stomata-ilima

This repository contains source code associated with the manuscript:

Amphistomy increases leaf photosynthesis more in coastal than montane plants of Hawaiian ʻilima (Sida fallax). 2024. The American Journal of Botany. 111(2):e16284.

Author contributions

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.

Contents

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

Prerequisites:

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.

Downloading data and code

1. Download or clone this repository to your machine.

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

2. Open stomata-ilima.Rproj in RStudio

Rendering manuscript

Software requirements

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.

Rendering manuscript with pre-saved outout

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

Generating all results

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