Event - Workshop

SICB Workshop: Accessing and working with NEON Small Mammal Data

Jan 5, 2023

Hosted By:

Society for Integrative and Comparative Biology

This is an in-person workshop at the Society for Integrative and Comparative Biology conference in Austin, TX.

Join Sara Paull for a 1.5hr workshop on January 5, 2023 at SICB: Accessing and Working with NEON Small Mammal Data

View the SICB program here

Workshop Description

This workshop will provide an introduction to discovering, accessing and preparing NEON data using R. The workshop will include an introduction to the NEON program and data collection procedures followed by a guided data access tutorial for the small mammal dataset.

NEON provides a diversity of open access ecological data from 81 sites across the United States. At these sites, data describing organismal observations, biogeochemistry, remote sensing, and micrometeorology are collected and published for public use. Numerous organismal and environmental samples are also collected and archived at the NEON Biorepository at Arizona State University. The organismal datasets include information on the diversity, abundance, and in some cases pathogens of small mammals, terrestrial invertebrates, aquatic macroinvertebrates, fish, birds and plants.

Prerequisites 

  • Walk-in participation is welcome and attendees will receive information about the NEON program and how to access data. There will be time at the end for questions.
  • Participants who wish to engage in the code-along format will benefit from having a basic level of familiarity with working with R, including installing and loading packages, and data import.
  • Participants who wish to engage in the code-along format should ensure R or R Studio and all relevant packages are installed (neonUtilities, neonOS, ggplot2, dplyr). View the "Workshop Materials" section below for more details. 

Logistics

Workshop Instructors

  • Sara Paull; Research Scientist; 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 should be completed prior to the workshop if you wish to participate in the code-along format.  Those wishing to sit in and learn about NEON are also welcome.

To participate in the code-along portion of 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 if you wish to code along.

  • neonUtilities: install.packages("neonUtilities")
  • neonOS: install.packages("neonOS")
  • ggplot2: install.packages("ggplot2")
  • dplyr: install.packages("dplyr")

#[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

Location:

Austin, TX
United States