Access & Use of NEON Data: Aquatics Training Palooza 2018

January 18, 2018
NEON

Through participation in this workshop,  full-time field ecologists on the NEON project will improve their ability to work with the local scientific community (site hosts, local researchers, and other potential NEON data users) by increasing their knowledge of the online resources available from NEON and the skills needed to access NEON data. In addition, the workshop will enable the field ecologists to directly work with NEON data by teaching them basic data skills that will increase their ability to conduct basic QA/QC on the data.

Objectives

At the end of the workshop, NEON aquatic field ecologists will be able to:

  • Explain to site hosts and researchers at the sites where to go for more information on NEON, NEON data collection methods, NEON data, and training on using NEON data (neonscience.org).
  • Explain to site hosts and researchers at field sites where to find information on what data is available for download (data.neonscience.org).
  • Explain to potential data users multiple methods for accessing NEON data:
    • through NEON data portal
    • direct API calls
    • through software packages, like the R package nneo
  • Download data for a specified data product, site, and time frame from the data portal.
  • Use the neonstackR package to combine multiple site/months .csv files to get a complete data set of interest.
  • Produce line/bar plots of data products of interest.

Things You’ll Need To Complete This Workshop

1) Install/Update Software

To participant in this workshop, you will need a laptop with the most current version of R, and, preferably, RStudio loaded on your computer. For details on installing RStudio in Mac, PC, or Linux operating systems, please see the Additional Set Up Instructions section at the bottom of this page.

Please note, while these packages are required, a working knowledge of using R and RStudio is not required.

If you already have these installed on your laptop, please be sure that you are running the most current version of RStudio, R and all packages that we'll be using in the workshop (listed below).

2) Install R Packages

  • neonDataStackR: devtools::install_github("NEONScience/NEON-utilities/neonDataStackR")

If you already have it installed, please update you version of neonDataStackR as it is frequently updated.

More on Packages in R

3) Data to Download

The link to download the example data will be posted in mid-December.

Please keep the downloaded data in your "Downloads" folder. This data is downloaded as back up in case there are issues with the internet connectivity or data portal during the workshop.

Workshop Instructor

  • Megan A. Jones; @meganahjones; Staff Scientists/Science Educator, NEON

Please get in touch with the instructor prior to the workshop with any questions.

Twitter?

Please tweet @NEON_sci and with the #WorkWithData hashtag during the workshop.

Schedule

Please note that the schedule listed below may change depending upon the pace of the workshop!

Time Topic
12:45 Information for Understanding NEON: neonscience.org
13:15 Accessing NEON data: data.neonscience.org
14:00 --------- BREAK ---------
14:15 Accessing NEON data, cont.
14:45 Using the neonDataStackR script in R
15:00 Working with NEON data products
15:30 --------- BREAK ---------
15:45 Working with NEON data products, cont.
16:45 Data Skills Assignment Description

Additional Set Up Resources

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

  • If your Mac is set up for UiO use, you can install R from Managed Software Center

  • 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 10.6+ (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.

Time Topic
12:45 Information for Understanding NEON: neonscience.org
13:15 Accessing NEON data: data.neonscience.org
14:00 --------- BREAK ---------
14:15 Accessing NEON data, cont.
Download via the Data Portal
Access through the NEON API
Access using software packages, like nneo R package
14:45 Using the neonDataStackR script in R
15:00 Working with NEON data products
15:30 --------- BREAK ---------
15:45 Working with NEON data products, cont.
16:45 Data skills assignment description

Related Tutorials

Tutorial: Use the neonDataStackR Package to Access NEON Data

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: Using the NEON API in R

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

R Tutorials for Working with NEON Data

During the working with NEON data products portion of the workshop we will primarily be working in spreadsheets. The tutorials below are a few of the available ones that show you have to do similar things with NEON data in R.

Series: Work with NEON OS & IS Data - Plant Phenology & Temperature

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Series: Introduction to Working With Time Series Data in Text Formats in R

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

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