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https://img.shields.io/badge/DOI-10.1002%2Fajb2.16038-green DOI License: MIT

Sources and consequences of mismatch between leaf disc and whole-leaf leaf mass per area (LMA)

Phisamai Maenpuen, Masatoshi Katabuchi, Yusuke Onoda, Cong Zhou, Jiao-Lin Zhang, Ya-Jun Chen

Code repository to run the analysis and generate the manuscript for Maenpuen et al. "Sources and consequences of mismatch between leaf disc and whole-leaf leaf mass per area (LMA)". https://doi.org/10.1002/ajb2.16038

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 2.29.2
  • pandoc
  • pandoc-crossref
  • latexdiff
  • R (4.1.3)
    • renv (renv::restore() will install all the R packages)

Running code in Apptainer (Linux)

First, change RENV_PATHS_CACHE in radian.def and tinytex.def to your path (i.e., RENV_PATHS_CACHE=<your_path>" ).

To build Apptainer containers:

sudo apptainer build radian.sif radian.def
sudo apptainer build tinytex.sif tinytex.def

To run analysis:

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

To generate the manuscript:

# To install R packages for the first run
# Rscript -e "renv::restore()"
apptainer exec tinytex.sif make

Requirements:

  • Apptainer (or Singularity)
  • cmdstan 2.29.2 (radian.sif does not contain cmdstan)