Workshop

Explore and work with NEON biodiversity data from aquatic ecosystems

Society for Freshwater Science

NEON data cover a wide range of subject areas within ecology, including organismal observations, biogeochemistry, remote sensing, and micrometeorology, this online workshop focuses on NEON biodiversity data collected from our 34 aquatic sites, including 24 wadable streams, 3 rivers, and 7 lakes.

Instruction will include an overview of the breadth of NEON biodiversity data before providing code-along with instruction on how to retrieve and convert NEON biodiversity data to standardized formats (long and wide species tables with relevant metadata to make cross data product comparisons possible) for taxonomic groups such as fishes, benthic macroinvertebrates, and algae. Participants will learn about the ecocomDP data model, a standardized data format designed by the Environmental Data Initiative (EDI) for biodiversity data, and how to import NEON data into this data pattern for synthesis work. Participants will also learn how to format and work with NEON data in a variety of standard R packages, including: Jost (2007)-style alpha, beta, and gamma diversity using the vegetarian package; alpha, beta, and gamma variability using ltmc R package; and ordinations using vegan package for R.

This workshop does not provide a general overview of NEON instrument data, nor the details of different ways of accessing NEON data. If you are interested in these topics, we recommend attending the ‘Access and explore open, continental-scale aquatic instrument data from NEON’ workshop instead of, or in addition to, this one. 

Required Prior Knowledge

The workshop will assume that participants have a basic level of familiarity with working with data in R, including installing and loading packages, and data import.

Participants

This 3-hr workshop is part of the 2020 Society for Freshwater Science (SFS) Summer of Science. The workshop, and other events in the Summer of Science, is free to members of SFS. However, registration is required and the workshop is limited to 40 participants.

The target audience for this workshop is a current or potential data user who wants to explore a range of aquatic organismal data products, learn how to download and work with NEON data, and apply popular biodiversity R packages to the data. If time allows, this workshop may also explore environmental data available from the NEON data portal and how biodiversity data and environmental data relate to one another.

A registration link will be provided once registration is open.

Workshop Schedule

All times are Eastern Daylight Time (UTC-4). See "Workshop Materials" at right for detailed workshop schedule.

Time Topic Instructor
13:45 Join the workshop early if you have any setup or installation issues
14:00 Welcome to the Workshop Donal O'Leary
14:20 Introduction to NEON (Video (4 mins) ) Stephanie Parker
14:30 Overview of NEON Aquatic Organismal Data Products Stephanie Parker
14:40 Access NEON data Donal O'Leary
15:30 NEON Data Munging Eric Sokol
16:00 Analyzing Biodiversity Data Eric Sokol
16:45 Final Questions & Evaluation Donal O'Leary
17:00 Workshop Ends

Workshop Instructors

  • Eric Sokol; Research Scientist, Science Education; NEON program, Battelle
  • Stephanie Parker; Research Scientist, Aquatic Ecologist; NEON program, Battelle
  • Donal O'Leary; Research Scientist, Science Education; NEON program, Battelle

Please get in touch with the instructors prior to the workshop with any questions.

Do you Twitter?

Please tweet at @NEON_Sci or use the hashtag #NEONData during this workshop!

Computer Set Up Instructions

These computer workshop instructions must be completed before starting the workshop.

R & RStudio

To participant in this workshop, you will need a computer with a version of R >3.4 and, preferably, RStudio loaded on your computer.

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Install R Packages

Please have these packages installed and updated prior to the start of the workshop.

 install.packages("neonUtilities")
 install.packages("devtools")
 install.packages("tidyverse")
 install.packages("vegetarian")
 install.packages("vegan")
 [additional packages may be added before the workshop]

Update R Packages

In RStudio, you can go to Tools --> Check for package updates to update previously installed packages on your computer. Or you can use update.packages() to update all packages that are installed in R automatically. More on Packages in R

API Tokens

In this workshop, we will be using an Application Programming Interface (API) process to download NEON data using R script. When using the NEON API, there is an optional step to include your 'User Token' to both increase your download speed, and to allow NEON to anonymously track data access statistics. Doing so helps us to optimize our data delivery platform, and is extremely helpful for our monthly and annual reporting to the NSF. Please consider following this quick tutorial to sign up for your user account, and using your user token, when downloading NEON data.

Monitors

To allow for participants to view the workshop instructors (including screensharing) and to follow along with the activities on their own computer, we recommend participants have two screens to view the workshop. If you do not have access to dual monitors, alternatives include calling into the virtual meeting on a tablet or extra-large cell phone (smaller cell phone screens will make it challenging to see the presentation materials). If these are not options, the workshop can still be completed with a single monitor/screen.

Workshop Schedule

All times are Eastern Daylight Time (UTC-4).

Time Topic Instructor
13:45 Join the workshop early if you have any setup or installation issues
14:00 Welcome to the Workshop Donal O'Leary
14:20 Introduction to NEON (Video (4 mins) ) Stephanie Parker
14:30 Overview of NEON Aquatic Organismal Data Products Stephanie Parker
14:40 Access NEON data Donal O'Leary
15:30 NEON Data Munging Eric Sokol
16:00 Analyzing Biodiversity Data Eric Sokol
16:45 Final Questions & Evaluation Donal O'Leary
17:00 Workshop Ends