simulation_parameters.json

{
  "simulation_directory": "simulations",
  "nruns": 100,
  "scaled_recombination_rate": 0.1,
  "msprime_parameters": {
    "samples": 50,
    "ploidy": 2,
    "sequence_length": 100,
    "num_replicates": 10000
  },
  "alphas": [
    1.05, 1.1, 1.15, 1.2, 1.25, 1.3, 1.35, 1.4, 1.45, 1.5, 1.55, 1.6, 1.65, 1.7,
    1.75, 1.8, 1.85, 1.9, 1.95
  ],
  "growth_rates": [0.5, 1.0, 2.0],
  "end_times": [0.5, 1.0, 2.0],
  "k_max": 20,
  "num_epochs": 5,
  "penalty_coef": 1e-6,
  "slim_parameters": {
    "num_samples": 100,
    "genome_length": 1e5,
    "recombination_rate": 1e-5,
    "num_bp": 100,
    "num_trees": 500,
    "genome_cutoff": 0.2,
    "nruns": 1000
  },
  "positive_sel_coeffs": [0.025, 0.05, 0.075, 0.1, 0.125, 0.15, 0.2],
  "positive_mut_rates": [1e-9, 1e-10],
  "power_pair_densities": [5000, 10000, 20000],
  "power_sequence_lengths": [25],
  "power_num_samples": 1000,
  "power_reps": 100,
  "search_r_low": 0.071,
  "search_r_high": 0.141,
  "search_iters": 5,
  "search_num_replicates": 500000
}