Add mammal traits from COMBINE (phylogenetically imputed values)

Joins the phylogenetically imputed COMBINE table to a taxify() result by looking up accepted_name. This is the companion to add_combine_reported(): the same ~6.2k mammal species, but with the cells the reported table leaves missing filled in by COMBINE's phylogenetic multiple-imputation model, giving near-complete coverage for the life-history traits. Imputed values are model estimates, not measurements, so they are attached under their own combine_imputed_* columns rather than replacing the reported values.

Usage

add_combine_imputed(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, mirroring add_combine_reported() but named combine_imputed_* (e.g. combine_imputed_adult_mass_g, combine_imputed_gestation_length_d). Traits COMBINE does not impute (for example biogeographical_realm and habitat_breadth_n) carry the reported coverage; the life-history traits (gestation, weaning, longevity, litter size, generation length, ...) are near-complete.

Details

Source: COMBINE (Soria et al. 2021, Ecology, CC0), imputed table (trait_data_imputed.csv). Same species set and column meanings as add_combine_reported(); the difference is coverage. Because imputation only fills gaps, applying both doors and comparing combine_* with combine_imputed_* shows which values are measured versus estimated.

References

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

Examples

if (FALSE) { # \dontrun{
# Compare reported vs imputed gestation length for a mammal:
taxify("Vulpes vulpes", backbone = "gbif") |>
  add_combine_reported() |>
  add_combine_imputed()
} # }