CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

The Tangled Bank is a Quarto-based educational website that serves University of the Western Cape’s Biodiversity and Conservation Biology modules. The repository contains academic content for undergraduate and honours-level biology and statistics courses.

Primary Modules: - BDC223: Plant Ecophysiology (undergraduate) - BDC334: Biogeography & Global Ecology (undergraduate) - BCB744: Introduction to R & Biostatistics (honours core) - BCB743: Quantitative Ecology (honours elective)

Architecture & Structure

Content Organization: - Each module lives in its own top-level directory (e.g., BDC223/, BDC334/, BCB744/, BCB743/) - Lectures are prefixed with Lec- or L##-, labs/practicals with Lab- - Assessment materials are centralized in assessments/ directory - Supporting R code in R/ directory, data files in data/ - Generated website content in _site/ directory

Key Configuration: - _quarto.yml: Main Quarto configuration with website structure, navigation, and rendering settings - tangled_bank.Rproj: R project configuration - Website uses Quarto with custom CSS styling (LesCodex2.css, styles.scss)

Development Commands

Website Building & Preview:

# Render the entire website
quarto render

# Preview website locally with live reload
quarto preview

# Clean build artifacts
quarto clean

Content Development:

# Render specific file
quarto render path/to/file.qmd

# Render specific directory
quarto render BDC334/

File Types & Conventions

Content Files: - .qmd - Quarto markdown (primary content format) - .Rmd - R Markdown (legacy format, some assessments) - .tex - LaTeX (for some assessment PDFs) - .html - Static content and self-assessments

Data & Resources: - Educational datasets in data/ - CSV, Excel, RData formats - Academic papers and references in docs/ - Images and media in images/, module-specific subdirectories - R utility functions in R/ directory

Assessment Workflow: - Assessment templates include both .qmd source and .xlsx answer sheets - Multi-format output (HTML, PDF, Word) configured per assessment

Important Notes

This is an academic repository focused on educational content delivery
R environment uses base R and tidyverse ecosystem primarily
Content includes statistical analysis, ecological modeling, and data visualization
Website deployment handled via Netlify (status badge in README)
Uses system R library (renv removed for simplicity and performance)

Module-Specific Details

BCB744 focuses on R programming fundamentals and basic statistics BCB743 covers advanced multivariate ecology and ordination methods
BDC334 emphasizes biogeography, macroecology, and biodiversity patterns BDC223 covers plant physiological ecology and ecophysiology calculations

Reuse

CC BY-NC-SA 4.0

Citation

BibTeX citation:

@online{smit,_a._j.,
  author = {Smit, A. J.,},
  url = {http://tangledbank.netlify.app/CLAUDE.html},
  langid = {en}
}

For attribution, please cite this work as:

Smit, A. J.http://tangledbank.netlify.app/CLAUDE.html.

# CLAUDE.md This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. ## Project Overview The Tangled Bank is a Quarto-based educational website that serves University of the Western Cape's Biodiversity and Conservation Biology modules. The repository contains academic content for undergraduate and honours-level biology and statistics courses. **Primary Modules:** - **BDC223**: Plant Ecophysiology (undergraduate) - **BDC334**: Biogeography & Global Ecology (undergraduate) - **BCB744**: Introduction to R & Biostatistics (honours core) - **BCB743**: Quantitative Ecology (honours elective) ## Architecture & Structure **Content Organization:** - Each module lives in its own top-level directory (e.g., `BDC223/`, `BDC334/`, `BCB744/`, `BCB743/`) - Lectures are prefixed with `Lec-` or `L##-`, labs/practicals with `Lab-` - Assessment materials are centralized in `assessments/` directory - Supporting R code in `R/` directory, data files in `data/` - Generated website content in `_site/` directory **Key Configuration:** - `_quarto.yml`: Main Quarto configuration with website structure, navigation, and rendering settings - `tangled_bank.Rproj`: R project configuration - Website uses Quarto with custom CSS styling (`LesCodex2.css`, `styles.scss`) ## Development Commands **Website Building & Preview:** ```bash # Render the entire website quarto render # Preview website locally with live reload quarto preview # Clean build artifacts quarto clean ``` **Content Development:** ```bash # Render specific file quarto render path/to/file.qmd # Render specific directory quarto render BDC334/ ``` ## File Types & Conventions **Content Files:** - `.qmd` - Quarto markdown (primary content format) - `.Rmd` - R Markdown (legacy format, some assessments) - `.tex` - LaTeX (for some assessment PDFs) - `.html` - Static content and self-assessments **Data & Resources:** - Educational datasets in `data/` - CSV, Excel, RData formats - Academic papers and references in `docs/` - Images and media in `images/`, module-specific subdirectories - R utility functions in `R/` directory **Assessment Workflow:** - Assessment templates include both `.qmd` source and `.xlsx` answer sheets - Multi-format output (HTML, PDF, Word) configured per assessment ## Important Notes - This is an academic repository focused on educational content delivery - R environment uses base R and tidyverse ecosystem primarily - Content includes statistical analysis, ecological modeling, and data visualization - Website deployment handled via Netlify (status badge in README) - Uses system R library (renv removed for simplicity and performance) ## Module-Specific Details **BCB744** focuses on R programming fundamentals and basic statistics **BCB743** covers advanced multivariate ecology and ordination methods **BDC334** emphasizes biogeography, macroecology, and biodiversity patterns **BDC223** covers plant physiological ecology and ecophysiology calculations