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NEON EDUCATION

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LiDAR (5)
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Hyperspectral Remote Sensing (7)
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R Bloggers
Date(s): - Aug 7, 2016

Overview

This workshop will focus on working with spatial time series data, raster GeoTIFF format, in R. The working dataset is derived from remote sensing data. Participants will learn how to efficiently explore raster metadata and address projection-related issues, how to automate processing a raster time series, and how work with raster stacks in support of both RGB and time series data.

The outcome goal of this workshop is a plot of NDVI over time derived from a raster time series that can be used to compare plant phenology at multiple sites. We will focus on the rasterand rgdal packages in R. rasterVis will be used to create raster time series plots.

All materials taught in this workshop were developed in collaborative effort between Data Carpentry and the National Ecological Observatory Network (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.


This 5-hr workshop will be taught at the 2016 meeting of the Ecological Society of America (ESA) in Ft. Lauderdale, FL. You must be a registered attendee of the conference and register for this workshop to participate in this workshop. For more information, visit the ESA 2016 annual meeting website.

Things You’ll Need For 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.

For details on setting up RStudio in Mac, PC, or Linux operating systems please see the instructions below.

Install R Packages

Please have these packages installed and updated prior to the start of the workshop.

  • raster: install.packages("raster")
  • rgdal: install.packages("rgdal")
  • rasterVis: install.packages("rasterVis")
  • ggplot2: install.packages("ggplot2")

Updating 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.

Download Data

Download NEON Teaching Data Subset: Airborne Remote Sensing Data

The LiDAR and imagery data used to create this raster teaching data subset were collected over the National Ecological Observatory Network’s Harvard Forest and San Joaquin Experimental Range field sites and processed at NEON headquarters. The entire dataset can be accessed by request from the NEON Airborne Data Request Page on the NEON website.

Download NEON Teaching Data Subset: Landsat-derived NDVI raster files

The imagery data used to create this raster teaching data subset were collected over the National Ecological Observatory Network’s Harvard Forest and San Joaquin Experimental Range field sites.
The imagery was created by the U.S. Geological Survey (USGS) using a multispectral scanner on a Landsat Satellite. The data files are Geographic Tagged Image-File Format (GeoTIFF).

Once you have downloaded the data, please set up a “data” directory as a parent directory to these three uncompressed directories. Set your R working directory to this “data” directory prior to the beginning of the workshop. If you would like further instruction please see the bottom of this page for detailed instructions.

Workshop Instructors

  • Megan A. Jones; @meganahjones, Staff Scientist/Science Educator; NEON program, Battelle
  • Mike Patterson; Science Technician & Geospatial Analyst; NEON program, Battelle
  • Tristan Goulden; Associate Scientist, Airborne Platform; NEON program, Battelle

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

#WorkWithData Hashtag

Please tweet using the hashtag #WorkWithData during this workshop!

Workshop Schedule

Location: Ft Lauderdale Convention Center, Rm 317 Please double check the conference schedule as rooms may change!

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

Time Topic
11:45 Please come early if you have any setup or installation issues.
12:00 Introduction to Working With Raster Data in R
  When Raster’s Don’t Line Up: Coordinate Reference System & Reprojection
13:30 ——— BREAK 1 ———
13:45 NEON Remote Sensing Data Products Overview
14:15 Raster Time Series Data in R: Tutorials 05–07
15:00 ——— BREAK 2 ———
15:15 Raster Time Series Data in R, continued
16:30 Final Questions & Evaluation
16:45 END with enough time to get to the ESA Opening Plenary

Online Tutorials

All NEON workshops and self-paced tutorials can be accessed via the NEON Data Skills portal.


Additional Set Up Resources

Set Working Directory to Downloaded Data

1) Download Data

First, download the data linked in the blue buttons above.

  • NEON Teaching Data Subset: Airborne Remote Sensing Data
  • NEON Teaching Data Subset: Landsat NDVI
Screenshot of the Data that you should download, prior to the workshop. (Note: the screenshots show a `NEON-DS-Site-Layout-Files` folder. This contains vector files we will not be using for this workshop. You will not be downloading this directory). Source: National Ecological Observatory Network (NEON)

After clicking on the Download Data button, the data will automatically download to the computer.

2) Locate .zip file

Second, find the downloaded .zip file. Many browsers default to downloading to the Downloads directory on your computer. Note: You may have previously specified a specific directory (folder) for files downloaded from the internet, if so, the .zip file will download there.

3) Move to data directory

Third, move the data files to a directory called data directory within the Documents directory on your computer.

4) Unzip/uncompress

Fourth, we need to unzip/uncompress the file so that the data files can be accessed. Use your favorite tool that can unpackage/open .zip files (e.g., winzip, Archive Utility, etc). The files will now be accessible in three directories:

  • NEON-DS-Airborne-Remote-Sensing
  • NEON-DS-Landsat-NDVI

These directories contain all of the subdirectories and files that we will use in this workshop.

Screenshot of the computer's Downloads folder containing the file structure. Source: National Ecological Observatory Network (NEON)

Windows R / RStudio Setup

Once R and R studio are installed, open RStudio to make sure it works and you don’t get any error messages.

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 R studio are installed, open RStudio to make sure it works and you don’t get any error messages.

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 R studio are installed, open RStudio to make sure it works and you don’t get any error messages.