Add plant chromosome numbers (Chromosome Counts Database)

Joins somatic chromosome numbers from the Chromosome Counts Database (Rice et al. 2015) to a taxify() result by looking up accepted_name. CCDB aggregates published counts per taxon; records are collapsed to the binomial and reduced to a per-species median with its observed range.

Usage

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

Arguments

x: A data.frame returned by taxify().
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:

ccdb_chromosome_2n: Median somatic chromosome number (2n).
ccdb_chromosome_2n_min: Lowest 2n reported for the species.
ccdb_chromosome_2n_max: Highest 2n reported for the species.

Details

Source: CCDB (ccdb.tau.ac.il), citation requested, no explicit licence, so taxify publishes no pre-built copy. The data is built on your machine from the original source, which needs taxifydb installed: remotes::install_github("gcol33/taxifydb").

CCDB's service reports gametic numbers, which taxifydb doubles to the somatic 2n reported here. The spread between min and max is real ploidy variation among a species' cytotypes rather than measurement error, so a polyploid complex legitimately spans a wide range (Sedum acre runs 2n = 40 to 120). Where a species is covered by both, this and the CC BY add_kew_cvalues() chromosome column agree exactly for 85% of the 7133 species they share; the rest are compilations differing over which cytotype is typical.

References

Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose I (2015) The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers. New Phytologist 206:19-26.

Examples

if (FALSE) { # \dontrun{
# Builds the enrichment on first use (requires taxifydb).
taxify("Zea mays", backbone = "gbif") |>
  add_ccdb()
} # }