Add root-nodule nitrogen fixation (NodDB)

Joins the nodulation status of a plant genus to a taxify() result. NodDB records nodulation per genus, so the join is on genus, the same grain as add_fungalroot().

Usage

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

Arguments

x: A data.frame returned by taxify().
cols: Which columns to attach: NULL (default) all, or a character vector of names. See enrichment_cols.
verbose: Logical. Default TRUE.

Value

The same data.frame with noddb_ columns: nodulation_consensus, nodulation_type, nodulation_clade, nodulation_family, spp_recognized, spp_studied, positive_reports, negative_reports.

Details

Source: Tedersoo et al. (2018), 824 plant genera. CC BY-SA 4.0.

nodulation_consensus is the authors' verdict verbatim, which distinguishes a confirmed record from a phylogenetic inference (Rhizobia against likely_Rhizobia) and carries their negative calls as unlikely_Rhizobia and unlikely_Frankia. nodulation_type collapses that to the symbiont involved – rhizobia, frankia, nostocaceae, present, none – reading both unlikely_ verdicts as none.

positive_reports and negative_reports are the counts of published observations behind the verdict, so a thinly evidenced call is visible.

References

Tedersoo L, Laanisto L, Rahimlou S, Toussaint A, Hallikma T, Partel M (2018) Global database of plants with root-symbiotic nitrogen fixation: NodDB. Journal of Vegetation Science 29:560-568. doi:10.1111/jvs.12627

Data: doi:10.15156/BIO/587469

Examples

if (FALSE) { # \dontrun{
taxify(c("Pisum sativum", "Alnus glutinosa", "Quercus robur")) |>
  add_noddb()
} # }