is_in_tree: Check that OTT ids occur in the Synthetic Tree

View source: R/is_in_tree.R

is_in_treeR Documentation

Check that OTT ids occur in the Synthetic Tree


Some valid taxonomic names do not occur in the Synthetic Tree. This convenience function allows you to check whether a given Open Tree Taxonomy identifier (OTT id) is in the tree. A taxonomic name may not occur in the synthetic tree because (1) it is an extinct or invalid taxon, or (2) it is part of a group that is not monophyletic in the tree.


is_in_tree(ott_ids, ...)



a vector of Open Tree Taxonomy identifiers


additional arguments to customize the API request (see rotl package documentation).


A named logical vector. TRUE indicates that the OTT id is in the synthetic tree, and FALSE that it is not.


## Not run: 
  plant_families <- c("Asteraceae", "Solanaceae", "Poaceae", "Amaranthaceae",
                      "Zamiaceae", "Araceae", "Juncaceae")
  matched_names <- tnrs_match_names(plant_families)
  ## This fails because some ott ids are not in the tree
  ## plant_tree <- tol_induced_subtree(ott_id(matched_names))
  ## So let's check which ones are actually in the tree first:
  in_tree <- is_in_tree(ott_id(matched_names))
  ## This now works:
  plant_tree <- tol_induced_subtree(ott_id(matched_names)[in_tree])

## End(Not run)

rotl documentation built on Oct. 7, 2022, 1:06 a.m.