This repository contains source code associated with the manuscript:

Amphistomy increases leaf photosynthesis more in coastal than montane plants of Hawaiian ʻilima (Sida fallax). Accepted at The American Journal of Botany.

Genevieve Triplett and Chris Muir contributed equally to all stages of this project; Tom Buckley contributed to development of the method and helped edit the manuscript.

This repository has the following file folders:

• figures: figures generated from original artwork and R code
• objects: saved objects generated from R code
• processed-data: processed data generated from R code
• ms: manuscript input (e.g. ms.qmd, si.qmd and stomata-ilima.bib) and output (e.g. ms.pdf, si.pdf) files
• r: R scripts for all data processing and analysis
• raw-data: raw data files

To run code and render manuscript:

• R version >4.3.0 and RStudio (recommended)
• LaTeX: you can install the full version or try tinytex
• GNU Make: In terminal, you can just type make paper to render the manuscript. You can also use it to re-run all scripts.

Before running scripts, you'll need to install the following R packages:

source("r/install-packages.R")

To fit brms model, set up cmdstanr.

1. Download or clone this repository to your machine.

git clone [email protected]:cdmuir/stomata-ilima.git

2. Open stomata-ilima.Rproj in RStudio

At minimum, you will need R version 4.3.0 or greater installed on your machine. Install additional packages by running r/install-packages.R.

Open ms/ms.qmd and knit using RStudio.

You can also run the following code from the terminal:

quarto render ms/ms.qmd
quarto render ms/si.qmd

or use make

make paper

You can re-run all analyses, figures, etc. using GNU make. Type make --version in a terminal/shell to see if it is already installed.

# Clear out previously saved output
make cleanall
# This will take a long time to run
make