2022 BIOME Institute Workshop - NEON Data and Resources for Undergraduate Classrooms

Workshop Background

This workshop, taught by NEON educators, is designed to provide faculty with information and resources to bring real-world, ecological data into their classroom.  NEON offers a variety of open ecological data from over 80 field sites across the United States with data applicable to a wide range of ecological subject areas, including microbes, organismal observations, biogeochemistry, remote sensing, and micrometeorology. Additionally, NEON provides a large variety of online resources designed for classroom curriculum development, as well as independent, asynchronous student learning. 

In this workshop we will explore the breadth of NEON educational resources, including our Tutorials, Teaching Modules, Protocol Documents, and Science Videos. We will also do some live hand-on programming in R to access and explore NEON data. 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 an in-classroom and. online curriculum. 

How this Workshop is Interactive

The keystone of our remote learning resources are the Tutorials, which are designed to teach specific data science skills related to ecology and analyzing NEON data. These tutorials are often adapted, or used directly, by faculty who seek to integrate open data science into their classroom. Together, we will walk through one of these tutorials to show the step-by-step process of downloading and working with NEON data. Along the way we will highlight the common problems that students run into while working with these tutorials, and pragmatic solutions to use during synchronous or asynchronous teaching. We will discuss the variety of topics that can be explored using these resources, from quantifying biodiversity, to analyzing LiDAR pointclouds in 3D. Finally, we will give an in-depth overview of our educational resources available on the NEON website as well as the BioQUEST QUBES hub. 

Required Prior Knowledge

This workshop has two main components. First, working with NEON resources and teaching materials that are available for educators. The final portion of the workshop goes into how to access NEON data programmatically from the NEON data portal using R. To follow along with this portion of the workshop on your personal computer, we expect participants have a basic level of familiarity with working with R, including installing and loading packages, and data import.

Introductory Assignment

• Required: watch the NEON: Open Data to Understand our Changing Ecosystems video to get a quick introduction to the Observatory
• Required: watch the Exploring and Downloading NEON Data Products video to get a quick introduction to the NEON Data Portal
• Required: read through the Download and Explore NEON data tutorial  to get an introduction on how our tutorials are set up
• Optional: if you want to code along during the workshop, install R studio and download relevant packages to the workshop. To do this, follow the instructions in the "Workshop Materials" section on the bottom of this page.
• Optional: if you are not familiar with R, we recommend you go through our Basic R Skills Tutorial

Logistics

Date & Time

Monday, July 18th, 1:00PM - 2:30PM ET

Registration

This workshop is open to participants in the BIOME Institute 2022: Sparking IDEAS: Inclusive, Diverse, Equitable, and Accessible Communities in STEM Classrooms

For more information, please see the BIOME Institute 2022 workshop page.

Workshop Schedule

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

Workshop Instructors

• Bridget Hass; Research Scientist; 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.

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.