Plant Breeding Data Analysis Course - Baku

This repository contains the Quarto project for the plant breeding data analysis course materials, specifically designed for breeders in Baku, in collaboration with ICARDA.

Project Structure

• `_quarto.yml`: Main configuration file for the Quarto project (defines book structure, output formats including slides).
• `index.qmd`: The main landing page/introduction chapter for the book format.
• `00_Setup_Intro/` to `06_GIGWA_AI/`: Folders containing course modules as Quarto (`.qmd`) files.
• `code/`: R scripts.
• `data/`: Datasets (`raw/`, `example/`, `processed/`).
• `figures/`: Saved plots.
• `output/`: Location for rendered outputs (HTML book, PDF book, slides).
  • `pdfs/`: Placeholder for final PDFs.
• `resources/`: Supplementary materials.
• `assets/`: Contains shared assets like logos.
  • `icarda_logo.png`: IMPORTANT: Replace this placeholder with the actual logo file.
• `custom.css`: Custom CSS rules, including adding the ICARDA logo to `revealjs` slides.
• `README.md`: This file.
• `gitignore`: Specifies files/directories for Git to ignore.

How to Use and Render

1. Prerequisites: R, RStudio, Quarto, LaTeX (e.g., run `tinytex::install_tinytex()` in R console).
2. Replace Logo: Put the actual `icarda_logo.png` file into the `assets/` directory. Adjust size/position in `custom.css` if needed.
3. Open Project: Open in RStudio (use `File > New Project > Existing Directory...`).
4. Install R Packages: Add necessary package installation commands (e.g., `install.packages(c("tidyverse", "rrBLUP", "qqman", "readxl", "writexl"))`) to `00_Setup_Intro/01_Setup_R_RStudio.qmd` and run them in the R console.
5. Render Specific Formats: Use the Terminal in RStudio:
   • HTML Book: `quarto render` (Default based on `project: type: book`) -> output in `output/_book/`
   • PDF Book: `quarto render --to pdf` -> output PDF in `output/`
   • HTML Slides (revealjs): `quarto render .qmd --to revealjs` (e.g., `quarto render 01_R_Basics/01_Intro_To_R.qmd --to revealjs`) -> output as `.html` in the source directory.
   • PDF Slides (beamer): `quarto render .qmd --to beamer` (e.g., `quarto render 01_R_Basics/01_Intro_To_R.qmd --to beamer`) -> output as `.pdf` in the source directory.
   • Note on Slide Warnings: The warnings "revealjs/beamer format is not supported by book projects" appear when rendering the whole book. They mean these formats are ignored for the book build, but you can still render individual files to these formats using the commands above.

Course Content Overview

See the `_quarto.yml` file or the rendered book's Table of Contents for module details. The `.qmd` files contain skeletal content that needs further development.