Workshop

Access and Work with NEON Data – ESA 2020

Ecological Society of America Annual Meeting

With ESA moving to an online format and cancelling the short course offerings, we will be offering this workshop as an independent, online workshop concurrent with the ESA meeting. 

NEON provides open ecological data from over 80 locations across the United States. NEON data cover a wide range of subject areas within ecology, including organismal observations, biogeochemistry, remote sensing, and micrometeorology. Some datasets already span several years of data collection.

This workshop will provide an introduction to discovering, accessing and preparing a variety of NEON data for your research, primarily using R. The workshop will be divided into two sections of roughly equal length.

  1. The workshop will begin will be a code-along guide to NEON data, including
    a. discovering and accessing NEON data, via the NEON data portal and the Application Programming Interface (API),
    b. understanding the contents and quality of various data packages, and
    c. performing common data merges, summarizations, and transformations.
    Instruction will include guidance in using R packages, including some that have been developed by NEON.
  2. In the final portion, participants will work with NEON data of their choice, while instructors circulate to answer questions about data and coding. Participants may break into groups based on the data or analyses they wish to explore. For participants who attend the workshop without a specific dataset or analysis of interest, a guided project will be available, analyzing data accessed in the first half of the workshop.

Required Prior Knowledge

The workshop will assume that participants have a basic level of familiarity with working with data in R, including installing and loading packages, and data import.

Registration

Registration for this online workshop will open in mid-July.

Workshop Schedule

All times are denoted in Eastern Daylight Time.

Time Topic
11:45 Please come early if you have any setup or installation issues.
12:00 Accessing NEON Data
1:30 --------- BREAK ---------
1:45 Working with NEON Data
2:45 Final Questions & Evaluation

Workshop Instructors & Helpers

  • Megan A. Jones; @meganahjones, Research Scientist, Science Education; NEON program, Battelle
  • Donal O'Leary; Data Science Educator; 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!

Before the Workshop

To participant in this workshop, you will need a laptop with R (at least version 3.4.0), and preferably RStudio, loaded on your computer.

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

Install R & RStudio

Windows R/RStudio Install

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 Install

  • 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 X.XX.XXXX - 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 Install

  • 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.

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

 #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

Please note that the schedule listed below may change depending upon the pace of the workshop! All times are Eastern Daylight Time

Time Topic
11:45 Please come early if you have any setup or installation issues.
12:00 Introductions & Workshop Plan
12:25 Accessing NEON Data
The NEON Data Portal
1:30 --------- BREAK ---------
1:45 Working with NEON Data
Use the neonUtilities Package to Access NEON Data
(Optional) Using the NEON Data API in R
2:15 Working with NEON Data of Interest
Compare tree height measured from the ground to a Lidar-based Canopy Height Model
Work with NEON OS & IS Data - Plant Phenology & Temperature
Introduction to working with NEON eddy flux data
2:45 Final Questions & Evaluation
3:00 Final Questions & Evaluation