Add benthic invertebrate traits (Cefas) — add_cefas

Joins biological traits of North-West European continental-shelf benthic macrofauna from the Cefas biological-traits database to a taxify() result by looking up genus. The source fuzzy-codes traits at genus level, and each trait is reduced to its highest-scoring modality, so the join is on genus rather than accepted_name: every species in a coded genus is annotated.

Usage

add_cefas_btrait(x, cols = NULL, verbose = TRUE)

Arguments

x: A data.frame returned by taxify().
cols: Which columns to attach: NULL (default) the curated set, "all" every column the source carries, or a character vector of names. See enrichment_cols.
verbose: Logical. Default TRUE.

Value

The same data.frame with additional columns. The default set:

cefas_body_size: Maximum body-size class.
cefas_morphology: Body morphology.
cefas_lifespan: Life-span class.
cefas_living_habit: Living habit.
cefas_feeding_mode: Feeding mode.
cefas_mobility: Mobility.
cefas_bioturbation: Bioturbation mode.

cols = "all" also attaches egg and larval development and sediment position.

Details

Source: North-West European continental-shelf benthos biological-traits database, Cefas Data Hub (doi:10.14466/CefasDataHub.123 ), Open Government Licence v3.0.

References

Centre for Environment, Fisheries and Aquaculture Science (2022) North-West European continental-shelf benthos biological-traits database. doi:10.14466/CefasDataHub.123

Examples

if (FALSE) { # \dontrun{
# Downloads the enrichment on first use.
taxify("Abra alba", backbone = "gbif") |>
  add_cefas_btrait()
} # }