Package index

Quick Start

Main functions for running simulations and analyzing results.

simulate_stand()

Simulate Forest Stand with Simulated Annealing

analyze_simulation_results()

Analyze and Report Simulation Results

pj_huffman_2009()

Create Pinyon-Juniper Configuration (Huffman et al. 2009)

Configuration System

Functions for creating, validating, and managing simulation configurations.

create_config()

Create Custom Simulation Configuration

validate_config()

Validate Configuration

print_config()

Print Configuration Summary

save_config()

Export Configuration to File

generate_config_template()

Generate Template Configuration File

Allometric Equations

Functions for calculating tree attributes from DBH and species.

calc_height()

Calculate tree height from DBH using allometric equations

calc_crown_radius()

Calculate crown radius from DBH and height using allometric equations

calc_crown_base_height()

Calculate crown base height from DBH and total height

calc_canopy_fuel_mass()

Calculate canopy fuel mass from DBH

get_default_allometric_params()

Get default allometric parameters for pinyon-juniper woodland

get_ponderosa_allometric_params()

Get default allometric parameters for ponderosa pine forest

allometric_equations

Allometric Equations for Forest Simulation

Stand Metrics

Functions for calculating stand-level characteristics.

calc_canopy_cover()

Calculate total canopy cover accounting for overlap

calc_canopy_cover_fast()

Fast Canopy Cover Calculation (Vectorized)

calc_stand_metrics()

Calculate all stand-level metrics

calc_stand_metrics_parallel()

Parallel Metric Calculation

calc_clark_evans_fast()

Fast Spatial Pattern Metrics

calc_tree_attributes()

Calculate all tree attributes from basic measurements

calc_tree_attributes_fast()

Batch Tree Attribute Calculation

Energy Calculation

Functions for evaluating how well a stand matches target patterns.

calc_energy()

Calculate energy (deviation from targets)

calc_energy_cached()

Energy Calculation with Caching

calc_mortality_probability()

Calculate Size-Dependent Mortality Probability

calc_nurse_tree_energy()

Calculate Nurse Tree Association Energy

should_full_update()

Batch Update Check

Perturbation Functions

Functions for modifying stand structure during optimization.

perturb_add()

Add a new tree

perturb_remove()

Remove a random tree

perturb_move()

Move a random tree to a new location

perturb_dbh()

Adjust DBH of a random tree

perturb_species()

Change species of a random tree

perturb_add_with_nurse()

Add Tree with Nurse Tree Effect

Mortality and History

Functions for simulating disturbance and tracking optimization.

simulate_mortality()

Simulate Post-Disturbance Mortality

update_history_efficient()

Memory-Efficient History Storage

adaptive_temperature()

Adaptive Temperature Schedule

Visualization

Functions for plotting simulation results and progress.

plot_simulation_results()

Plot Simulation Results

plot_progress()

Plot progress during simulation - showing objective progress

print_simulation_summary()

Print Simulation Summary

Performance Utilities

Optimized versions of calculation functions.

precompute_ce_table()

Pre-compute Clark-Evans Lookup Table

Package Documentation

EmpericalPatternR-package EmpericalPatternR

EmpericalPatternR: Forest Stand Pattern Simulation