# Getting Started With PhotoGEA

# 1 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.

# 2 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')

# 3 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.