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adding documentation slowly using pdoc
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‎bash_scripts/run_phase1.sh‎

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# =============================================================================
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#
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# PHASE 1: Find critical point via 2D sweep of prey_birth × prey_death
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# - 15 × 15 × 15 reps × 2 (evo/non-evo) = 6,750 simulations
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# - Estimated runtime: ~2 min on 32 cores
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# - Memory: ~8 GB peak
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#
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# SUBMIT: sbatch run_phase1.sh
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# MONITOR: squeue -u $USER
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echo ""
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echo "Output files:"
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ls -lh $OUTPUT_DIR/
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echo ""
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echo "Next steps:"
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echo " 1. Download phase1_results.jsonl"
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echo " 2. Run analysis.py to find critical point"
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echo " 3. Update config.py with critical_prey_birth/death"
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echo " 4. Run phase 2-5"
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echo "========================================"
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echo ""

‎bash_scripts/run_phase2.sh‎

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# PP Hydra Effect - Phase 2: Self-Organization (SOC Test)
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# =============================================================================
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#
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# PHASE 2: Test if prey_death evolves toward critical point
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# - 6 initial prey_death values × 30 reps = 180 simulations
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# - Longer runs (5000 steps) for evolution to equilibrate
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# - Tracks evolved_prey_death_timeseries
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#
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# SUBMIT: sbatch run_phase2.sh
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# MONITOR: squeue -u $USER
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# CANCEL: scancel <job_id>
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echo ""
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echo "Output files:"
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ls -lh $OUTPUT_DIR/
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echo ""
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echo "Next steps:"
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echo " 1. Download phase2_results.jsonl"
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echo " 2. Plot evolved_prey_death_final vs initial prey_death"
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echo " 3. Check if all runs converge to ~0.095-0.105 (critical point)"
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echo " 4. If SOC confirmed, proceed to Phase 3 (finite-size scaling)"
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echo "========================================"
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echo ""

‎bash_scripts/run_phase3.sh‎

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# PP Hydra Effect - Phase 3: Finite-Size Scaling
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# =============================================================================
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#
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# PHASE 3: Test finite-size scaling at critical point
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# - Grid sizes: 50, 100, 250, 500, 1000
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# - 20 replicates per size = 100 simulations
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# - Cluster size distributions for power-law analysis
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#
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# SUBMIT: sbatch run_phase3.sh
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# MONITOR: squeue -u $USER
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# CANCEL: scancel <job_id>
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echo ""
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echo "Output files:"
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ls -lh $OUTPUT_DIR/
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echo ""
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echo "Next steps:"
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echo " 1. Download phase3_results.jsonl"
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echo " 2. Analyze cluster size distributions P(s) for each grid size"
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echo " 3. Fit power-law exponent tau from P(s) ~ s^(-tau)"
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echo " 4. Check finite-size cutoff s_max ~ L^D (fractal dimension)"
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echo "========================================"
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echo ""

‎bash_scripts/run_phase4.sh‎

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# PP Hydra Effect - Phase 4: Global Sensitivity Analysis
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# =============================================================================
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#
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# PHASE 4: Full 4D Parameter Sweep (Global Sensitivity)
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# - Parameters: prey_birth, prey_death, pred_birth, pred_death
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# - Sweep: 0.0 to 1.0 (11 values each) = 14,641 combinations
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# - Replicates: 10 per combination
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# - Total Simulations: ~146,410
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# - Grid Size: 250x250
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#
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# SUBMIT: sbatch run_phase4.sh
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# MONITOR: squeue -u $USER
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# CANCEL: scancel <job_id>
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echo ""
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echo "Output files:"
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ls -lh $OUTPUT_DIR/
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echo ""
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echo "Next steps:"
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echo " 1. Download phase4_results.jsonl"
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echo " 2. Perform Global Sensitivity Analysis (Sobol Indices)"
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echo " 3. Identify parameter dominance for extinction events"
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echo " 4. Plot parameter heatmaps for predator/prey survival"
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echo "========================================"
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echo ""

‎bash_scripts/run_phase5.sh‎

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#SBATCH --error=pp_phase6_%j.err
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# =============================================================================
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# PP Hydra Effect - Phase 6: Directed Hunting 4D Sweep
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# PP Hydra Effect - Phase 5: Directed Hunting 4D Sweep
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# =============================================================================
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#
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# PHASE 6: Full 4D parameter sweep with directed hunting enabled
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# - Same structure as Phase 4 but with directed_hunting=True
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# - 11^4 × 10 reps = 146,410 simulations
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# - Grid size: 250
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# - Collects time series for comparison with Phase 4
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# - Estimated runtime: ~4-6 hours on 128 cores
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# - Memory: mem=0 (use all available node memory)
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#
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# PURPOSE: Test if Hydra effect and SOC persist under directed hunting
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#
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# SUBMIT: sbatch run_phase6.sh
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echo ""
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echo "Output files:"
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ls -lh $OUTPUT_DIR/
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echo ""
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echo "Next steps:"
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echo " 1. Download phase6_results.jsonl"
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echo " 2. Compare with Phase 4 results (random hunting baseline)"
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echo " 3. Analyze if Hydra effect persists under directed hunting"
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echo " 4. Compare critical point locations between Phase 4 and Phase 6"
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echo " 5. Check for differences in SOC signatures"
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echo "========================================"
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echo ""

‎docs/index.html‎

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‎docs/models.html‎

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‎docs/models/CA.html‎

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‎docs/models/config.html‎

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‎docs/models/numba_optimized.html‎

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