Enhance Fritsche Lab coding guide with new features and updates

- Added custom footer and title includes for branding consistency.
- Introduced a new SCSS file for shared visual styles, aligning with Fritsche Lab's identity.
- Created setup SCSS for body font and color palette.
- Added favicon and brand mark SVGs for visual identity.
- Implemented accessibility improvements for table navigation.
- Developed "Agentic Coding Playbook" and "Hands-on Quick Start" documentation for practical coding tasks.
- Updated "Guide Updates" to reflect September 2026 revisions and evidence for changes.
- Introduced templates for Agent Task Brief and Session Handoff to standardize task delegation.

Author: ilarsf

CITATION.cff

@@ -6,9 +6,9 @@ authors:
   - family-names: "Fritsche"
     given-names: "Lars G."
     affiliation: "University of Michigan"
-    website: "https://medschool.umich.edu/profile/4980/lars-fritsche"
+    website: "http://fritschelab.org"
 repository-code: "https://github.com/FritscheLab/practical-genai-coding-guide"
-url: "https://FritscheLab.github.io/practical-genai-coding-guide/"
+url: "https://fritschelab.org/practical-genai-coding-guide/"
 license: "GPL-3.0-only"
 keywords:
   - "generative AI"

README.md

@@ -1,83 +1,43 @@
-# GenAI Tools for Coding & Research Workflows — A Practical 8-Step Process
+# Practical GenAI Coding Guide
 
-Welcome to this repository containing a **practical textbook** on integrating Large Language Models (LLMs) into coding and research workflows. This guide is geared toward **biostatisticians, bioinformaticians, and data scientists**, providing hands-on steps and examples to enhance productivity and maintain rigorous standards when employing GenAI tools.
+A Fritsche Lab guide to using AI assistants in biostatistics, bioinformatics, and research coding. Follow eight steps from a clear analysis plan to reviewed code, tested behavior, and reproducible documentation.
 
-## Authorship and Maintainer
+**[Read the guide](https://fritschelab.org/practical-genai-coding-guide/)** · **[Fritsche Lab](https://fritschelab.org/)**
 
-This guide is created and maintained by [Lars G. Fritsche, PhD](https://medschool.umich.edu/profile/4980/lars-fritsche), Research Associate Professor of Anesthesiology in the University of Michigan Medical School and Research Associate Professor of Biostatistics in the University of Michigan School of Public Health. Repository stewardship is through the [Fritsche Lab](https://github.com/FritscheLab).
+## Start here
 
-## How to Cite
+- **[Try the hands-on quick start](docs/QuickStart.md):** a small synthetic dataset, an R task, and checks with independently specified results.
+- **[Read the eight chapters](chapters/index.md):** planning, research, prompting, review, refinement, testing, standardization, and documentation.
+- **[Use the coding agent playbook](docs/AgenticCodingPlaybook.md):** task scope, context handoffs, review, permissions, and reproducible R workflows.
+- **[Copy a template](docs/templates/index.md):** task briefs, handoffs, project plans, code review, and documentation prompts.
 
-If you use this guide in teaching, documentation, analysis workflows, or publications, please cite the repository:
+The [September 2026 update notes](docs/Updates.md) explain the source-backed content changes and alignment with the lab website. The guide uses synthetic examples; keep protected data in its approved environment.
 
-> Fritsche, Lars G. *Practical GenAI Coding Guide: A practical 8-step process for integrating GenAI tools into coding and research workflows*. Fritsche Lab, University of Michigan. https://FritscheLab.github.io/practical-genai-coding-guide/. Accessed YYYY-MM-DD.
+## Repository map
 
-Citation metadata is available in [`CITATION.cff`](CITATION.cff) for GitHub and reference managers.
+| Path | Contents |
+| --- | --- |
+| `chapters/` | The eight-step learning sequence and conclusions. |
+| `docs/` | Quick start, playbook, appendices, references, and contributor setup. |
+| `docs/templates/` | Copyable prompts, project plans, and an R script skeleton to adapt and test. |
+| `scripts/` | Synthetic EHR and demographic data generator. |
+| `_sass/custom/`, `_includes/`, `assets/` | Lab styling and Just the Docs extension hooks. |
 
-## Repository Overview
+## Build and preview
 
-- **Chapters**  
-  1. [Chapter 1: Laying the Foundation — Plan & Context](chapters/Chapter01_PlanAndContext.md)  
-  2. [Chapter 2: Knowledge is Power — Do Your Research](chapters/Chapter02_KnowledgeIsPower.md)  
-  3. [Chapter 3: The AI Assistant — Prompt LLM to Generate Code](chapters/Chapter03_TheAIAssistant.md)  
-  4. [Chapter 4: Critical Eye — Review & Understand the Code](chapters/Chapter04_CriticalEye.md)  
-     - Introduces **Git-based version control** practices for managing LLM-generated code iterations.  
-  5. [Chapter 5: Making it Better — Refine Code & Add Features](chapters/Chapter05_MakingItBetter.md)  
-  6. [Chapter 6: The Iterative Journey — Iterate Until Satisfied](chapters/Chapter06_TheIterativeJourney.md)  
-  7. [Chapter 7: Standardization — Refactor to Lab Template](chapters/Chapter07_Standardization.md)  
-     - Explains using the **R Code Refactoring Prompt** and an **R Code Template** to enforce lab-wide coding standards.  
-  8. [Chapter 8: Sharing Your Work — Generate Documentation](chapters/Chapter08_SharingYourWork.md)  
-     - Demonstrates how to leverage the **GitHub Repository Documentation Guidelines** for creating robust project docs.  
-  - [Conclusions](chapters/Conclusions.md)  
-     - A concise, **optimized conclusion** summarizing the eight-step process and emphasizing the importance of version control, collaboration, and reproducibility.
+Use Ruby 3.3 and Bundler from the repository root:
 
-- **Docs**  
-  - [Appendix A: Recommended LLM Tools and Platforms](docs/AppendixA_RecommendedLLMTools.md)  
-  - [Appendix B: Prompt Library for Biostatistics, Bioinformatics, and Data Science](docs/AppendixB_PromptLibrary.md)  
-  - [Appendix C: Further Reading and Resources](docs/AppendixC_FurtherReading.md)  
-  - [Appendix D: Project Plans and Code Templates](docs/AppendixD_ProjectPlansAndTemplates.md)  
-    - Directs you to the individual plan and template files under `docs/templates`.  
-  - [References](docs/References.md)  
-    - Hyperlinked citations used throughout the textbook.
-
-- **Templates** (in `docs/templates/`)  
-  - **R Code Templates & Prompts**  
-    - [`R_CodeTemplate.R`](docs/templates/R_CodeTemplate.R): A production-quality script template featuring metadata, library management, CLI parsing, and more.  
-    - [`R_CodeRefactoringPromptExample.md`](docs/templates/R_CodeRefactoringPromptExample.md): Guidance for prompting an LLM to refactor your existing code according to lab standards.  
-  - **GitHub Documentation Guide**  
-    - [`GitHubRepoDocumentationGuidelines.md`](docs/templates/GitHubRepoDocumentationGuidelines.md): A prompt and template for creating comprehensive `README.md` files, environment setup instructions, and usage docs.  
-  - **Project Plans**  
-    - [`ProjectPlan_InitialDraft.md`](docs/templates/ProjectPlan_InitialDraft.md)  
-    - [`ProjectPlan_Improved.md`](docs/templates/ProjectPlan_Improved.md)  
-    - [`ProjectPlan_Advanced.md`](docs/templates/ProjectPlan_Advanced.md)  
-  - **Coding Prompt**  
-    - [`CodingPromptForRScript.md`](docs/templates/CodingPromptForRScript.md): An example prompt for generating production-ready R scripts with `data.table` and `optparse`.
-
-## How to Use This Repository
-
-1. **Follow the 8-Step Process**  
-   Read the chapters in order to learn how to plan, prompt, refine, and document your AI-assisted code effectively.  
-
-2. **Leverage the Appendices**  
-   - Check out the recommended LLM tools, curated prompts, further reading, and code templates to accelerate your workflow.
-
-3. **Explore the Templates**  
-   - Use the R templates, refactoring prompts, and documentation guidelines in `docs/templates/` to standardize your code and streamline collaboration.
-
-4. **Apply Version Control**  
-   - As described in [Chapter 4](chapters/Chapter04_CriticalEye.md), store each LLM-generated or refined code iteration in Git (e.g., GitHub) to maintain a clear history, review diffs, and revert if needed.
-
-5. **Stay Tuned for References**  
-   - All references are hyperlinked and listed in [docs/References.md](docs/References.md).
-
-## Data Simulation Script
+```bash
+bundle install
+bundle exec jekyll build
+bundle exec jekyll serve --host 127.0.0.1 --port 4000
+```
 
-If you'd like to **test your workflows** or the 8-step process on example data, we provide a script that **simulates EHR and demographic records** with realistic data quality issues:
+Open `http://127.0.0.1:4000/practical-genai-coding-guide/`. See [Development Setup](docs/DevelopmentSetup.md) for platform-specific setup, the Conda/Miniforge compiler workaround, and GitHub Pages deployment. Generated site and dependency directories stay ignored.
 
-- **Script**: [`scripts/simulate_ehr_data.R`](scripts/simulate_ehr_data.R)  
-- **Purpose**: Generates BMI, height, weight, and demographic data for a specified number of individuals, optionally introducing missing or implausible values.
+## Practice with larger synthetic data
 
-### Example Usage
+The [EHR simulator](scripts/simulate_ehr_data.md) creates measurements, demographic records, and data dictionaries. Install its documented R dependency before running, then use explicit output paths:
 
 ```bash
 Rscript scripts/simulate_ehr_data.R \
@@ -89,27 +49,20 @@ Rscript scripts/simulate_ehr_data.R \
   --n_individuals 1000
 ```
 
-**Explanation of Arguments:**
+For a first exercise requiring no R packages, use the [quick start](docs/QuickStart.md).
 
-- `--output_ehr`: Where to save the simulated EHR (BMI) data (TSV).  
-- `--output_ehr_dict`: Where to write the EHR data dictionary (TXT).  
-- `--output_demo`: Where to save the demographics data (TSV).  
-- `--output_demo_dict`: Where to write the demographics data dictionary (TXT).  
-- `--seed`: Random seed for reproducibility.  
-- `--n_individuals`: Number of unique individuals to simulate (default=1000).  
+## Contribute
 
-By running this script, you can quickly produce **synthetic data** for testing code-refinement prompts, checking your data-cleaning pipelines, or practicing the entire 8-step process from ingestion to documentation.
+Open an issue or pull request with a concrete correction, a useful research-code example, or a source-backed workflow improvement. Keep existing page paths, use synthetic fixtures, and build the site before submitting. Repository conventions are in [AGENTS.md](AGENTS.md); [Codex Agent Setup](docs/CodexAgentSetup.md) describes the project's automation support.
 
-## Contributing
+## Authorship and citation
 
-- We welcome pull requests for refinements, corrections, or extensions.  
-- Please open issues for any questions, or join discussions to keep this textbook accurate and helpful.  
-- To build or preview the Just the Docs site locally, see [Development Setup](docs/DevelopmentSetup.md).
+Created and maintained by [Lars G. Fritsche](https://medschool.umich.edu/profile/4980/lars-fritsche) and the [Fritsche Lab](https://fritschelab.org/) at the University of Michigan.
 
-## License
+> Fritsche, Lars G. *Practical GenAI Coding Guide: A practical 8-step process for integrating GenAI tools into coding and research workflows*. Fritsche Lab, University of Michigan. https://fritschelab.org/practical-genai-coding-guide/. Accessed YYYY-MM-DD.
 
-This repository is licensed under the [GNU General Public License v3.0](./LICENSE).  
+[CITATION.cff](CITATION.cff) provides citation metadata for GitHub and reference managers.
 
----
+## License
 
-**Happy learning and coding with GenAI tools!**
+[GNU General Public License v3.0](LICENSE).

_config.yml

@@ -1,6 +1,7 @@
 title: Practical GenAI Coding Guide
 description: A practical 8-step process for integrating GenAI tools into coding and research workflows.
 theme: just-the-docs
+color_scheme: light
 
 author:
   name: "Lars G. Fritsche"
@@ -9,7 +10,7 @@ author:
   biostat_profile_url: "https://sph.umich.edu/faculty-profiles/fritsche-lars.html"
   github_org: "https://github.com/FritscheLab"
 
-url: "https://FritscheLab.github.io"
+url: "https://fritschelab.org"
 baseurl: "/practical-genai-coding-guide"
 repository: FritscheLab/practical-genai-coding-guide
 
@@ -41,7 +42,7 @@ back_to_top_text: "Back to top"
 
 footer_content: >-
   Maintained by <a href="https://medschool.umich.edu/profile/4980/lars-fritsche">Lars G. Fritsche, PhD</a>
-  and the <a href="https://github.com/FritscheLab">Fritsche Lab</a>
+  and the <a href="https://fritschelab.org/">Fritsche Lab</a> at the University of Michigan
   (<a href="https://sph.umich.edu/faculty-profiles/fritsche-lars.html">Biostatistics profile</a>).
   Distributed under the <a href="https://www.gnu.org/licenses/gpl-3.0.html">GNU GPL v3.0</a>.
 
@@ -67,6 +68,8 @@ mermaid:
   version: "9.1.3"
 
 aux_links:
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   "Repository":
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 aux_links_new_tab: true

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@@ -0,0 +1,3 @@
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+<script src="{{ '/assets/js/guide-accessibility.js' | relative_url }}" defer></script>

_includes/mermaid_config.js

@@ -1,5 +1,19 @@
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_includes/nav_footer_custom.html

@@ -0,0 +1,5 @@
+<div class="guide-lab-note">
+  <a href="https://fritschelab.org/">Fritsche Lab <span aria-hidden="true">↗</span></a>
+  <span>University of Michigan</span>
+  <span>Research · Methods · Teaching</span>
+</div>

_includes/title.html

@@ -0,0 +1,2 @@
+<img class="guide-brand-mark" src="{{ '/assets/images/fritsche-lab-mark.svg' | relative_url }}" alt="" width="42" height="42">
+<span class="guide-brand-copy"><strong>Fritsche Lab</strong><span>Practical GenAI coding</span></span>