ESA Workshop: The Only Constant is Change: Programmatic Workflows to Access, Prepare and Work with NEON Plant Phenology Data to Detect Seasonal Trends

Workshop Description

The National Ecological Observatory Network (NEON) collects and provides open ecological data from over 80 locations across the United States to better understand how U.S. ecosystems are changing. 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 plant phenology observation data, primarily using R. The workshop will be divided into three sections of roughly equal length. The first section will feature an introductory presentation highlighting NEON educational resources for accessing and working with NEON data, an overview of the NEON phenology data collection protocol, and an introduction to the NEON data portal. The second section will include a code-along guide to (a) accessing data through the NEON API from an R environment using the neonUtilities and geoNEON R packages, (b) understanding the contents and quality of various data packages, and (c) performing common data merges, visualizations, summarizations, and transformations with NEON plant phenology data. In the last section, we will discuss available datasets that are relevant to NEON phenology data, including meteorological data from the NEON towers and data hosted by external partners (e.g. phenocam network and national phenology network).  Basic familiarity with R is required for participation in the workshop.

This session and the supporting materials are designed to align with the goals of the NEON project and the National Science Foundation to not only broaden participation in climate change research but to increase access to raw data and promote data literacy. The communities most vulnerable to climate change are the same that are underrepresented in climate science. Increasing access to data and analysis tools is one component of the mission to increase diversity, representation and equity in ecology and climate change science. The educational resources shared here are designed to be portable and customizable to integrate with the environmental studies curriculum or facilitate self-directed learning.

Required Prior Knowledge

The second portion of the workshop goes into how to access NEON data programmatically from the NEON data portal using R. To follow along with this portion of the workshop on your personal computer, we expect participants have a basic level of familiarity with working with R, including installing and loading packages, and data import.

Optional Introductory Assignment

• Watch the NEON: Open Data to Understand our Changing Ecosystems video to get a quick introduction to the Observatory
• Watch the Exploring and Downloading NEON Data Products video to get a quick introduction to the NEON Data Portal
• If you want to code along during the workshop, install R studio and download relevant packages to the workshop. To do this, follow the instructions in the "Workshop Materials" section on the bottom of this page.
• If you are not familiar with R, we recommend you go through our Basic R Skills Tutorial

Logistics

Date & Time

Monday, August 15th, 11:45AM - 1:15PM ET

Location: 

Montréal, Québec, Canada- Palais des congrès de Montréal 

Registration

This workshop is open to participants attending the 2022 Annual ESA Meeting in-person. Registration details can be found on the 2022 ESA meeting website. 

Workshop Schedule

All times are Eastern Daylight Time (UTC-4). 

Workshop Instructors

• Katie Jones; Research Scientist; NEON program, Battelle
• Bridget Hass; Research Scientist; NEON program, Battelle
• Marie Faust; Science Outreach Specialist; 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!

Workshop Materials

Computer Set Up Instructions

These computer workshop instructions must be completed before starting the workshop.

To participant in this workshop, you will need a computer with a version of R >3.4 and, preferably, RStudio loaded on your computer.

Setting Up R & RStudio

Windows R/RStudio Setup

• Download R for Windows here
• Run the .exe file that was just downloaded
• Go to the RStudio Download page
• Under Installers select RStudio X.XX.XXX - Windows Vista/7/8/10
• 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.

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.

install.packages("neonUtilities") install.packages("devtools") devtools::install_github("NEONScience/NEON-geolocation/geoNEON") install.packages("raster") # [additional packages may be added before the workshop]

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

Monitors

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.