A NEON #WorkWithData Event
Date: 09 August 2015 - Ecological Society of America Meeting
Location: Baltimore, Maryland
Ecologists working across scales and integrating disparate datasets face new data management and analysis challenges that demand tools beyond the spreadsheet. This workshop will overview three key data formats: ASCII, HDF5 and las and several key data types including temperature data from a tower, vegetation structure data, hyperspectral imagery and lidar data, that are often encountered when working with ‘Big Data’. It will provide an introduction to available tools in R for working with these formats and types.
Things to Do Before the Workshop
Download The DataPlease save your data in a directory called ESA2015. National Ecological Observatory Network's San Joaquin Experimental Range and Soaproot Saddle field sites. This data is intended for educational purposes, for access to all the data for research purposes visit the NEON Data Portal. National Ecological Observatory Network's San Joaquin Experimental Range field site. The data were collected over the San Joaquin field site located in California (Domain 17) and processed at NEON headquarters. The entire dataset can be accessed from the NEON website. National Ecological Observatory Network's Airborne Observation Platform group. The .las file format is a commonly used file format to store LIDAR point cloud data.
Set Up Your Working DirectoryPlease setup your workshop working directory, which will contain all of the data downloaded above, as follows:
- Create a folder somewhere on your computer called ESA2015. this is where we will save all of the data.
- Copy all of the data downloaded above to this directory. It should look like the image below.
Setup RStudioTo participate in the workshop, we recommend that you come with R and RSTUDIO installed. R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we STRONGLY recommend RStudio, an interactive development environment (IDE).
If You Already Have R / RStudio -- please updateIf you already have R / RStudio installed on your laptop, please be sure that you are running the most current version of R-Studio, R AND all packages that we'll be using in the workshop (listed below). HINT: you can use
update.packages()to update all packages that are installed in R automatically.
Install R PackagesYou can chose to install each library individually if you already have some installed. Or you can download the script below and run it to install all libraries at once. In RStudio, you can go to `Tools --> Check for package updates` to update already installed libraries on your computer!
- sp: (installs with the raster library)
Download the Free H5 Viewer
The free H5 viewer will allow you to explore H5 data, using a graphic interface.More on the HDF viewer here
Please review the following prior to the workshop:
- A brief introduction to Lidar Data
- About the basic Lidar Derived Data Products - CHM, DEM, DSM
- Documentation for the
rasterpackage in R.
- A brief intro to the Hierarchical Data Format (HDF5) format.
- A brief intro to Hyperspectral Remote Sensing data format.
- A 5 minute video on imagery / optical remote sensing.
- Leah Wasser @leahawasser, Supervising Scientist, NEON, Inc
- Natalie Robinson, Staff Scientist, NEON, Inc
Workshop Fearless Instruction Assistants
- Claire Lunch @dr_lunch, Staff Scientist
- Kate Thibault @fluby, Senior Staff Scientist
- Christine Laney @cmlaney, Staff Scientist, NEON, Inc
- Mike Smorul @msmorul, Associate Director of Cyberinfrastructure, SESYNC
- Philippe Marchand, Scientific Support Specialist, SESYNC
Please tweet using the hashtag: “#WorkWithData” during this workshop!
Also you can tweet at @NEON_Sci !
Please note that we are still developing the agenda for this workshop. The schedule below is subject to change.
|8:00||Welcome / Introductions / Logistics|
|8:05||Getting Started with Rasters in R||Natalie|
|9:30||Raster Resolution, Extent & CRS in R||Natalie|
|10:15||——- BREAK ——-|
|10:30||LiDAR Data Derived Rasters in R||Leah|
|11:45 - 1:00 PM||Lunch on Your Own|
|1:00||Introduction to HDF5 in R||Leah|
|2:30||——- BREAK ——-|
|2:45||Hyperspectral Imagery in R||Leah|
|Done Early?||Create Raster Stacks & NDVI in R||Leah|
|3:45||——- BREAK ——-|
|4:00||Hands On Activity Options|