Add Collembola traits (Data INRAE deposits) — add_inrae_collembola

Joins fuzzy-coded springtail functional traits to a taxify() result by looking up accepted_name. Output columns are prefixed inrae_.

Usage

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

Arguments

x: A data.frame returned by taxify().
cols: Which columns to attach: NULL (default) all, or a character vector of names. See enrichment_cols.
verbose: Logical. Default TRUE.

Value

The same data.frame with additional columns, one per modality bin of seven fuzzy-coded traits: number of ocelli, furca, post-antennal organ, pigmentation, body shape, scales and reproduction. Each trait is fuzzy coded, so a species' affinities across the bins of one trait (columns sharing an inrae_<trait>__ stem) sum to 100. The source is sparse, so a trait a species was not scored for is NA across its bins. See enrichment_cols for the full column list.

Details

Source: fuzzy-coded Collembola traits compiled from the BETSI database (Pey et al. 2014) across two Data INRAE deposits, the datasets behind Joimel et al. (2021). Coverage: 135 species. The deposits' species codes carry no published legend and are decoded against a Collembola reference pool; codes that cannot be resolved are dropped, never guessed. The fuzzy affinity vectors are not passed to the scalar add_trait() verb.

References

Joimel S et al. (2021) Collembola are among the most flexible soil fauna: a comparison across land uses. Frontiers in Ecology and Evolution 9:630919. doi:10.3389/fevo.2021.630919

Examples

if (FALSE) { # \dontrun{
taxify("Isotoma viridis", backbone = "gbif") |>
  add_inrae_collembola_traits()
} # }