Metabolic and structural leaf mass

Code repostitory to run the analysis and generate the manuscript for Katabuchi et al. "Decomposing leaf mass into metabolic and structural components explains divergent patterns of trait variation within and among plant species"

Masatoshi Katabuchi, Kaoru Kitajima, S. Joseph Wright, Sunshine A. Van Bael, Jeanne L. D. Osnas and Jeremy W. Lichstein

Reproduce the results

Codes (R and STAN) and workflow are managed with the R package targets (https://github.com/ropensci/targets).

Running code on local

To run analysis:

# To install R packages for the first run
# Rscript -e "renv::restore()"
Rscript run.R

To generate the manuscript:

make

Requirements:

• cmdstan 2.34.1
• quarto
• latexdiff
• R (4.3.2)
  • renv (renv::restore() will install all the R packages)

Running code in Apptainer (Linux)

To build the Apptainer container:

sudo apptainer build radian.sif radian.def

or you can download the container from XXX.

To run analysis or to render the manuscript:

# To install R packages for the first run
# apptainer exec --env RENV_PATHS_CACHE=/home/${USER}/renv \
		# --env RENV_PATHS_PREFIX_AUTO=TRUE \
 		# radian.sif Rscript run.R -e "renv::restore()"

> ./run.sh
1) tar_make() on local
2) tar_make() on Apptainer
3) Enter in the Apptainer container
4) make (render manuscript) on the Apptainer container
Enter number：

Requirements:

• Apptainer (or singularity)
• renv directory on your home