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.
a vector of Open Tree Taxonomy identifiers
additional arguments to customize the API request (see
A named logical vector.
TRUE indicates that the OTT
id is in the synthetic tree, and
FALSE that it is not.
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## 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)
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