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Add UCD-SeRG Lab Manual reference to copilot-instructions #184

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Add UCD-SeRG Lab Manual reference to copilot-instructions #184

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Initial plan
Copilot Jan 27, 2026
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Add UCD-SeRG Lab Manual reference to copilot-instructions
Copilot Jan 27, 2026
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18 changes: 18 additions & 0 deletions .github/copilot-instructions.md
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- **Key Dependencies**: runjags, rjags, JAGS 4.3.1, serocalculator, ggmcmc, dplyr, ggplot2
- **Lifecycle**: Experimental (under active development)

## Lab-Wide Guidance

**Follow the guidance in the [UCD-SeRG Lab Manual](https://ucd-serg.github.io/lab-manual/)**, which provides comprehensive best practices for:
- Culture and conduct
- Communication
- Reproducibility
- Code repositories and version control
- Coding practices and style
- Working with big data
- Quarto and documentation
- GitHub workflows
- Reproducible environments
- Code and data publication
- AI tools usage
- And more

If the web version is inaccessible, refer to the [source files on GitHub](https://github.com/UCD-SERG/lab-manual) for easier reading.
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## Critical Setup Requirements

### Copilot Setup Workflow (Automatic Environment Configuration)
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: serodynamics
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9047
Version: 0.0.0.9048
Authors@R: c(
person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
comment = "Author of the method and original code."),
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1 change: 1 addition & 0 deletions NEWS.md
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Workspace sessions much faster.
* Reorganized pkgdown documentation with new "Getting Started" guide demonstrating main API workflow, organized articles into "Get started" and "Developer Notes" sections (#73).
* Added `.github/workflows/copilot-setup-steps.yml` GitHub Actions workflow to automate environment setup for GitHub Copilot coding agent, preinstalling R, JAGS, and all dependencies.
* Added reference to UCD-SeRG Lab Manual in copilot-instructions for lab-wide best practices guidance.

* Consolidated OS-specific snapshot variants: removed redundant Linux and Windows
snapshot directories (which were identical), keeping only base snapshots and
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