<commit_before>---
layout: workshop
title: "NEON Intro to HDF5 Workshop"
estimatedTime: 3.0 - 3.5 Hours
packagesLibraries: RHDF5
date:   2015-1-15 20:49:52
dateCreated:   2015-2-23 10:49:52
lastModified: 2015-05-21 22:11:52
authors: <NAME>
tags: [Data-Workshops]
mainTag: Data-Workshops
description: "This workshop introduces the concept of Hierarchical Data Formats. Learn what an HDF5 file is. Explore HDF5 files in the free HDFviewer. Create and open HDF5 file sin R."
code1: 
image:
  feature: hierarchy_folder_green.png
  credit: <NAME> NEON, Inc.
  creditlink: http://www.neoninc.org
permalink: /Data-Workshops/NEON-HDF5-TimeSeries-In-R
comments: true 
---

###A NEON #WorkWithData Workshop

**Date:** Spring 2015

This workshop will provide hands on experience with working hierarchical data formats(HDF5) in R.


<div id="objectives">

<h3>Goals / Objectives</h3>
After completing this workshop, you will:
<ol>
<li>Know what the Hierarchical Data Format (HDF5) is.</li>
<li>Know How to create and read from HDF5 files in R.</li>
<li>Know how to read and visualization time series data stored in an HDF5 format.</li>
</ol>

<h3>Before the Workshop Please</h3>

<h4>Data to Download</h4>
<ul>
<li><a href="{{ site.baseurl }}/data/NEON_TowerDataD3_D10.hdf5" class="btn btn-success">Download the National Ecological Observatory Network (NEON) Flux Tower Temperature data HERE.</a> </li>
<li><a href="http://neonhighered.org/Data/HDF5/SJER_140123_chip.h5" class="btn btn-success">Download the NEON Airborne Observation Platform Spectrometer Data HDF5 File.</a> </li>

<li><a href="http://neonhighered.org/Data/D17_2013_SJER_vegStr.zip" class="btn btn-success">Download the sample NEON vegetation structure data from California.</a> </li>

</ul>
NOTE: The second file downloaded above has an ".h5" extension while the first has an HDF5 extension. Both extensions represent the HDF5 data type.


<h4>Install R Libraries</h4>
<ul>
<li>rhdf5: <code>source("http://bioconductor.org/biocLite.R")
biocLite("rhdf5")</code></li>
<li>ggplot2: A great plotting library. <code>install.packages("ggplot2")</code> </li>
<li>dplyr: data manipulation at its finest! <code>install.packages("dplyr")</code></li>
<li>scales: this library makes it easier to plot time series data. <code>install.packages("scales")</code></li>
</ul>

</div>


##SCHEDULE


| Time        | Topic         | Instructor | 
|-------------|---------------|------------|<commit_msg>Added link to background material<commit_after>---
layout: workshop
title: "NEON Intro to HDF5 Workshop"
estimatedTime: 3.0 - 3.5 Hours
packagesLibraries: RHDF5
date:   2015-1-15 20:49:52
dateCreated:   2015-2-23 10:49:52
lastModified: 2015-05-21 22:11:52
authors: <NAME>
tags: [Data-Workshops]
mainTag: Data-Workshops
description: "This workshop introduces the concept of Hierarchical Data Formats. Learn what an HDF5 file is. Explore HDF5 files in the free HDFviewer. Create and open HDF5 file sin R."
code1: 
image:
  feature: hierarchy_folder_green.png
  credit: <NAME> NEON, Inc.
  creditlink: http://www.neoninc.org
permalink: /Data-Workshops/NEON-HDF5-TimeSeries-In-R
comments: true 
---

###A NEON #WorkWithData Workshop

**Date:** Spring 2015

This workshop will provide hands on experience with working hierarchical data formats(HDF5) in R.


<div id="objectives">

<h3>Goals / Objectives</h3>
After completing this workshop, you will:
<ol>
<li>Know what the Hierarchical Data Format (HDF5) is.</li>
<li>Know How to create and read from HDF5 files in R.</li>
<li>Know how to read and visualization time series data stored in an HDF5 format.</li>
</ol>

<h3>Before the Workshop Please</h3>

<h4>Data to Download</h4>
<ul>
<li><a href="{{ site.baseurl }}/data/NEON_TowerDataD3_D10.hdf5" class="btn btn-success">Download the National Ecological Observatory Network (NEON) Flux Tower Temperature data HERE.</a> </li>
<li><a href="http://neonhighered.org/Data/HDF5/SJER_140123_chip.h5" class="btn btn-success">Download the NEON Airborne Observation Platform Spectrometer Data HDF5 File.</a> </li>

<li><a href="http://neonhighered.org/Data/D17_2013_SJER_vegStr.zip" class="btn btn-success">Download the sample NEON vegetation structure data from California.</a> </li>

</ul>
NOTE: The second file downloaded above has an ".h5" extension while the first has an HDF5 extension. Both extensions represent the HDF5 data type.


<h4>Install R Libraries</h4>
<ul>
<li>rhdf5: <code>source("http://bioconductor.org/biocLite.R")
biocLite("rhdf5")</code></li>
<li>ggplot2: A great plotting library. <code>install.packages("ggplot2")</code> </li>
<li>dplyr: data manipulation at its finest! <code>install.packages("dplyr")</code></li>
<li>scales: this library makes it easier to plot time series data. <code>install.packages("scales")</code></li>
</ul>

<h4>Review These Materials</h4>
<ul>
<li>[Please review this page on the HDF5 format.]({{ site.baseurl }}/HDF5/About/) </li>
</ul>
</div>


##SCHEDULE


| Time        | Topic         | Instructor | 
|-------------|---------------|------------|
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