Event - Workshop

2020 AAG Annual Meeting | Virtual NEON Workshop

Apr 8, 2020

Hosted By:

NEON and AAG

Update: With the transition of AAG 2020 to a virtual meeting due to the COVID-19 pandemic, this workshop will also be virtual.  Participants still need to register through AAG to participate and new registrations are allowed.  

  1. If not already registered for AAG 2020, register for the AAG Virtual Conference: AAG Virtual Meeting info page 
  2. While signed in, visit this workshop's abstract page on AAG and click on "Join Virtual Session". You'll be redirected to a link to register with us for the workshop & to receive the virtual workshop link. 
  3. Prior to the workshop starting, please ensure your computer is set up (instructions below).  

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.  

NEON provides open data from 81 locations across the United States. NEON data cover a wide range of subject areas of interest to AAG members, including spatially explicit micrometeorology, biogeochemistry, organismal observations, and both lidar and hyperspectral remote sensing. Data collection is projected to occur for the next 30 years. This virtual workshop will provide an introduction to the basics of data availability, and hands-on work to explore and accessing data via the NEON data portal, accessing data via the neonUtilities R package, understanding the content and quality of the data downloaded, and performing common data merges and transformations. Portions of the workshop will feature instruction will be in R but options for Python and ArcGIS will also be available. 

The workshop will begin with an introduction to the design and purpose of NEON including discovering and accessing NEON data via the data portal (data.neonscience.org) and understanding the contents and quality of various data packages. 

The second section of the workshop will include R code-along guide to downloading and using NEON data with the neonUtilitites R package (can be adapted to Python).  Instruction will include guidance in using R packages, including some that have been developed by NEON.

In the final section of the workshop, participants will have the option to join one of three small breakout groups to explore data closer to their interest of choice, each led by an instructor:

  • Compare tree height measured from the ground to a lidar-based Canopy Height Model.
  • Access and work with NEON geolocation data using the geoNEON R package.
  • A more detailed, look at NEON data using ArcGIS Online.

Required Prior Knowledge

In the R coding portions of the workshop, we will assume that participants have a basic level of familiarity with working with data in R, including installing and loading packages, and data import. We will be explaining NEON specific information but not providing an introduction to the R programming language.

However, resources for working with NEON data in ArcGIS and Python will also be presented. Participants preferring to work with these platforms will still benefit from attending the workshop.

This 3-hr virtual workshop is taught as part of the 2020 virtual meeting of the American Association of Geographers (AAG) originally scheduled for Denver, CO. You must be registered for this workshop with AAG to participate. For more information, visit the AAG Virtual Meeting info page and the workshop specific page on AAG.

Workshop Schedule

Location: Online. Virtual meeting information sent to registered participants. As the conference was originally scheduled to be held in Denver, CO, all times remain Mountain Daylight Time (UTC -6).

Please note that the schedule listed below may change depending upon the pace of the workshop.

Time Topic
09:35 Introductions
09:45 Introduction to NEON
10:00 The NEON Spatial Design
10:10 Accessing NEON Data
11:05 Working with NEON Data
11:55 Working with NEON Data of Interest - Breakout Rooms
  R: Compare tree height measured from the ground to a lidar-based Canopy Height Model
  R: Access and Work with NEON Geolocation Data
  ArcGIS: A more detailed look at NEON data using ArcGIS online
12:30 Final Questions & Evaluation

Workshop Instructors

  • Megan A. Jones; Twitter: @meganahjones, Science Education; NEON program, Battelle
  • Donal O'Leary; Data Science Educator; NEON program, Battelle
  • Melissa Slater; Research Scientist, GIScience; NEON program, Battelle

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

Twitter?

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

Before the Workshop

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

Prior to the workshop you should have R and, preferably, RStudio installed on your computer.

Setting Up R & RStudio

Windows R/RStudio Setup

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.

  • neonUtilities: install.packages("neonUtilities"); neonUtiltities only works with R version 3.4 or higher. For further directions, see the start of the Use the neonUtilities Package to Access NEON Data tutorial.
  • raster: install.packages("raster"); to work with raster files in R.
  • devtools: install.packages("devtools"); required to install using the install_github() function.
  • geoNEON: install_github("NEONScience/NEON-geolocation/geoNEON”); to get specific location data for NEON data and samples. Optional for workshop.

If you want to participate in "Compare tree height measured from the ground to a lidar-based Canopy Height Model" breakout session:

  • rhdf5: install.packages("BiocManager"), BiocManager::install("rhdf5"); to work with HDF5 files in R

If you want to install all of them, you can use the following code.

 install.packages("neonUtilities")
 install.packages("raster")
 install.packages("devtools")
 library(devtools)
 install_github("NEONScience/NEON-geolocation/geoNEON")
 install.packages("BiocManager")
 BiocManager::install("rhdf5")

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

Learn More

Location:

Denver, CO
United States