Changelog

Source: NEWS.md

EmpericalPatternR 0.1.0

Major Changes

Documentation

• Added comprehensive pkgdown documentation website
• Created three detailed vignettes:
  • getting-started: Installation, quick start, and configuration basics
  • pinyon-juniper: Complete workflow for P-J woodland simulations with nurse effects
  • ponderosa-pine: Custom configurations for different forest types
• Enhanced README with:
  • Professional badges (R-CMD-check, License)
  • Package logo and banner image
  • Quick start examples
  • Workflow diagram
  • Performance benchmarks table
  • Updated citations to Pommerening (2006, 2008) framework
• Organized function reference into 9 logical topic groups
• Created deployment documentation:
  • DOCUMENTATION_SUMMARY.md: Technical build summary
  • GETTING_STARTED_WITH_DOCS.md: User-friendly documentation guide
  • DEPLOYMENT_CHECKLIST.md: GitHub Pages deployment steps

Package Infrastructure

• Added build_pkgdown.R helper script for easy documentation rebuilding
• Updated DESCRIPTION with pkgdown URL and vignette support
• Added knitr and rmarkdown to Suggests for vignette building
• Configured VignetteBuilder for proper vignette compilation
• Added package logo (man/figures/logo.png)
• Added package banner (man/figures/banner.png)

Project Organization

• Moved example R files to misc/ folder:
  • example_pjwoodland_simulation.R
  • my_simulation.R
  • run_example.R
  • test_template.R
• Cleaned up root directory for better package structure

License

• Changed license from MIT to GPL-3
• Added LICENSE file with full GPL-3 text

Citations

• Updated from empirical data citations (Huffman, Reese, Miller, Grier) to methodological framework:
  • Pommerening, A., 2006. Evaluating structural indices by reversing forest structural analysis
  • Pommerening, A. and Stoyan, D., 2008. Reconstructing spatial tree point patterns from nearest neighbour summary statistics

Initial Release (0.1.0)

Core Features

• Simulated annealing optimization for forest stand pattern matching
• Pre-built configuration for pinyon-juniper woodlands (pj_huffman_2009())
• Flexible configuration system with create_config()
• Species-specific allometric equations
• OpenMP-parallelized C++ functions for performance
• Canopy fuel load (CFL) optimization
• Nurse tree effects for facilitation patterns
• Comprehensive analysis and visualization functions
• 62 unit tests covering all major functions

Functions

• Quick Start: pj_huffman_2009(), simulate_stand()
• Configuration: create_config(), validate_config(), print_config(), save_config()
• Allometry: calc_height(), calc_crown_radius(), calc_crown_base_height(), calc_canopy_fuel_mass()
• Stand Metrics: calc_stand_metrics(), calc_canopy_cover(), calc_clark_evans_fast()
• Energy Calculation: calc_energy(), calc_energy_cached(), calc_nurse_tree_energy()
• Perturbations: perturb_add(), perturb_remove(), perturb_move(), perturb_dbh(), perturb_species(), perturb_add_with_nurse()
• Analysis: analyze_simulation_results(), plot_simulation_results(), plot_progress()
• Utilities: adaptive_temperature(), precompute_ce_table(), Performance optimization functions