Introduction to Hierarchical Data Format (HDF5) - Using HDFView and R

Series Overview

This series goes through what the HDF5 format is and how to open, read, and create HDF5 files in R. We also cover extracting and plotting data from HDF5 files.

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

Series 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 using RStudio, an interactive development environment (IDE).

Download Data

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

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