Event - Workshop

Access and Work with NEON Data | AGU 2019

Dec 11, 2019

Hosted By:

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 both lidar and hyperspectral remote sensing. 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.

Registration 

The workshop is limited to 40 participants – make sure to secure your spot by signing up by Dec 2, 2019! 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. 

REGISTER NOW

Schedule

Location: San Francisco, CA. Additional details will be provided to registered participants.

Date: Wednesday December 11th from 11:00 AM–12:30 PM PT (local time)

Time Topic
11:00 Navigating the NEON website and data portal
11:30 Downloading and wrangling NEON data
12:20 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; Data Science Educator; 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 laptop 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. 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.

Optional:

  • 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 install all of them, you can use the following code.

 install.packages("neonUtilities")
 install.packages("raster")

 #optional, if wanting to do Compare Canopy Height exercise or NEON API tutorial
 install.packages("devtools")
 library(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

Location:

TBD