Rules of phyteclub

I’m preparing my poster for the Gordon Research Conference on CO$_2$ Assimilation, which will introduce what I’m provisionally calling phyteclub, a suite of R packages for modeling and data analysis in plant ecophysiology. My poster will include a very short tutorial on how to get started in phyteclub, so I’m reproducing that here as a blog post.

Rules of phyteclub

  1. The first rule of phyteclub is: you do talk about phyteclub! Please email me ot file issues on GitHub.

  2. The second rule of phyteclub is: you do talk about phyteclub! If you find one of these packages useful in your research or teaching, please cite it. You can find citation information using citation("package_name"). Mahalo!

  3. Install R

  4. (Optional but recommended) Install RStudio

  5. Install maturing1 packages from CRAN. Open the R application and install packages using the following code:

    install.packages("gunit")
    install.packages("photosynthesis")
    install.packages("tealeaves")
    
  6. Install experimental2 packages from GitHub. Open the R application and install packages using the following code:

    install.packages("remotes")
    remotes::install_github("leafoptimizer")
    
  7. You’re ready to go! See Vignettes associated with the {tealeaves} and {photosynthesis} packages.

I want to provide an update on work I’ve been doing lately to improve the computational toolkit for plant ecophysiologists, specifically using R. This is very much a work-in-progress, but since I’ve recently released the first R packages related to this work on CRAN (see here, here, and here), I wanted to write a short post explaining my motivation and how these packages fit into the big-picture changes I would like to make in plant ecophysiology and its integration with evolutionary biology.


  1. “The API (application programming interface) of a maturing package has been roughed out, but finer details likely to change. Once released to CRAN, we will strive to maintain backward compatibility, but the package needs wider usage in order to get more feedback and find the optimal API.” https://www.tidyverse.org/lifecycle/ ^
  2. “An experimental package is in the very early stages of development. The API (application programming interface) will be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental packages will make API breaking changes without deprecation, so you are generally best off waiting until the package is more mature before you use it. Experimental packages will not be released on CRAN.” https://www.tidyverse.org/lifecycle/ ^

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