Add mammal traits from COMBINE (reported values)

Joins the COMBINE mammal trait database to a taxify() result by looking up accepted_name, attaching the reported (directly measured or literature-compiled) trait values. COMBINE ships two parallel tables over the same ~6.2k mammal species: the reported table used here, and a phylogenetically imputed table with the missing cells filled in by a model (add_combine_imputed()). They are offered as two separate sources so the distinction between a measured value and a model estimate stays explicit.

Usage

add_combine_reported(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 (reported values):

combine_adult_mass_g

Adult body mass (g).

combine_adult_body_length_mm

Adult head-body length (mm).

combine_litter_size_n

Litter size (count).

combine_litters_per_year_n

Litters per year (count).

combine_max_longevity_d

Maximum longevity (days).

combine_gestation_length_d

Gestation length (days).

combine_weaning_age_d

Weaning age (days).

combine_generation_length_d

Generation length (days).

combine_dispersal_km

Natal dispersal distance (km).

combine_habitat_breadth_n

Number of IUCN habitats (count).

combine_diet_breadth_n

Number of diet categories (count).

combine_trophic_level

Trophic level (1 herbivore, 2 omnivore, 3 carnivore).

combine_activity_cycle

Activity cycle (1 nocturnal, 2 cathemeral, 3 diurnal).

combine_foraging_stratum

Foraging stratum (G/Ar/A/S/M).

combine_biogeographical_realm

Biogeographical realm(s).

Details

Source: COMBINE (Soria et al. 2021, Ecology, CC0), reported table. Coverage: ~6.2k mammal species, keyed on the IUCN 2020 binomial. The reported table leaves a cell missing when no source measured that trait for a species; use add_combine_imputed() for the higher-coverage phylogenetically imputed values.

References

Soria CD et al. (2021) COMBINE: a coalesced mammal database of intrinsic and extrinsic traits. Ecology 102:e03344. doi:10.1002/ecy.3344

See also

add_combine() for reported values with imputed gaps filled and per-trait provenance; add_combine_imputed() for the imputed values; add_pantheria(), add_anage() for other mammal trait sources.

Examples

if (FALSE) { # \dontrun{
taxify("Vulpes vulpes", backbone = "gbif") |>
  add_combine_reported()
} # }