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Add invasive-species impact (EICAT / SEICAT, GIDIAS)

Source: R/add-gidias.R
add_gidias.Rd

Joins per-species environmental- and socio-economic-impact aggregates from GIDIAS (Bacher et al. 2025), the IPBES invasive-species assessment's global impact compilation, to a taxify() result by looking up accepted_name. GIDIAS's individual impact records are reduced to per-species indicators; the raw impact records are not distributed.

Usage

add_gidias(x, group = "Any", cols = NULL, verbose = TRUE)

Arguments

x

A data.frame returned by taxify().

group

Character. Which affected native taxon the impact is measured against:

  • "Any" (default): every impact record for the species, the species-level summary.

  • One of "Plant", "Invertebrate", "Vertebrate", "Microbe", "Fungi": only the impacts recorded against that group.

  • Several (e.g. c("Plant", "Vertebrate")): adds columns with a group suffix (e.g. gidias_eicat_category_Plant).

  • "all": one column set per group, "Any" included.

List them with enrichment_groups("gidias").

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. The default set:

gidias_eicat_category

EICAT environmental-impact category (MC/MN/MO/MR/MV/DD, or NA when no negative impact is recorded).

gidias_eicat_mechanism

IUCN EICAT impact mechanism(s) behind the species' negative environmental impacts.

gidias_seicat_category

SEICAT socio-economic-impact category (MC/MN/MO/MR/DD, or NA).

gidias_ncp_direction

Direction of the species' impact on nature's contributions to people: "Negative", "Positive", "Neutral", or a combination ("Negative; Positive") where the records disagree. GIDIAS scores no magnitude for this block, so there is no category to report.

gidias_ias_taxon

Functional group: Plant, Invertebrate, Vertebrate, or Microbe.

gidias_realms

Realm(s) the impacts span: terrestrial, freshwater, and/or marine.

gidias_n_records

Number of impact records for the species.

gidias_n_sources

Number of distinct sources documenting the impacts.

cols = "all" additionally attaches the numeric EICAT/SEICAT magnitudes (0-3), the affected well-being constituents and contributions to people (gidias_ncp_affected), kingdom, the negative-record count, and a global-extinction flag.

Details

A species' EICAT category is the most severe magnitude among its negative (harmful) environmental-impact records, on the IUCN scale "MC" (Minimal Concern), "MN" (Minor), "MO" (Moderate), "MR" (Major, local extinction), "MV" (Massive, global extinction), or "DD" (Data Deficient); gidias_seicat_category applies the same rule to socio-economic impact (SEICAT, "MC" to "MR"). For impact reconciled across sources, use add_trait() with "environmental_impact" or "socioeconomic_impact".

Source: GIDIAS (Bacher et al. 2025, Scientific Data; CC BY 4.0), compiled for the IPBES thematic assessment report on invasive alien species. Only the derived per-species aggregates are distributed here, not the raw impact records.

What a species impacts

GIDIAS records the affected native taxon per impact record, so group asks the question at that grain: add_gidias(group = "Invertebrate") scores Felis catus "MO" (reduced populations) where the default "Any" scores it "MV", the global extinctions it drove among vertebrates. 28% of species with a recorded affected taxon impact two or more of the five groups, so for those the species-level category is the most severe impact on anything, not the impact on each thing.

The vocabulary is the coarse one GIDIAS controls: "Vertebrate", not "Aves". "Any" is the only group carrying the impact records with no affected taxon recorded (12% of the negative ones) and the two people-facing blocks, so gidias_seicat_category and gidias_ncp_direction are NA on every other group: impact on people is not a question the affected-native-taxon axis can answer.

References

Bacher S et al. (2025) Global Impacts Dataset of Invasive Alien Species (GIDIAS). Scientific Data 12:832. doi:10.1038/s41597-025-05184-5

Examples

if (FALSE) { # \dontrun{
# Downloads the GIDIAS enrichment on first use.
taxify("Felis catus", backbone = "gbif") |>
  add_gidias()

# What the cat does to invertebrates, rather than to anything at all.
taxify("Felis catus", backbone = "gbif") |>
  add_gidias(group = "Invertebrate")

taxify("Felis catus", backbone = "gbif") |>
  add_gidias(group = c("Invertebrate", "Vertebrate"))
} # }