Getting Started With PhotoGEA

Overview

PhotoGEA (short for photosynthetic gas exchange analysis) is an R package that provides a suite of tools for loading, processing, and analyzing photosynthetic gas exchange data. See Lochocki, Salesse-Smith, & McGrath (2025) for more information.

Installing PhotoGEA

PhotoGEA is available on CRAN, so the easiest way to install the latest release is to type the following from within an R terminal:

install.packages('PhotoGEA')

Using PhotoGEA

The PhotoGEA package includes extensive documentation, and more articles are being added all the time:

• Analysis guides:
  • Analyzing C3 A-Ci Curves
  • Analyzing C4 A-Ci Curves
  • Analyzing Ball-Berry Data
  • Analyzing TDL Data
  • Analyzing Mesophyll Conductance Data
• Frequently Asked Questions: Provides answers to frequently asked questions about PhotoGEA.
• Publication Gallery: Includes a list of publications that describe or use PhotoGEA, along with links to their corresponding analysis scripts.
• General PhotoGEA advice:
  • Creating Your Own Processing Tools: Discusses how to create functions compatible with PhotoGEA that apply new types of processing.
  • Combining PhotoGEA With Other Packages: Discusses how to create wrappers for functions from other packages to extend the processing capabilities of PhotoGEA.
  • Developing a Data Analysis Pipeline: Discusses how PhotoGEA provides functionality for all parts of a data analysis pipeline, including loading and validating the data – and how it can help save your time and improve the reproducibility of your data analysis!
  • Working With Extended Data Frames: Discusses how to work with extended data frames, which are a critical part of PhotoGEA.
• General gas exchange advice:
  • Guide to Licor LI-6800 User Constants: Discusses how to include metadata in log files when using a Licor LI-6800 gas exchange measurement system, and provides advice for dealing with data sets that do not contain user constants.