licorer: Read and process LI-COR photosynthesis data files in R

Getting your LI-COR photosynthesis data into R

A lot of plant ecophysiologists are using languages like R and python to process, analyze, and visualize their photosynthetic data in a more rigorous and reproducible way. But anyone who has done this knows that importing LI-COR files into R, for example, can be annoying. We’d like this to be easier, and we’d also like to automate or script some of the basic data checks and tweeks that scientists routinely do. Ultimately, we want raw data that we can trust before it goes into an analysis pipeline.

Introducing licorer version 0.0.1 (alpha release)

With these objectives in mind, Daniel Trupp, a computational biology student in the lab, has been developing an R package to read and process LI-COR photosynthesis files. We’re really excited to make this alpha release publically available on GitHub today.

This version of licorer reads in LI-6800 raw data files, stores header information as attributes, correctly assigns units, and allows for easy data processing. In the future, other phyteclub packages will have special methods for licor-class data.

Please try it out and let us know what you think!

We need to see how the packages performs in the wild. To help with that, we’d appreciate if potential users with raw LI-6800 files could do the following:

  1. Download and install the package:
# install.packages("remotes")
remotes::install_github("muir-lab/licorer")
  1. Read in a dataset:

library(licorer)
my_data <- read_li6800_raw(system.file("/path/to/my/data")

  1. File issues:

If you run into a bug while installing or using licorer, let us know! Comments, criticisms, and contributions are welcomed! GitHub issues are the preferred way to report bugs, ask questions, or request new features. You can submit issues here: https://github.com/muir-lab/licorer/issues

  1. Request a new feature:

If there’s something you’ve always wanted to streamline or improve about your photosynthesis data processing, let us know by requesting a new feature in the issues tab: https://github.com/muir-lab/licorer/issues

Current limitations

  • licorer only working with raw LI-6800 files now. We plan to expand to LI-6400 files soon. It also doesn’t currently work with Excel files. This could change, but it will require a lot of work with limited utility since the intention is that data processing and manipulation would all be done with R scripts, making Excel unnecessary.

  • A function to batch read and combine multiple files is still in a prototype phase, but a working version will be released soon.

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