rotl: is_in_tree – R documentation

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is_in_tree

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

Interface to the 'Open Tree of Life' API

v3.0.11

BSD_2_clause + file LICENSE

Authors

Francois Michonneau [aut, cre] (<https://orcid.org/0000-0002-9092-966X>), Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>), David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)

Initial release