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Add mammal traits (COMBINE)

Source: R/add-combine.R
add_combine.Rd

The default COMBINE door. Attaches the reported (measured or literature compiled) trait values and fills each still-missing cell from COMBINE's phylogenetically imputed table, so a single call reaches the fullest coverage COMBINE offers. A measurement is never overwritten: the reported value wins wherever it exists and the imputed model only fills gaps. Beside every trait sits a <trait>_src column recording where that cell came from – "reported", "imputed", or NA when neither table has it – so a model estimate is always distinguishable from a measurement.

Usage

add_combine(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 the combine_* trait columns (reported values, gaps filled from the imputed table) and, beside each, a combine_*_src column tagging that cell as "reported", "imputed", or NA. Traits COMBINE does not impute (for example combine_biogeographical_realm) come out "reported" wherever present. If the imputed table is unavailable, the reported values are returned with every _src tag "reported" or NA.

Details

For a single-table view use add_combine_reported() (measured values only) or add_combine_imputed() (the imputed table on its own).

See also

add_combine_reported(), add_combine_imputed()

Examples

if (FALSE) { # \dontrun{
# Coverage-filled values with per-trait provenance:
res <- taxify("Osphranter rufus", backbone = "col") |>
  add_combine()
res[, c("combine_gestation_length_d", "combine_gestation_length_d_src")]
} # }