Check scientific or vernacular name(s) — check

Checks if a given scientific or vernacular name(s) can be found in the metadata (package$taxonomic) and returns error if not.

Usage

check_species(
  package = NULL,
  species,
  arg_name = "species",
  datapkg = lifecycle::deprecated()
)

Arguments

package: Camera trap data package object, as returned by read_camtrap_dp().
species: Character vector with scientific or vernacular names.
arg_name: Character with argument name to return in error message Default: "species".
datapkg: Deprecated. Use package instead.

Value

A character vector with the correspondent scientific names.

Examples

# Species is a scientific name
check_species(mica, "Martes foina")
#> [1] "Martes foina"

# Species is a vector of vernacular names
check_species(mica, c("beech marten", "european polecat"))
#> Scientific name of beech marten: Martes foina
#> Scientific name of european polecat: Mustela putorius
#> [1] "Martes foina"     "Mustela putorius"

# Vernacular names can be specified in any language available
check_species(mica, c("vos", "blauwe reiger"))
#> Scientific name of vos: Vulpes vulpes
#> Scientific name of blauwe reiger: Ardea cinerea
#> [1] "Vulpes vulpes" "Ardea cinerea"

# Vernacular names and scientific names can be mixed up
check_species(mica, c("beech marten", "blauwe reiger", "Anas strepera"))
#> Scientific name of beech marten: Martes foina
#> Scientific name of blauwe reiger: Ardea cinerea
#> [1] "Martes foina"  "Ardea cinerea" "Anas strepera"

# Case insensitive
check_species(mica, "AnaS StrePeRa")
#> [1] "Anas strepera"
check_species(mica, "bEEch mARteN")
#> Scientific name of bEEch mARteN: Martes foina
#> [1] "Martes foina"

if (FALSE) { # \dontrun{
check_species(mica, "bad name")
} # }