environment.yml

# Conda Environment for Cross-Language Reproducibility
# Alternative to renv for users who need R + Python + system dependencies
name: quick-start-template
channels:
  - conda-forge
  - r
  - nodefaults

dependencies:
  # R Base
  - r-base>=4.0
  
  # Core R packages for data analysis
  - r-tidyverse>=1.3.0
  - r-dplyr>=1.0.0
  - r-ggplot2>=3.3.0
  - r-tidyr>=1.2.0
  - r-stringr>=1.4.0
  - r-readr>=2.0.0
  - r-purrr>=0.3.0
  
  # R packages for reproducible research
  - r-knitr>=1.30
  - r-rmarkdown>=2.0
  - r-bookdown>=0.20
  - r-config>=0.3
  - r-here>=1.0
  
  # R packages for data manipulation and analysis
  - r-janitor>=2.0
  - r-lubridate>=1.7
  - r-forcats>=0.5
  - r-scales>=1.1
  - r-broom>=0.7
  
  # R packages for modeling and statistics  
  - r-caret>=6.0
  - r-randomforest>=4.6
  - r-glmnet>=4.0
  - r-mass>=7.3
  
  # R packages for visualization
  - r-cowplot>=1.1
  - r-gridextra>=2.3
  - r-ggbeeswarm>=0.6
  
  # R database connectivity
  - r-dbi>=1.1
  - r-rsqlite>=2.2
  - r-odbc>=1.3  # For SQL Server connectivity
  
  # Python (if needed for mixed workflows)
  - python>=3.8
  - pandas>=1.3
  - numpy>=1.20
  - matplotlib>=3.3
  - seaborn>=0.11
  - jupyter>=1.0
  - ipykernel>=6.0
  
  # System tools and utilities
  - git>=2.30
  - curl>=7.70
  - openssl>=1.1
  
  # Development tools
  - make>=4.3
  - cmake>=3.18
  
  # Additional dependencies via pip (if needed)
  - pip
  - pip:
    - quarto-cli  # Document rendering
    # Add any Python packages not available via conda

# Environment configuration
variables:
  R_LIBS_USER: $CONDA_PREFIX/lib/R/library
  PYTHONPATH: $CONDA_PREFIX/lib/python3.8/site-packages