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vegbankr: An R client for the VegBank API


vegbank

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This package is an R client for VegBank, the vegetation plot database of the Ecological Society of America’s Panel on Vegetation Classification, hosted by the National Center for Ecological Analysis and Synthesis (NCEAS). VegBank contains vegetation plot data, community types recognized by the U.S. National Vegetation Classification and others, and all ITIS/USDA plant taxa along with other taxa recorded in plot records. As a VegBank API client, the vegbankr package currently supports querying and downloading vegetation plot records and other supporting information from the VegBank database, and will soon support validating and uploading new data to the VegBank database as well.

VegBank in general, and the vegbankr package in particular, are open source, community projects. We welcome contributions in many forms, including code, data, documentation, bug reports, testing, etc. Use the VegBank discussions to discuss these contributions with us.

Installation

The vegbankr package is not yet available on CRAN, but you can install it directly from this GitHub repository using either the remotes or devtools package. First install one of those packages, and then use it to install vegbankr as follows:

# or use `devtools::` if you prefer
remotes::install_github("nceas/vegbankr")

Usage examples

To view more details about the VegBank API … you’ll have to be a little patient. It’s still in development! Keep an eye on the core VegBank repo at https://github.com/NCEAS/vegbank2 for developments and announcements.

On that note, prior to its production release, the main VegBank API (https://api.vegbank.org) may or may not be available at any given time. However, until then, you should be able to explore and prototype against the development API (https://api-dev.vegbank.org). Configure vegbankr to use the dev API using the following expression:

library(vegbankr)

# the package default URL is https://api.vegbank.org
vb_set_base_url("https://api-dev.vegbank.org")

How many projects are currently registered in VegBank?

Search for “GAP” related projects, returning them sorted in descending order by observation count.

vb_get_projects(search = "GAP", sort = "-obs_count") |>
  dplyr::select(pj_code, project_name, obs_count)

Get the first 100 plot observations associated with project pj.11044 (Pennsylvania HP Delaware Water Gap), sorted by author_obs_code, then check out where they are located.

obs <- vb_get_plot_observations("pj.11044", sort = "author_obs_code",
  limit = 100)
obs |> dplyr::count(state_province)

Grab a single plot observation record based on its “ob” code.

ob.135454 <- vb_get_plot_observations("ob.135454", detail = "full",
  with_nested = TRUE)

Get the taxon (plant) observations associated with this plot obseration, displaying them in order based on the plant code of the current taxon interpretation.

vb_get_taxon_observations("ob.135454") |>
  dplyr::arrange(int_curr_plant_code) |>
  print(n = 35)

Now search for community concepts with the string “sequoiadendron”.

sequoia_communities <- vb_get_community_concepts(search = "sequoiadendron")

Determine which concept has the most plot observations, then retrieve all of those plot obervations from VegBank.

sequoia_plots <- sequoia_communities |>
  dplyr::arrange(-obs_count) |>
  dplyr::slice(1) |>
  dplyr::pull(cc_code) |>
  vb_get_plot_observations()

License 

Copyright [2025] [Regents of the University of California]

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

Acknowledgements

Work on this package was supported by:

  • California Department of Fish and Wildlife
  • The ESA Panel on Vegetation Classification

Additional support was provided for collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.

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