Workshop

Explore NEON Workshop - Virginia Commonwealth

University of Virginia Commonwealth

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This two-day workshop introduces participants to NEON, teaches them how to access and work with NEON data, and allows 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. 

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 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. For detailed schedule, see Workshop Materials.

Location:
25th October - Rice River Center (with social hour at 5:00 PM)

26th October - Virginia Commonwealth University T. Edward Temple Building, Room 2223

NOTE: participation is expected for both days even though the locations are different each day

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. Details provided in Workshop Materials in right menu.

Day 1: Friday 25 October

Time Topic
8:45 Room open, participants should be ready for start at 9:00
9:00 Welcome & Introductions
9:30 Exploring NEON & Accessing Data from the Data Portal
10:30 --------- BREAK ---------
10:45 Reproducible Workflows & Open Science
12:00 LUNCH (provided) w/ Poster Session of Local Research Using NEON
13:00 Access NEON Data using the neonUtilities Package
15:00 --------- BREAK ---------
15:15 Access & Explore NEON Data of Interest
17:00 End of Workshop & Start of Happy Hour

Day 2: Saturday 26 October

Time Topic
8:45 Room open, participants should be ready for start at 9:00
9:00 Access & work with NEON spatial data
10:45 --------- BREAK ---------
11:00 NEON Data Processing & Data QA/QC
12:00 --------- LUNCH (provided) ---------
13:00 Funding research involving NEON & Assignable Assets
13:30 NEON Data Activities
14:00 --------- BREAK ---------
14:15 NEON Data Activities cont.
16:30 Workshop Questions & Evaluation
17:00 End of Day

Workshop Hosts

  • Catherine Hulshof; Biology - Macroecology; Virginia Commonwealth University
  • Chris Gough; Biology - Forest Ecology; Virginia Commonwealth University
  • Lesley Bulluck; Center for Environmental Studies - Avian Ecology; Virginia Commonwealth University

Workshop Instructors

  • Natalie Robinson; Research Scientist, Data Science/Ecology/GIS; 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!

Before the Workshop

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.

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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")

Introduction to the National Ecological Observatory Network (NEON)

Here we will provide an overview of the National Ecological Observatory Network (NEON). Please carefully read through these materials and links that discuss NEON’s mission and design.

Learning Objectives

At the end of this activity, you will be able to:

  • Explain the mission of the National Ecological Observatory Network (NEON).
  • Explain the how sites are located within the NEON project design.
  • Explain the different types of data that will be collected and provided by NEON.

The NEON Project Mission & Design

To capture ecological heterogeneity across the United States, NEON’s design divides the continent into 20 statistically different eco-climatic domains. Each NEON field site is located within an eco-climatic domain.

The Science and Design of NEON

To gain a better understanding of the broad scope fo NEON watch this 4 minute long video.

Please, read the following page about NEON's mission.

Data Institute Participants -- Thought Question: How might/does the NEON project intersect with your current research or future career goals?

NEON's Spatial Design

The Spatial Design of NEON

Watch this 4:22 minute video exploring the spatial design of NEON field sites.

Please read the following page about NEON's Spatial Design:

Read this primer on NEON's Sampling Design

Read about the different types of field sites - core and relocatable

NEON Field Site Locations

Explore the NEON Field Site map taking note of the locations of

  1. Aquatic & terrestrial field sites.
  2. Core & relocatable field sites.
Click here to view the NEON Field Site Map

Explore the NEON field site map. Do the following:

  • Zoom in on a study area of interest to see if there are any NEON field sites that are nearby.
  • Use the menu below the map to filter sites by name, type, domain, or state.
  • Select one field site of interest.
    • Click on the marker in the map.
    • Then click on Site Details to jump to the field site landing page.

Data Institute Participant -- Thought Questions: Use the map above to answer these questions. Consider the research question that you may explore as your Capstone Project at the Institute or about a current project that you are working on and answer the following questions:

  • Are there NEON field sites that are in study regions of interest to you?
  • What domains are the sites located in?
  • What NEON field sites do your current research or Capstone Project ideas coincide with?
  • Is the site(s) core or relocatable?
  • Is it/are they terrestrial or aquatic?
  • Are there data available for the NEON field site(s) that you are most interested in? What kind of data are available?

NEON Data

How NEON Collects Data

Watch this 3:06 minute video exploring the data that NEON collects.

Read the Data Collection Methods page to learn more about the different types of data that NEON collects and provides. Then, follow the links below to learn more about each collection method:

All data collection protocols and processing documents are publicly available. Read more about the standardized protocols and how to access these documents.

Specimens & Samples

NEON also collects samples and specimens from which the other data products are based. These samples are also available for research and education purposes. Learn more: NEON Biorepository.

Airborne Remote Sensing

Watch this 5 minute video to better understand the NEON Airborne Observation Platform (AOP).

Data Institute Participant – Thought Questions: Consider either your current or future research or the question you’d like to address at the Institute.

  • Which types of NEON data may be more useful to address these questions?
  • What non-NEON data resources could be combined with NEON data to help address your question?
  • What challenges, if any, could you foresee when beginning to work with these data?

Data Tip: NEON also provides support to your own research including proposals to fly the AOP over other study sites, a mobile tower/instrumentation setup and others. Learn more here the Assignable Assets programs .

Access NEON Data

NEON data are processed and go through quality assurance quality control checks at NEON headquarters in Boulder, CO. NEON carefully documents every aspect of sampling design, data collection, processing and delivery. This documentation is freely available through the NEON data portal.

Pathways to access NEON Data

There are several ways to access data from NEON:

  1. Via the NEON data portal. Explore and download data. Note that much of the tabular data is available in zipped .csv files for each month and site of interest. To combine these files, use the neonUtilities package (R tutorial, Python tutorial).
  2. Use R or Python to programmatically access the data. NEON and community members have created code packages to directly access the data through an API. Learn more about the available resources by reading the Code Resources page or visiting the NEONScience GitHub repo.
  3. Using the NEON API. Access NEON data directly using a custom API call.
  4. Access NEON data through partner's portals. Where NEON data directly overlap with other community resources, NEON data can be accessed through the portals. Examples include Phenocam, BOLD, Ameriflux, and others. You can learn more in the documentation for individual data products.

Data Institute Participant – Thought Questions: Use the Data Portal tools to investigate the data availability for the field sites you’ve already identified in the previous Thought Questions.

  • What types of aquatic/terrestrial data are currently available? Remote sensing data?
  • Of these, what type of data are you most interested in working with for your project while at the Institute.
  • For what time period does the data cover?
  • What format is the downloadable file available in?
  • Where is the metadata to support this data?

Data Institute Participants: Intro to NEON Culmination Activity

Write up a brief summary of a project that you might want to explore while at the Data Institute in Boulder, CO. Include the types of NEON (and other data) that you will need to implement this project. Save this summary as you will be refining and adding to your ideas over the next few weeks.

The goal of this activity if for you to begin to think about a Capstone Project that you wish to work on at the end of the Data Institute. This project will ideally be performed in groups, so over the next few weeks you'll have a chance to view the other project proposals and merge projects to collaborate with your colleagues.

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. This activity is option and those familiar with the tool will have the opportunity to use GitHub for online code collaboration during the workshop during the Data Activities section.

Version Control with GitHub

Day 1: Friday 25 October

Time Topic
8:45 Room open, participants should be ready for start at 9:00
9:00 Welcome & Introductions
9:30 NEON Introduction ( video)
9:45 Accessing NEON Information (neonscience.org and biorepo.neonscience.org)
10:00 Exploring & Accessing NEON Data from the Data Portal
Access NEON Data using The Data Portal Visual Guide (direct download of PPT)
10:30 --------- BREAK ---------
10:45 Reproducible Workflows & Open Science
Importance of Reproducible Research
Download for File Organization activity (5.6 MB)
Optional: Importance of Sharing, Publishing, and Archiving Code & Data
RStudio help: Using R Projects
12:00 --- LUNCH (provided) with Poster Session of local research being done using NEON data ---
13:00 Access NEON Data using the neonUtilities Package
14:15 Understanding NEON Data - Documentation & Structure
15:00 --------- BREAK ---------
15:15 Access & Explore NEON Data of Interest
17:00 End of Instruction & Start of Happy Hour

Day 2: Saturday 26 October

Time Topic
8:45 Room open, participants should be ready for start at 9:00
9:00 Access & work with NEON spatial data
10:45 --------- BREAK ---------
11:00 NEON Data Processing & Data QA/QC
Data processing videos – Observational Sampling, Instrumented Sampling, Airborne Observation Platform.
12:00 --------- LUNCH (provided) ---------
13:00 NEON Data Activities (specific activities will depend on participant interest)
Work with NEON OS & IS Data - Plant Phenology & Temperature
Introduction to working with NEON eddy flux data
Compare tree height measured from the ground to a Lidar-based Canopy Height Model
Introduction to working with PhenoCam Images
14:00 --------- BREAK ---------
14:15 NEON Data Activities cont.
16:30 Workshop Questions & Evaluation
17:00 End of Day