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R Bloggers

A NEON #WorkWithData Workshop

Date: Spring 2015

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

Goals / Objectives

After completing this workshop, you will:
  1. Know what the Hierarchical Data Format (HDF5) is.
  2. Know How to create and read from HDF5 files in R.
  3. Know how to read and visualization time series data stored in an HDF5 format.

Before the Workshop Please

Data to Download

Install R Libraries

  • rhdf5: source("") biocLite("rhdf5")
  • ggplot2: A great plotting library. install.packages("ggplot2")
  • dplyr: data manipulation at its finest! install.packages("dplyr")
  • scales: this library makes it easier to plot time series data. install.packages("scales")

Review These Materials

Click here for the Etherpad


Time Topic Instructor
11:30 DPLYR Basics  
12:30 What is HDF5?  
12:30 Explore an HDF5 File (HDFviewer)  
12:45 Create an HDF5 file in R  
2:00 Working with and visualizing time series data in HDF5 format ??


To participate in the workshop, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of the workshop.


Hierarchical Data Format 5 (HDF5) is a file format used to store, package, and simultaneously organize large quantities of related data. Although we will use R to analyze data stored in this format, HDFView is free-ware that allows for quick and easy viewing and editing of these files.


R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we recommend, RStudio, an interactive development environment (IDE).