Get rogue taxa that break the monophyly of defined taxa

For groups that were recovered as paraphyletic in the phylogenetic analysis, uses the Fish Tree of Life API to identify which species prevented that clade from being recovered as monophyletic.

Usage

fishtree_rogues(
  taxon,
  release = getOption("fishtree.release", .default_release),
  rank = deprecated()
)

Arguments

taxon: the (possibly paraphyletic) taxon for which rogue or intruder species should be identified.
release: The tree release to use, from fishtree_releases. Defaults to `getOption("fishtree.release")`, or `"R2018"` if that is unset. Looking up a `taxon` is only available for `"R2018"`.
rank: Deprecated; use `taxon` instead.

Value

A vector of species names, potentially empty.

References

Rabosky, D. L., Chang, J., Title, P. O., Cowman, P. F., Sallan, L., Friedman, M., Kashner, K., Garilao, C., Near, T. J., Coll, M., Alfaro, M. E. (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714), 392–395. doi:10.1038/s41586-018-0273-1

Examples

if (FALSE) { # \dontrun{
fishtree_rogues("Gobiidae")   # several rogue taxa!
fishtree_rogues("Labridae")   # nice and monophlyetic
} # }