Workshop
Access and Work with Open, Continental-Scale Data from NEON | AAG 2020
American Association of Geographers
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.
- If not already registered for AAG 2020, register for the AAG Virtual Conference: AAG Virtual Meeting info page
- 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.
- 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.
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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 theinstall_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.
Schedule
Please note that the schedule listed below may change depending upon the pace of the workshop!
| Time | Topic | Instructor |
|---|---|---|
| 09:20 | Please come early if you have any setup or installation issues. | |
| 09:35 | Introductions & Using the Zoom Virtual Platform | Megan Jones |
| 09:45 | Introduction to NEON | Megan Jones |
| NEON: Open Data to Understand our Changing Ecosystems (video) | ||
| 10:00 | The NEON Spatial Design | Donal O'Leary |
| 10:10 | Accessing NEON Data | |
| Spatial Data & Maps | Melissa Slater | |
| ArcGIS Online | Melissa Slater | |
| Specimens & Samples from the NEON Biorepository | Megan Jones | |
| The NEON Data Portal | Megan Jones | |
| 11:05 | Working with NEON Data | Donal O'Leary |
| Download & Explore NEON Data | ||
| (Supplemental) Use the neonUtilities Package to Access NEON Data | ||
| (Supplemental) Using neonUtilities in Python | ||
| (Supplemental) Using the NEON Data API in R | ||
| 11:55 | Working with NEON Data of Interest - Breakout Rooms | |
| (A 10 minute break will be take between selection of the breakout room & starting this section of the workshop) | ||
| R: Compare tree height measured from the ground to a lidar-based Canopy Height Model | Donal O'Leary | |
| R: Access and Work with NEON Geolocation Data | Megan Jones | |
| ArcGIS: A more detailed look at NEON data using ArcGIS online | Melissa Slater | |
| 12:30 | Final Questions & Evaluation |