taxonomyGet: Load a bird taxonomy into the R environment

In clootl: Fetch and Explore the Cornell Lab of Ornithology Open Tree of Life Avian Phylogeny

Load a bird taxonomy into the R environment

Description

taxonomyGet either reads a taxonomy file and loads it as a ⁠data frame⁠, or loads the default taxonomy data object.

Usage

taxonomyGet(taxonomy_year, data_path = FALSE, from_file = FALSE)

Arguments

taxonomy_year	The eBird taxonomy year the tree should be output in. Current options are 2021-2024. Both numeric and character inputs are acceptable here. Any value aside from these years will result in an error. Default is most recent year.
data_path	Default to FALSE. If a summary, dated tree is desired, this is sufficient and does not need to be modified. However, if a user wishes to extract a set of complete dated trees, for example to iterate an analysis across a cloud of trees, or to use an older version of the tree than the current one packed in the data object, this function can also accept a path to the downloaded set of trees. If you have already downloaded the AvesData repo available at https://github.com/McTavishLab/AvesData use data_path= the path to the download location. Alternately, you can download the full data repo using get_avesdata_repo(). This approach will download the data and set an environmental variable AVESDATA_PATH. When AVESDATA_PATH is set, the data_path will default to this value. To manually set AVESDATA_PATH to the location of your downloaded AvesData repo use set_avesdata_repo_path()
from_file	Default to FALSE. If TRUE forces taxonomyGet to use a local copy of the the taxonomy. This is useful for testing changes and/or updating the clootl_data object.

Details

This will return a data object that has the taxonomy of the requested year.

Value

A data.frame with 17 columns of taxonomic information: order, species code, taxon concept, common name, scientific name, family, OpenTree Taxonomy data, etc.

clootl documentation built on April 24, 2026, 1:07 a.m.