Explore NEON Workshop

November 08, 2018 - November 09, 2018
NEON

This two-day workshop introduces graduate students to NEON, teach them how to access and work with NEON data, and allow them to interact with NEON science staff. The workshop includes hands-on, interactive instruction on how to access and work with NEON data, both through the NEON data portal and programmatically via the API.

Required Prior Knowledge

All participants are expected to have some coding experience. All coding instruction will be conducted in R. Participants using other programming languages are welcome to attend, however, instruction and assistance in the language may not be available.

Workshop Schedule

Location: NEON Headquarters, Boulder, CO

Schedule subject to change.

Day 1: Thursday 8 November

Time Topic
8:30 Arrival at NEON Headquarters
8:45 Welcome to NEON
9:30 Accessing NEON Data from the Data Portal
10:15 --------- BREAK ---------
10:30 Use the neonUtilities Package to Access NEON Data
11:15 Understanding NEON Data
12:00 --------- LUNCH ---------
13:00 NEON Tour
15:00 --------- BREAK ---------
15:15 Working with NEON Data of Interest
15:45 (Optional) NEON API tutorial
16:30 Networking with NEON Scientists

Day 2: Friday 9 November

Time Topic
8:30 NEON Biorepository & Archival Samples
9:30 Reproducible Workflows & Open Science
10:45 --------- BREAK ---------
11:00 Career Paths; NEON Scientist Panel
12:00 --------- LUNCH ---------
13:00 NEON Data Processing & Data QA/QC
14:00 --------- BREAK ---------
14:15 NEON Data Activities
16:30 Workshop Questions & Evaluation

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 the hashtag #NEONData & @NEON_Sci during this workshop!

Workshop & Travel Logistics

Only selected applicants are allowed to attend this workshop. All travel & hotel arrangements will be made through Battelle/NEON – please do not make any of your own travel arrangements (other than getting to/from your local airport). For more on workshop logistics and getting around Boulder, please see the Workshop Logistics page.

Before the Workshop

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.

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 RStudi, 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.

  • devtools: install.packages("devtools"); required to install using the install_github() function.
  • neonUtilities: install_github("NEONScience/NEON-utilities/neonUtilities", dependencies=TRUE). 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.
  • geoNEON: install_github("NEONScience/NEON-geolocation/geoNEON”); to get specific location data for NEON data and samples.
  • raster: install.packages("raster"); to work with raster files in R.
  • rhdf5: source("https://bioconductor.org/biocLite.R"), biocLite("rhdf5"); to work with HDF5 files in R

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

 install.packages("raster")
 install.package("neonUtilities")
 install.packages("devtools")


 source("http://bioconductor.org/biocLite.R")
 biocLite("rhdf5")
 library(devtools)
 install_github("NEONScience/NEON-geolocation/geoNEON")

Schedule

Day 1: Thursday 8 November

Time Topic
8:30 Arrival at NEON Headquarters
8:40 Welcome to NEON ( video)
9:30 Accessing NEON Data from the Data Portal
10:15 --------- BREAK ---------
10:30 Use the neonUtilities Package to Access NEON Data
Download and Explore NEON data - specific script used in workshop
11:15 Understanding NEON Data
12:00 --------- LUNCH ---------
13:00 NEON Tour
15:00 --------- BREAK ---------
15:15 Working with NEON Data of Interest
15:45 (Optional) NEON API tutorial
16:30 Networking with NEON Scientists

Day 2: Friday 9 November

Time Topic
8:30 Beyond the Downloadable Data: NEON Biorepository & More
9:30 Reproducible Workflows & Open Science
Reproducible Research Slideshow
Messy Directory Exercise (direct download 5MB)
Version Control with GitHub
10:45 --------- BREAK ---------
11:00 Career Paths; NEON Scientist Panel
12:00 --------- LUNCH ---------
13:00 NEON Data Processing & Data QA/QC
14:00 --------- BREAK ---------
14:15 NEON Data Activities
16:30 Workshop Questions & Evaluation

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