Event - Workshop

SFS 2021 NEON Aquatic Biodiversity Workshop

May 23, 2021

Registration

Registration is required - please Register Here prior to the event.

Workshop Description

Title: Explore and work with NEON biodiversity data from aquatic ecosystems

The National Ecological Observatory Network (NEON) provides open ecological data from 81 locations across the United States. NEON data cover a wide range of subject areas within ecology, including organismal observations, biogeochemistry, remote sensing, and micrometeorology. This workshop will focus on NEON biodiversity data collected from our 34 aquatic sites, including 24 wadeable streams, 3 rivers, and 7 lakes.

Instruction will include an overview of the breadth of NEON organismal data available for taxonomic groups such as fishes, benthic macroinvertebrates, and algae, before providing code-along instruction on how to access and convert NEON organismal data into standardized formats for use with a variety of R packages commonly used to calculate standard biodiversity metrics. Examples will include Jost (2007)-style alpha, beta, and gamma diversity using the vegetarian and/or iNEXT packages; alpha, beta, and gamma variability using the ltmc package; and ordinations using the vegan package. Additionally, participants will learn about interoperability with the ecocomDP data format developed by the Environmental Data Initiative (EDI) and data discovery and visualization tools available in the ecocomDP package (https://github.com/EDIorg/ecocomDP). 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.

This workshop follows two NEON data tutorials:

  1. Explore and work with NEON biodiversity data from aquatic ecosystems
  2. Explore biodiversity with NEON algae data

This workshop does not cover the NEON Aquatic Instrument System (AIS). If you are interested in this topic, we recommend attending the ‘Explore and work with NEON aquatic instrument system data’.

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.

Participants

This 3-hr workshop is part of the 2021 Society for Freshwater Science (SFS) Virtual Meeting and will occur during the meeting on Sunday, May 23rd, 1PM - 4PM EDT (the local time zone of the event). The workshop is open to all meeting attendees. However, registration is required and the workshop is limited to 30 participants.  

NEON’s target audience for this specific workshop are those interested in learning more about the observatory’s aquatic observational system design and data collection. Instruction will guide participants in data organization and preparation approaches using the R software, with no prior experience with R necessary.

Workshop Instructors

  • Eric Sokol; Research Scientist, Quantitative Ecology; NEON program, Battelle
  • Stephanie Parker; Research Scientist, Aquatic Ecology; NEON program, Battelle
  • Donal O'Leary; Research Scientist, Science Education; 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.

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

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")
 [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.

 

Location:

TBD