Workshop

Access and Work with NEON Data | AGU 2020

NEON - AGU

NEON provides open ecological data from over 80 locations across the United States. NEON data cover a wide range of subject areas of interest to AGU members, including micrometeorology, biogeochemistry, organismal observations, and remote sensing data including lidar, hyperspectral, and high-resolution RGB imagery. Some datasets already span several years of data collection. This workshop will provide an introduction to the basics of data access and data navigation: discovering 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. Basic familiarity with R is recommended for participation in the workshop. To make the most of our time together, please see the software and R package installation instructions below under the heading 'Before the Workshop.'

Registration

Register HERE on our Zoom account page

The number of registrations for the workshop is limited - make sure to secure your spot by signing up by Dec 1, 2020! If spaces are available, registration may be extended beyond this date.

This workshop is not affiliated with the AGU Annual Meeting and participants in this workshop do not have to be registered for the AGU meeting.

Workshop Learning Objectives

The participants of the workshop will learn about the available datasets and tools to study ecological processes using NEON data. By the end of the workshop, participants will understand how they can use the suite of NEON data products to address their research questions. After attending the workshop, the attendees will be able to:

  • Find, access, and interpret NEON data.
  • Find additional resources to learn to work with the NEON data of their choice.

Schedule

Note that times are listed in Pacific Standard Time to align with AGU's programming.

Location: Virtual meeting via Zoom (see registration link above)

Date: Wednesday December 2nd from 11 AM–12:30 PM PST

Time Topic
11:00am Pacific Time Navigating the NEON website and Data Portal
11:30am Pacific Time Downloading and wrangling NEON data
(Optional: Using an API Token when Accessing NEON Data with neonUtilities)
(Optional: Advanced usage of the neonUtilities package in R)
(Optional: Using the neonUtilities package in Python using rpy2)
12:20pm Pacific Time Post-workshop suggested resources, questions, and wrap up

Workshop Instructors & Helpers

  • Claire Lunch; @dr_lunch, Research Scientist, Data Science; NEON program, Battelle
  • Donal O'Leary; Research Scientist, Data Science; NEON program, Battelle

If you have questions about the workshop materials, please contact one of the instructors.

Twitter?

Please tweet using #NEONData & @NEON_Sci 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 machine.

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. The last two are optional if you want to do the Compare Canopy Height exercise or the NEON API tutorial.

  • 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 packages using the install_github() function.
  • geoNEON: devtools::install_github("NEONScience/NEON-geolocation/geoNEON”); to get specific location data for NEON data and samples. Optional for workshop.

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

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

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