SFS Access & Explore NEON Aquatic Instrument Data Workshop

NEON data cover a wide range of subject areas, this virtual workshop focuses on NEON aquatic instrument systems (AIS) data collected continuously from our 34 aquatic sites, including 24 wadable streams, 3 rivers, and 7 lakes. AIS data products span water quality, surface and groundwater elevations, and meteorological instrumentation.

Instruction will include an overview of the breadth of available NEON AIS data and data product naming conventions, before jumping using the neonUtilities R package to access NEON AIS data. Participants will then learn how to interpret NEON data by referencing metadata records and standardized quality flags. In the final portion of the workshop, participants will be able to explore the individual AIS data products of interest to their research while NEON staff are on hand to address specific questions.  

This is an introductory workshop for individuals interested in learning how to access NEON data and understanding the details associated with interpreting instrument data and quality flags. Participants will then learn to apply common data preparation approaches for applications to time series analyses and modeling. While participants with no prior coding experience are welcome to participate, some live-coding and instruction will be provided in R. This is not an introduction to R workshop and a basic understanding of R will facilitate participation.  

For users interested in aquatic observational data in the context of biodiversity, we suggest participating in the Explore and work with NEON biodiversity data from aquatic ecosystems workshop. 

Workshop Recording

A recording of this workshop is available for 1 year from the workshop date on the Society for Freshwater Science Summer of Science webpage: https://www.sfssummerofscience.com/30-neon

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 2020 Society for Freshwater Science (SFS) Summer of Science. The workshop, and other events in the Summer of Science, is free to members of SFS. However, registration is required and the workshop is limited to 40 participants.

NEON’s target audience for this specific workshop are those interested in learning more about the observatory’s aquatic instrument system design, and/or wish to better understand the formatting and quality flagging of NEON instrument data. Instruction will guide participants in data organization and preparation approaches using the R software, with no prior experience with R necessary.

A registration link will be provided once registration is open.

Workshop Schedule

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

Workshop Instructors

• Guy Litt; Research Scientist, Hydrology/Aquatic Instrumentation; NEON program, Battelle
• Bobby Hensley; Research Scientist, Aquatic Biogeochemist; NEON program, Battelle
• Claire Lunch; Twitter: @dr_lunch, Data 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 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")
 [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.