Access and Work with NEON Data

August 05, 2018
Ecological Society of America Annual 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 data portal (http://neondata.org) 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 third half, 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.


This 5-hr workshop will be taught at the 2018 meeting of the Ecological Society of America (ESA) in New Orleans, LA. You must be a registered attendee of the conference and register for this workshop with your ESA registration to participate in this workshop. For more information, visit the ESA 2018 annual meeting website.


Workshop Schedule

Location: Room 353, New Orleans Ernest N. Morial Convention Center Please double check the conference schedule as rooms can change!

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

Time Topic
11:45 Please come early if you have any setup or installation issues.
12:00 Accessing NEON Data
13:30 --------- BREAK 1 ---------
13:45 Working with NEON Data
15:00 --------- BREAK 2 ---------
15:15 Working with NEON Data of Interest
16:30 Final Questions & Evaluation

Workshop Instructors

  • Claire Lunch; @dr_lunch, Research Scientist, Data Science; NEON program, Battelle
  • Megan A. Jones; @meganahjones, Research Scientist, Science Education; NEON program, Battelle
  • Christine Laney; @cmlaney, Research Scientist, Data Science/Ecoinformatics; NEON program, Battelle

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

Twitter?

Please tweet using the hashtag #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 RStudi, 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.

  • devtools: install.packages("devtools"); required to install using the install_github() function.
  • neonUtilities: install_github("NEONScience/NEON-utilities/neonUtilities", dependencies=TRUE). You must have devtools installed and running ( library(devtools)) prior to installing with install_github(). For further directions, see the start of the Use the neonUtilities Package to Access NEON Data tutorial.
  • geoNEON: install_github("NEONScience/NEON-geolocation/geoNEON”); to get specific location data for NEON data and samples.
  • raster: install.packages("raster"); to work with raster files in R.
  • rhdf5: source("https://bioconductor.org/biocLite.R"), biocLite("rhdf5"); to work with HDF5 files in R

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

 install.packages("devtools")
 install.packages("raster")
 source("http://bioconductor.org/biocLite.R")
 library(devtools)
 install_github("NEONScience/NEON-utilities/neonUtilities")
 install_github("NEONScience/NEON-geolocation/geoNEON")
 biocLite("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

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

Time Topic
11:45 Please come early if you have any setup or installation issues.
12:00 Accessing NEON Data
The NEON Data Portal
13:30 --------- BREAK 1 ---------
13:45 Working with NEON Data
Use the neonUtilities Package to Access NEON Data
(Optional) Using the NEON Data API in R
15:00 --------- BREAK 2 ---------
15:15 Working with NEON Data of Interest
Work with NEON OS & IS Data - Plant Phenology & Temperature
16:30 Final Questions & Evaluation
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