ovatum  TRUE
#> 3     Homo sapiens FALSE
CompadreSubset <- cdb_check_species(Compadre, species, return_db = TRUE)