Event - Workshop

ESA Workshop: Explore and work with biodiversity data from NEON and LTER

Aug 19, 2022

Join NEON staff for a workshop at the ESA/CSEE 2022 meeting: Explore and work with harmonized continental-scale biodiversity data from NEON and the US LTER!

When: 8/19/2022; 8:00 AM - 11:00 AM
Sign up when you register for the ESA/CSEE 2022 conference!

The National Ecological Observatory Network (NEON) and the Environmental Data Initiative (EDI) provide open ecological data from across the United States. NEON provides data from automated instruments, observational sampling, and airborne remote sensing across 81 sites. EDI hosts data from the U.S. Long Term Ecological Research (LTER) network and a diverse set of field stations, non-profits, state agencies, and projects focused on environmental research.

This short course will focus on tools to work with biodiversity data holdings from NEON and EDI that can be accessed in a standardized format using the ecocomDP package for R. Instruction will include an overview of the breadth of NEON and EDI organismal datasets before an introduction to data discovery and visualization tools available in the ecocomDP package. We will provide code-along instruction using the RStudio IDE in the CyVerse Discovery Environment, with all packages required for this course pre-installed. Participants will learn how to access and work with NEON and LTER datasets in the ecocomDP data format. We will then provide guidance on how biodiversity data in the ecomcomDP format can be used with a variety of R packages commonly used to analyze biodiversity data. Examples will include calculating Jost (2007)-style alpha, beta, and gamma diversity metrics and plotting ordinations using the vegan package.
 

INFORMATION FOR PARTICIPANTS:

We are looking forward to seeing you all at the “Explore and work with biodiversity data from NEON and LTER” short course at ESA this year! To participate in the course, you will need to bring a laptop and have some familiarity with the R programming language. Additionally, we suggest you complete the following tasks ahead of time:

  1. Visit the short course/workshop event page here: https://www.neonscience.org/get-involved/events/esa-workshop-explore-and-work-biodiversity-data-neon-and-lter. We will update this page with any information you need to know during the week leading up to the short course. 
  2. [OPTIONAL] Sign up for a NEON user account and set up an API token to access NEON data following the instructions outlined in this tutorial: https://www.neonscience.org/resources/learning-hub/tutorials/neon-api-tokens-tutorial. This is not required. You can download NEON data without a token, but using an API token will enable faster download speeds. 
  3. Create a CyVerse account and request access to the Visual Interactive Computing Environment (VICE):
    • CREATING A CYVERSE ACCOUNT
      • To create a CyVerse account, navigate to user.cyverse.org and click "Sign Up". You will be prompted to fill in your name, a username, and an email. It is highly recommended that you use a .edu, .org, or .gov email address if you have one. Cloud computing platforms are a prime target for cryptocurrency miners, and using an institutional email address makes it easier to verify that you aren't one.
      • You will be prompted to fill out a few more pieces of information about yourself and what you intend to use CyVerse for. Once you have completed the registration process, you will have a CyVerse account and can proceed to the next step.
    • REQUESTING VICE ACCESS
      • Next, you will have to request access to the Visual Interactive Computing Environment (VICE), which is a platform for running interactive applications, like RStudio or JupyterLab, on the cloud. VICE access requires a one-time approval, due to the cryptocurrency miner issue mentioned above. You can navigate to user.cyverse.org/services to find services you have access to.
      • You can locate DE-VICE and click "Request Access", where you will be prompted to provide information about why you are using VICE. It may take up to a day for VICE access to be approved, so it is worth doing this step ahead of time.
  4. For background on the ecocomDP data model and its intended use for biodiversity data harmonization and synthesis efforts, please see O’Brien et al. (2021, https://doi.org/10.1016/j.ecoinf.2021.101374). For background on how NEON organismal data products have been mapped to the ecocomDP model, please see Li et al. (2022, https://doi.org/10.1002/ecs2.4141).

Please feel free to contact us if you have any questions leading up to the workshop! (esokol@battelleecology.org)

Location:

TBD