✨ Set up comprehensive Copilot instructions with modern R tooling

.gitignore

@@ -10,3 +10,10 @@ inst/doc
 docs
 /doc/
 /Meta/
+
+# R CMD check build artifacts
+.Rcheck/
+*.Rcheck/
+..Rcheck/
+*.tar.gz
+bregr_*.tar.gz

copilot-instructions.md

@@ -0,0 +1,237 @@
+# GitHub Copilot Instructions for bregr R Package
+
+This file contains comprehensive instructions for GitHub Copilot to effectively work with the `bregr` R package repository.
+
+## Repository Overview
+
+The `bregr` package is an R package for easy and efficient batch processing of regression models. It provides tools for running univariate and multivariate regression models in batch, returning results in tidy format with visualization capabilities.
+
+### Package Structure
+- **Type**: Standard R package
+- **Language**: R (>= 4.1.0)
+- **Testing**: testthat framework
+- **Documentation**: roxygen2 + pkgdown
+- **CI/CD**: GitHub Actions with R-CMD-check
+- **Dependencies**: tidyverse ecosystem, statistical modeling packages
+
+### Key Components
+- `R/`: Core R functions for batch regression modeling
+- `tests/testthat/`: Unit tests and example tests
+- `man/`: Auto-generated documentation files
+- `vignettes/`: Package vignettes and tutorials
+- `data-raw/`: Raw data processing scripts
+- `DESCRIPTION`: Package metadata and dependencies
+
+## Development Environment Setup
+
+### R Installation (Using rig + pak - RECOMMENDED)
+
+Use the modern R installation manager `rig` and package installer `pak` for optimal development experience:
+
+```bash
+# Install rig (R Installation Manager)
+curl -Ls https://github.com/r-lib/rig/releases/download/latest/rig-linux-latest.tar.gz | sudo tar xz -C /usr/local
+
+# Install latest R release
+sudo rig add release
+
+# Verify installation
+rig list
+R --version
+```
+
+**Timing**: rig installation ~1 minute, R installation ~5-8 minutes
+
+### Package Dependencies Installation
+
+```bash
+# Navigate to package directory
+cd /path/to/bregr
+
+# Install all package dependencies using pak (much faster than install.packages)
+R --slave -e "pak::local_install_deps()"
+
+# Install additional development tools
+R --slave -e "pak::pak(c('knitr', 'rmarkdown', 'testthat', 'pkgdown'))"
+```
+
+**Timing**: Dependencies installation ~4-6 minutes, dev tools ~2-3 minutes
+
+### System Dependencies
+
+Essential system packages (automatically handled by pak):
+- `pandoc` (for vignettes and documentation)
+- `libxml2-dev`, `libcurl4-openssl-dev`, `libssl-dev` (for various R packages)
+- Graphics libraries: `libfreetype6-dev`, `libjpeg-dev`, `libpng-dev`, `libtiff-dev`
+
+## Build and Testing Commands
+
+### Package Building
+
+```bash
+# Quick build (without vignettes) - recommended for development
+R CMD build . --no-build-vignettes
+
+# Full build (with vignettes) - for release
+R CMD build .
+```
+
+**Timing**: Quick build ~10-20 seconds, Full build ~5-10 minutes
+
+### Package Checking
+
+```bash
+# Quick check (skip suggested packages)
+_R_CHECK_FORCE_SUGGESTS_=false R CMD check package_*.tar.gz --no-manual
+
+# Full check (requires all suggested packages)
+R CMD check package_*.tar.gz --no-manual
+```
+
+**Timing**: Quick check ~2-3 minutes, Full check ~10-15 minutes
+
+### Running Tests
+
+```bash
+# Install package locally first
+R --slave -e "pak::local_install('.')"
+
+# Run tests
+R --slave -e "testthat::test_dir('tests/testthat')"
+
+# Test basic functionality
+R --slave -e "library(bregr); mtcars_result <- br_pipeline(mtcars[1:10,], y='mpg', x=c('cyl','disp'), method='gaussian'); print('Success!')"
+```
+
+**Timing**: Local install ~10-15 seconds, Tests ~30-60 seconds
+
+### Documentation Building
+
+```bash
+# Build pkgdown site
+R --slave -e "pkgdown::build_site()"
+
+# Update documentation
+R --slave -e "devtools::document()"
+```
+
+**Timing**: pkgdown build ~2-5 minutes, documentation update ~30 seconds
+
+## Package Functionality
+
+### Core Features
+- `br_pipeline()`: Main function for batch regression modeling
+- `br_show_*()`: Visualization functions (forest plots, tables, networks)
+- Support for multiple regression methods: gaussian, binomial, cox, etc.
+- Tidy output format compatible with broom ecosystem
+
+### Supported Models
+- Linear regression (`gaussian`)
+- Logistic regression (`binomial`)
+- Cox proportional hazards (`coxph`)
+- Poisson regression (`poisson`)
+- And more (see vignettes for full list)
+
+### Example Usage
+```r
+library(bregr)
+
+# Simple linear regression example
+result <- br_pipeline(
+  data = mtcars,
+  y = "mpg",
+  x = c("cyl", "disp", "hp"),
+  method = "gaussian"
+)
+
+# Visualize results
+br_show_forest(result)
+br_show_table(result)
+```
+
+## Development Workflow
+
+### Making Changes
+1. Edit R functions in `R/` directory
+2. Update documentation with roxygen2 comments
+3. Run `devtools::document()` to update man files
+4. Test changes with `testthat::test_dir('tests/testthat')`
+5. Build and check package with `R CMD build` and `R CMD check`
+
+### Adding New Functions
+1. Create function in appropriate R file in `R/` directory
+2. Add roxygen2 documentation with `@export` if public function
+3. Add unit tests in `tests/testthat/`
+4. Update `NAMESPACE` with `devtools::document()`
+5. Consider adding examples to vignettes if it's a major feature
+
+### Performance Considerations
+- Use `pak` instead of `install.packages()` for faster package management
+- Skip vignette building during development iterations
+- Use `_R_CHECK_FORCE_SUGGESTS_=false` for faster checking
+- Consider parallel testing for large test suites
+
+## Common Issues and Solutions
+
+### Build Issues
+- **Vignette build failures**: Often due to missing suggested packages, build without vignettes for development
+- **Dependency conflicts**: Use `pak::pak_sitrep()` to diagnose issues
+- **System library missing**: pak will usually install automatically, but check error messages
+
+### Testing Issues
+- **Package not found errors**: Make sure to install package locally with `pak::local_install('.')`
+- **Suggested package errors**: Install missing packages or use `_R_CHECK_FORCE_SUGGESTS_=false`
+
+### Documentation Issues
+- **Missing exports**: Add `@export` to roxygen2 comments and run `devtools::document()`
+- **Cross-reference errors**: Check that referenced packages are available
+
+## Performance Metrics (Typical Timings)
+
+- **rig setup**: ~1 minute
+- **R installation**: ~5-8 minutes  
+- **Package dependencies**: ~4-6 minutes
+- **Quick build**: ~10-20 seconds
+- **Quick check**: ~2-3 minutes
+- **Local install**: ~10-15 seconds
+- **Test suite**: ~30-60 seconds
+- **pkgdown build**: ~2-5 minutes
+- **Full check**: ~10-15 minutes
+- **Full build with vignettes**: ~5-10 minutes
+
+## Best Practices
+
+1. **Use rig and pak**: Modern, faster alternatives to traditional R installation and package management
+2. **Incremental development**: Use quick builds and checks during development
+3. **Test early and often**: Install locally and test after each significant change
+4. **Documentation-driven development**: Keep roxygen2 comments up to date
+5. **Leverage CI/CD**: Let GitHub Actions handle full checks for pull requests
+6. **Version control**: Use meaningful commit messages and atomic commits
+
+## Troubleshooting
+
+### Package Manager Issues
+```bash
+# Update pak
+R --slave -e "pak::pak_update()"
+
+# Clear pak cache
+R --slave -e "pak::cache_clean()"
+
+# Check pak status
+R --slave -e "pak::pak_sitrep()"
+```
+
+### R Environment Issues
+```bash
+# List installed R versions
+rig list
+
+# Switch R version if needed
+rig default 4.5.1
+
+# Check R configuration
+R --slave -e "sessionInfo()"
+```
+
+This setup provides a modern, efficient development environment for the bregr R package using best practices and contemporary tools.