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Add plant traits from GIFT

Source: R/enrichment-gift.R
add_gift.Rd

Joins species-level plant traits from GIFT, the Global Inventory of Floras and Traits (Weigelt et al. 2020), to a taxify() result by accepted_name. GIFT aggregates published trait records to one value per species (mean for numeric traits, most frequent entry for categorical ones). You choose which traits to attach with cols; browse the available columns with gift_traits().

Usage

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

Arguments

x

A data.frame returned by taxify().

cols

Which GIFT trait columns to attach. One of: NULL (the default) for a convenient set of well-populated traits; the string "all" for every bundled trait; or a character vector of gift_ column names (e.g. "plant_height_max", with or without the gift_ prefix). See gift_traits(). When left NULL, a one-time message notes the default set and how to request all traits.

verbose

Logical. Default TRUE.

Value

The same data.frame with one added column per requested trait, named gift_<trait>. Numeric traits (heights, masses, areas) are doubles, the rest character. Rows with no value in GIFT get NA. With the default cols, the added columns are gift_woodiness_1, gift_growth_form_1, gift_lifecycle_1, gift_life_form_1, gift_climber_1, gift_epiphyte_1, gift_parasite_1, gift_aquatic_1, gift_plant_height_max, gift_photosynthetic_pathway, gift_seed_mass_mean, gift_dispersal_syndrome_1, gift_flowering_start, gift_flowering_end, gift_deciduousness_1, and gift_sla_mean.

Details

The GIFT trait table is bundled as a pre-built .vtr and joined offline, so no internet access is needed once it is present (the first use downloads it, or builds it from source if taxifydb is installed). GIFT's API exposes only the redistributable subset of its data (CC BY 4.0; references whose underlying source is restricted are excluded), and that subset is what is bundled here. Cite GIFT and, where applicable, the underlying references (GIFT::GIFT_references()) when you use the values.

References

Weigelt P, Konig C, Kreft H (2020) GIFT - A Global Inventory of Floras and Traits for macroecology and biogeography. Journal of Biogeography 47:16-43. doi:10.1111/jbi.13623 Denelle P, Weigelt P, Kreft H (2023) GIFT: an R package to access the Global Inventory of Floras and Traits. Methods in Ecology and Evolution 14:2738-2748. doi:10.1111/2041-210X.14213

See also

gift_traits() to browse the available columns.

Examples

old <- options(taxify.data_dir = taxify_example_data())

taxify("Abies alba") |>
  add_gift()

options(old)