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Cite data sources used in a taxify result

Source: R/cite.R
cite.Rd

Prints formatted citations for the taxonomic backbone(s), enrichment layers, and the taxify package itself. Optionally writes a BibTeX file.

Usage

cite(x, ...)

# Default S3 method
cite(x, file = NULL, ...)

# S3 method for class 'character'
cite(x, file = NULL, source = NULL, ...)

Arguments

x

A taxify_result object, or a character vector of reference ids (cells of <enrichment>:<id> joined by |, as in <trait>_refs).

...

Unused.

file

Optional file path. If provided, BibTeX entries are written to this file (extension should be .bib).

source

For a character x only: NULL (default) when the ids carry their enrichment prefix, or the enrichment the bare ids belong to (e.g. "austraits" for the dispersal_syndrome_source column of add_austraits(cols = "all")).

Value

For a taxify_result, x, invisibly (pipe-friendly). For reference ids, invisibly, a data.frame with one row per distinct id: ref (the qualified id), source, ref_id, citation, doi, and any further columns the source's reference table carries.

Details

Given reference ids instead of a result, cite() resolves them to the works a trait value was taken from: the per-value references add_trait() returns with provenance = TRUE (<trait>_refs), or a door's <col>_source column read with source =.

Examples

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

result <- taxify("Quercus robur", backbone = "wfo")
result |> cite()
result |> cite(file = tempfile(fileext = ".bib"))

options(old)