Add mammal traits including extinct species (PHYLACINE)

Joins PHYLACINE mammal traits to a taxify() result by looking up accepted_name. PHYLACINE covers extant plus recently and prehistorically extinct mammals; it is offered alongside add_pantheria() and add_combine(), not as a replacement.

Usage

add_phylacine(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:

phylacine_mass_g

Body mass (g).

phylacine_diet_plant_pct

Percent of diet that is plant.

phylacine_diet_vertebrate_pct

Percent of diet that is vertebrate.

phylacine_diet_invertebrate_pct

Percent of diet that is invertebrate.

phylacine_terrestrial

Terrestrial habit (0/1).

phylacine_marine

Marine habit (0/1).

phylacine_freshwater

Freshwater habit (0/1).

phylacine_aerial

Aerial habit (0/1).

phylacine_island_endemicity

Island endemicity class.

phylacine_iucn_status

IUCN status (includes EP = extinct in prehistory, EX, EW).

phylacine_mass_method

How the body mass was obtained (the PHYLACINE Mass.Method field, verbatim): Reported, Imputed, or an allometric estimate (e.g. "Assumed isometric based on head-body length").

phylacine_mass_method_class

Coarse provenance of the body mass: reported (measured/compiled), estimated (allometric or same-size analogy), or imputed (phylogenetic gap-fill). Only reported is an observation; the others are model estimates.

Details

Source: PHYLACINE v1.2 (Faurby et al. 2018, Ecology, CC0). Coverage: ~5.8k mammal species including extinct taxa. Mass.g is partly modelled (PHYLACINE gap-fills data-poor and extinct species); phylacine_mass_method / phylacine_mass_method_class record how each mass was derived, so a modelled mass is not mistaken for a measurement where PHYLACINE is the only source.

References

Faurby S et al. (2018) PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology. Ecology 99:2626. doi:10.1002/ecy.2443

Examples

if (FALSE) { # \dontrun{
taxify("Mammuthus primigenius", backbone = "gbif") |>
  add_phylacine()
} # }