Work with NEON Biodiversity Data – ESA 2020

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. 

This workshop focuses on NEON biodiversity data collected from the over 80 NEON field sites. Instruction will include an overview of the breadth of NEON biodiversity data before providing code-along instruction on how to get NEON biodiversity data into standardized formats (long and wide species tables with relevant metadata to make cross data product comparisons possible).

Participants will learn about the ecocomDP data format from Environmental Data Initiative (EDI) with instruction on to convert NEON data to the format. Participants will also learn how to format and work with NEON data in a variety of standard R packages, including: Jost (2007)-style alpha, beta, and gamma diversity using the vegetarian package; alpha, beta, and gamma variability using ltmc R package; and ordinations using vegan package for R. At the end of the workshop, time will be reserved for participants to work with the NEON data of their choice with instructors present to address any questions that arise while working with the individual data sets. Basic familiarity with R is required for participation in 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 workshop is now open: Register Here. Registration is limited to 60 participants.

Workshop Schedule

All times are Eastern Daylight Time (UTC-4). See "Workshop Materials" at right for detailed workshop schedule.

Workshop Instructors

• Eric Sokol; Research Scientist, Science Education; NEON program, Battelle
• Natalie Robinson; Research Scientist, Science Education; NEON program, Battelle
• Cody Flagg; Research Scientist, Science Education; NEON program, Battelle
• Donal O'Leary; Research Scientist, Science Education; NEON program, Battelle
• Megan A. Jones; @meganahjones, Research Scientist, Science Education; NEON program, Battelle

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

Workshop Materials

Computer Set Up Instructions

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

R & RStudio

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("tidyverse")
  install.packages("vegetarian")
  install.packages("vegan")
  install.packages("devtools")
  devtools::install_github("sokole/ecocomDP@neon_demo")

More 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.

Do you Twitter?

Please tweet at @NEON_Sci or use the hashtag #NEONData during this workshop!