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R Bloggers
Date(s): - Aug 9, 2015

A NEON #WorkWithData Event

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.

Visit the Workshop Etherpad

Background Materials

Things to Do Before the Workshop

Download The Data

Please save your data in a directory called ESA2015.
Download NEON Teaching Data Subset: Field Site Spatial Data
These remote sensing data files provide information on the vegetation at the 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.
Download NEON Teaching Data Subset: Imaging Spectrometer Data - HDF5
These hyperspectral remote sensing data provide information on the 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.
Download NEON Teaching Data Subset: Sample LiDAR Point Cloud Data (.las)
This .las file contains sample LiDAR point cloud data collected by 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 Directory

Please setup your workshop working directory, which will contain all of the data downloaded above, as follows:
  1. Create a folder somewhere on your computer called ESA2015. this is where we will save all of the data.
  2. Copy all of the data downloaded above to this directory. It should look like the image below.
Your working directory should look like the above image. NOTE: we will setup the ESA2015.Rproj file together at the beginning of the workshop.
We will be setting up an R-Studio project within this working directory. Read more about R-Studio projects, here. In R studio, your working directory space will look like this:
Your working directory in R should look like the above image. NOTE: we will setup the ESA2015.Rproj file together at the beginning of the workshop.

Setup RStudio

To 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 update

If 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 Packages

You 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!
  • raster: install.packages("raster")
  • sp: (installs with the raster library) install.packages("sp")
  • rgdal: install.packages("rgdal")
  • maptools: install.packages("maptools")
  • ggplot2: install.packages("ggplot2")
  • rgeos: install.packages("rgeos")
  • dplyr: install.packages("dplyr")
  • rhdf5: source(""); biocLite("rhdf5")

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:

Workshop Instructors

Workshop Fearless Instruction Assistants

#WorkWithData Hashtag

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.

Time Topic Instructor
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  

Morning Session - Working with Rasters in R

Afternoon Session - Working with HDF5 files