Explore NEON Workshop - University of Puerto Rico

This three-day workshop introduces participants to NEON, teaches them how to access and work with NEON data, and to allow them to interact with NEON science staff to get assistance working on the data they are interested in using. The workshop includes hands-on, interactive instruction on how to access and work with NEON data, both through the NEON data portal and programmatically. The third day is an optional site visit to the NEON Guanica field site. 

Participation & Registration

Workshop space is limited and the workshop hosts welcome applications from anyone with interest in using and learning more about NEON data (graduate students, postdocs, researchers, motivated undergraduates). 

Registration for this workshop is now closed. 

Required Prior Knowledge

All coding instruction will be conducted in R and participants will be able to complete the workshop best if they have at least an introduction to coding. Participants without past experience working in a programming environment are encouraged to complete a basic introduction to R to understand the basics -- training options can be found on the Resources for Learning R page. Participants using other programming languages are welcome to attend, however, instruction and assistance in the language may not be available.

Workshop Schedule

Schedule subject to change. 

Location: University of Puerto Rico - Rio Piedras, Room C-236 (Natural Sciences)

Pre-Workshop

All participants will be asked to complete self-paced online tutorials before the workshop to have their laptops set up for the workshop and to learn about version control & online collaboration with GitHub. 

Day 1: Friday 20 September

Day 2: Saturday 21 September

Day 3: Sunday 22 September

Workshop Hosts

• Carla López Lloreda, Luquillo Critical Zone Observatory
• Jess Zimmerman, Institute for Tropical Ecosystem Studies, University of Puerto Rico, Rio Piedras
• Carla Restrepo, Dept. Biology, University of Puerto Rico, Rio Piedras
• Elvia Meléndez-Ackerman, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras

Workshop Instructors

• Claire Lunch; @dr_lunch, Research Scientist, Data Science; 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.

Additional NEON scientists will be active in the Explore NEON Workshop.

Twitter?

Please tweet using #NEONData & @NEON_Sci during this workshop!

Workshop Materials

R

To participant in this workshop, you will need a laptop with the most current version of R, and preferably RStudio, loaded on your computer. Prior to the workshop you should have R and, preferably, RStudio installed on your computer. If you have no prior experience using R or a programming language, please consider taking the time to do a brief introduction to R. Suggestions are provided on Resources for Learning R.

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.

• neonUtilities: install.packages("neonUtilities"); to access NEON data specific functions
• raster: install.packages("raster"); to work with raster files in R
• rhdf5: install.packages("BiocManager"), BiocManager::install("rhdf5"); to work with HDF5 files in R
• devtools: install.packages("devtools"); required to install using the install_github() function.
• geoNEON: install_github("NEONScience/NEON-geolocation/geoNEON”); to get specific location data for NEON data and samples. You must have devtools installed and running ( library(devtools)) prior to installing with install_github(). For further directions, see the start of the Use the neonUtilities Package to Access NEON Data tutorial.

If you want to install all of them, you can use the following code.

 install.packages("neonUtilities")
 install.packages("raster")
 install.packages("BiocManager")
 BiocManager::install("rhdf5")
 install.packages("devtools")
 library(devtools)
 install_github("NEONScience/NEON-geolocation/geoNEON")

Version Control & Online Collaboration with GitHub

Please complete the self-paced online training on Version Control and Online Collaboration using GitHub prior to the workshop so that we can use these tools during the workshop.

Series: Version Control with GitHub

GET STARTED

Tutorial: Introduction to the National Ecological Observatory Network (NEON)

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