Add reptile ecological traits and distribution (ReptTraits)

Joins species-level reptile traits from ReptTraits (Oskyrko et al. 2024) to a taxify() result by looking up accepted_name. ReptTraits is built on the Reptile Database taxonomy, so it joins cleanly against the reptiledb backbone (and any backbone that resolves to Reptile Database accepted names).

Usage

add_repttraits(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:

biogeographic_realm

Main biogeographic realm (e.g. Neotropic, Palearctic, Afrotropic, Australo-Pacific, Marine).

microhabitat

Microhabitat (e.g. Terrestrial, Saxicolous, Arboreal).

habitat_type

Habitat type(s) (e.g. Forest, Desert, Wetlands).

elevation_min_m

Minimum recorded elevation in metres.

elevation_max_m

Maximum recorded elevation in metres.

mean_annual_temp_c

Mean annual temperature across the range (degrees Celsius).

insular_endemic

Whether the species is insular/endemic ("Yes"/"No").

body_mass_g

Maximum body mass in grams.

svl_mm

Maximum snout-vent length (straight carapace length for turtles) in mm.

total_length_mm

Maximum total length in mm.

longevity_yr

Maximum longevity in years.

diet

Diet category (e.g. Carnivorous, Herbivorous, Omnivorous).

reproductive_mode

Reproductive mode (oviparous/viviparous/...).

clutch_size

Mean clutch or litter size.

active_time

Activity time (Diurnal/Nocturnal/Cathemeral).

foraging_mode

Foraging mode (ACT active / AMB ambush / Mixed).

Details

The layer carries a per-species distribution signal – biogeographic realm, elevation range and mean climate – alongside body-size and life-history traits, across all reptiles (snakes, lizards, amphisbaenians, turtles, crocodiles and the tuatara), not lizards only.

Source: ReptTraits v1.2 (Oskyrko et al. 2024, Scientific Data, CC BY 4.0). Coverage: 12,060 reptile species. The biogeographic realm and climate fields give a coarse, realm-level range signal; they are not a fine-grained (TDWG-level) range like the plant ranges used by the region constraint.

References

Oskyrko O, Mi C, Meiri S, Du W (2024) ReptTraits: a comprehensive dataset of ecological traits in reptiles. Scientific Data 11:243. doi:10.1038/s41597-024-03079-5

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

taxify("Pogona vitticeps", backbone = "reptiledb") |>
  add_repttraits()

options(old)