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Cross-check taxonomic names using GBIF backbone and GNA Verifier

Source: R/tax_crosscheck_pq.R
tax_crosscheck_pq.Rd

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Compares name-verification results from two independent sources:

  • GNA Verifier (via [taxize::gna_verifier()]) with `data_sources = 11` (GBIF Backbone Taxonomy)

  • rgbif backbone (via [rgbif::name_backbone_checklist()])

Because the two services use different matching algorithms and update schedules, discrepancies highlight taxa that may need manual review. A Venn-style summary shows the overlap in matched canonical names.

Usage

tax_crosscheck_pq(
  physeq = NULL,
  taxnames = NULL,
  taxonomic_rank = c("Genus", "Species"),
  data_sources = 11,
  plot = TRUE,
  verbose = TRUE,
  ...
)

Arguments

physeq

(optional) A phyloseq object. Either `physeq` or `taxnames` must be provided, but not both.

taxnames

(optional) A character vector of taxonomic names.

taxonomic_rank

Character vector. The column(s) in the `@tax_table` slot used to construct taxon names when `physeq` is provided. Default `c("Genus", "Species")`.

data_sources

Integer or character vector passed to [taxize::gna_verifier()]. Default `11` (GBIF Backbone Taxonomy). Use `c(1, 11)` to also include Catalogue of Life, for example.

plot

(logical, default `TRUE`). If `TRUE` and ggVennDiagram is installed, a Venn diagram of the two sets of matched canonical names is included in the returned list.

verbose

(logical, default `TRUE`). Print progress messages.

...

Additional arguments passed to [gna_verifier_pq()].

Value

A list with the following elements:

  • gna_results: tibble returned by [gna_verifier_pq()] (with `add_to_phyloseq = FALSE`).

  • backbone_results: tibble returned by [rgbif::name_backbone_checklist()].

  • comparison: data.frame with one row per submitted taxon, columns for the canonical name from each source, and a status column ("match", "mismatch", "gna_only", "backbone_only", or "both_na").

  • summary: named numeric vector with counts of each status category.

  • venn_plot: (optional) a ggVennDiagram object comparing the two sets of matched canonical names.

See also

[gna_verifier_pq()], [rgbif::name_backbone_checklist()]

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Cross-check a phyloseq object
res <- tax_crosscheck_pq(data_fungi)
res$summary
res$comparison |> filter(status == "mismatch")

res$venn_plot

res_taxref <- tax_crosscheck_pq(data_fungi, data_sources = 12)

# Cross-check a vector of names
res2 <- tax_crosscheck_pq(taxnames = c(
  "Trametopsis brasiliensis",
  "Fake species Waller 2022",
  "Russula"
))
res2$summary
} # }