added currenlty colllected metrics

Author: codegithubka

docs/experiments.md

@@ -22,4 +22,175 @@ These phases should be completed sequentially, deepening our understanding at ea
 - Create autocorrelation plot of mean population count, following perturbations around the critical point
 	- Look for critical slowing down: perturbations to states closer to the critical point should more slowly return to the steady state
 ### Phase 4: model extensions
-- Investigate whether hydra effect and SOC still occur with diffusion and directed movement
+- Investigate whether hydra effect and SOC still occur with diffusion and directed movement
+
+---
+
+
+## What we are currently collecting:
+
+### 2D Parameter Sweep
+
+We map the full phase space to find:
+- Hydra regions
+- Critical points
+- Coexistence boundaries
+- Evolutionary advantage zones
+
+For now at least we sweep:
+
+```
+prey_birth in [0.10, 0.35]  
+prey_death in [0.001, 0.10]
+```
+
+Metrics Collected (so far):
+
+1. Population Dynamics
+
+```
+
+prey_mean: time-averaged prey pop
+prey_std: variability in prey
+
+# same for predator as above
+
+prey_survived: did prey persist
+pred_survived: did pred perist
+
+```
+
+2. Cluster structure
+
+```
+
+prey_n_clusters: total number of prey clusters
+pred_n_clusters: total number of pred clusters
+prey_tau: power law exp
+prey_s_c: cutoff cluster sizes
+pred_tau: pred cluster exp
+pred_s_c: pred cutoff
+
+```
+
+3. Order Parameters
+
+```
+prey_largest_fraction_mean
+prey_largest_fraction_std
+pred_largest_fraction_mean
+prey_percolation_prob: fraction of samples with spanning cluster
+pred_percolation_prob: predator percolation prob
+
+```
+
+
+4. Spatial Correlations
+
+```
+
+pcf_distances: distance bins in lattice units
+pcf_prey_prey_mean: prey-prey correlation function
+pcf_pred_pred_mean
+pcf_prey_pred_mean
+segregation_index: measure spatial mixing
+prey_clustering_index: short range prey clustering
+pred_clustering_index
+
+```
+
+5. Evolutionary dynamics
+
+```
+evolved_prey_death_mean: time avg evolved mortality rate
+evolved_prey_death_std
+evolved_prey_death_final
+evolve_sd: mutation strength used
+
+```
+
+---
+
+### Finite-size scaling
+
+We choose a fixed point identified in the main simulation run ```(target_prey_birth, target_prey_death)``` ideally near hydra boundary.
+
+
+For selected grid sizes (TBD) we run independent reps for each size.
+
+
+Metrics:
+
+```
+grid_size
+prey_mean, prey_std
+prey_survived: bool
+prey_largest_fraction: order parameter
+prey_percolation_prob
+prey_tau: grid size dependent exponent
+prey_tau_se: SE on tau
+prey_s_c: cutoff scales
+```
+
+---
+
+### Evo Sensitivity
+
+How does mutation strength affect evolutionary advantage in Hydra regions, speed of adaptation and final evolved mortality rates.
+
+Again. choose fixed point identified from main analysis.
+
+Metrics Dict:
+
+```
+prey_mean: in cell units as the below metrics as well
+prey_std
+pred_mean
+pred_std
+prey_survived: bool
+
++ same cluster metrics and spatial correlation metrics
+
+
+evolved_prey_death_mean: avg mortality across all prey
+evolved_prey_death_std
+evolved_prey_death_final
+evolve_sd
+```
+
+
+## Additions Required:
+
+1. Temporal dynamics for time series analysis. Needed to add critical slowing down effect near phase transitions.
+
+```
+result["prey_timeseries"] = prey_pops[::10]  # Subsample every 10 steps
+result["pred_timeseries"] = pred_pops[::10]
+
+```
+
+```
+def run_perturbation_experiment(...):
+    # Save full time series only for these special runs
+```
+
+2. Snapshots of spatial configurations. This is a costly operation so we need to figure out how and when to do it in the sim.
+
+3. Saving final grid states?
+
+```
+result["final_grid"] = model.grid.copy()
+```
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/kimon_updates.md

@@ -292,19 +292,11 @@ Options:
 2. Coarse initial parameter sweep grid
 3. Discard non-evo runs and use mean field baseline instead or the opposite
 
-NOTE: Without the optimization kernels for a 1000x1000 grid the simulation (using 50 reps for statistical power) would run for 548 hours (approximately 23 days)
+NOTE:
 
-### Results Dict
+Warmup and Measurement time must be scaled according to grid size. We need to write a method to estimate the approximate simulaiton time required. (Sary is working on that.)
 
-Add clustering size index.
-Pertrubtion on the prey count.
-Cluster size distribution mesauremnt.
 
-Sary:
-
-Bifuraction
-Clustering Measurement
-Warmpup and Measurement size