Introduction to Hierarchical Data Format (HDF5) - Using HDFView and R feature image Source: National Ecological Observatory Network
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Series: Introduction to Hierarchical Data Format (HDF5) - Using HDFView and R

In this series we cover what a HDF5 format is and how to open, read, and create HDF5 files in R. We also cover extracting and plotting data from HDF5 files.

ata used in this series are from the National Ecological Observatory Network (NEON) and are in HDF5 format.

Series Goals / Objectives

After completing the series you will:

  • Understand how data can be structured and stored in HDF5
  • Understand how metadata can be added to an HDF5 file
  • Know how to explore HDF5 files using HDFView, a free tool for viewing HDF4 and HDF5 files
  • Know how to work with HDF5 files in R
  • Know how to work with time-series data within a nested HDF5 file

Things You’ll Need To Complete This Series

You will need the most current version of R and, preferably, RStudio loaded on your computer to complete this tutorial.

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).

Download Data

Data is available for download in those tutorials that focus on teaching data skills.


Set Working Directory: This lesson assumes that you have set your working directory to the location of the downloaded and unzipped data subsets. An overview of setting the working directory in R can be found here.

R Script & Challenge Code: NEON data lessons often contain challenges that reinforce learned skills. If available, the code for challenge solutions is found in the downloadable R script of the entire lesson, available in the footer of each lesson page.

Tutorials in Series