Explore NEON – ISU Workshop

NEON provides open ecological data from over 80 locations across the United States. NEON data cover a wide range of subject areas within ecology, including organismal observations, biogeochemistry, remote sensing, and micrometeorology. Some datasets already span several years of data collection.

In this workshop we will provide an introduction to discovering, accessing and preparing a variety of NEON data for your research, primarily using R. We will also explore a variety of educational resources designed to help familiarize you with NEON data, including but not limited to Tutorials, Teaching Modules, and Science Videos. The goals for this workshop are to increase your awareness of NEON resources (documents and staff!), understand the workflow for working with NEON data in R, and to highlight how each of these can fit into your research. The workshop will be divided into two sections, each on a separate day.

1. Day 1: an overview of the NEON program, website, and educational resources, followed by a deep dive into the neonscience.org data portal.
2. Day 2: Using NEON data in R: a code- along guide to discovering and accessing NEON data, via the NEON data portal and the Application Programming Interface (API), followed by a discussion on potential research questions you can explore with NEON data and a code-along guide to NEON data, including
   1. understanding the contents and quality of various data packages, and
   2. performing common data merges, summarizations, and transformations. Instruction will include guidance in using R packages, including some that have been developed by NEON.

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. Please click on the blue "Workshop Materials" button on the right navigation panel to view setup and installation instructions.

Workshop Schedule

All times are Central Daylight Time (UTC-5). See "Workshop Materials" at right for detailed workshop schedule.

Pre-Workshop Materials

Watch our 4-minute NEON overview video: "Open Data to Understand our Changing Ecosystems", and while you're there, feel free to explore the many other resources on our YouTube Page.

Day 1: Friday 4 September: Understanding NEON Data and Resources

Day 2: Friday 11 May: Using NEON Data in R

Workshop Instructors

• Donal O'Leary; Research Scientist, Science Education; NEON program, Battelle
• Marie Faust; Science Outreach Specialist; 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!

Workshop Materials

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.

Setting Up R & RStudio

Windows R/RStudio Setup

• Download R for Windows here
• Run the .exe file that was just downloaded
• Go to the RStudio Download page
• Under Installers select RStudio X.XX.XXX - Windows Vista/7/8/10
• Double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Mac R/RStudio Setup

• Go to CRAN and click on Download R for (Mac) OS X
• Select the .pkg file for the version of OS X that you have and the file will download.
• Double click on the file that was downloaded and R will install
• Go to the RStudio Download page
• Under Installers select RStudio 0.98.1103 - Mac OS X XX.X (64-bit) to download it.
• Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Linux R/RStudio Setup

• R is available through most Linux package managers. You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R).
• To install RStudio, go to the RStudio Download page
• Under Installers select the version for your distribution.
• Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Install R Packages

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

 install.packages("neonUtilities")
 install.packages("devtools")
 devtools::install_github("NEONScience/NEON-geolocation/geoNEON")
 install.packages("raster")
 # [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

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). In these are not options, the workshop can still be completed with a single monitor/screen.

Post-Workshop Materials

• Did you miss a day? Or want to review what we covered? Here is a link to a similar (shorter) webinar that we put on for the ESA: Watch Recorded Webinar (note that you will need to enter your name and email to gain access to the recording)
• Have questions about the Data Portal? Download this excellent step-by-step guide PPT for working in the Data Portal
• See detailed information about our protocols, sampling design, and more in our Document Library
• Check out our many Data Skills Tutorials that cover everything from geospatial analysis to hyperspectral imagery
• Consider signing up for a Data Portal User Account, which will give you access to an API token that you can use to faster download speeds
• Visit our YouTube Playlists page to learn more about topics such as:
  • NEON Science Explained
  • NEON's Spatial Sampling Design
  • The theoretical and technical basis of our Aerial Observation Platform Remote Sensing Data