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

Description

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.

Usage

is_in_tree(ott_ids, ...)

Arguments

ott_ids

a vector of Open Tree Taxonomy identifiers

...

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

Value

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

Examples

## 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.