R: Check that OTT ids occur in the Synthetic Tree

is_in_tree {rotl} | R 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)

[Package rotl version 3.0.3 Index]