run_genetic_simulation: Run a high-level genetic simulation with configurable model

Description

Run a high-level genetic simulation with configurable model

Usage

run_genetic_simulation(
  n_pops = 30,
  n_major_groups = 4,
  n_subgroups = 8,
  model = "mixed",
  geo_dims = NULL,
  isolation_factor = NULL,
  genetic_dims = NULL,
  group_separation = 15,
  subgroup_separation = NULL,
  pop_dispersion = 0.5,
  admixture_prob = 0.15,
  bottleneck_prob = 0.1,
  use_subgroups = TRUE,
  use_genetic_dims = NULL,
  use_admixture = TRUE,
  use_bottlenecks = TRUE,
  use_isolation_by_distance = NULL,
  use_nonlinear = TRUE,
  use_noise = TRUE,
  seed = NULL,
  output_file = NULL,
  verbose = TRUE
)

Value

List with results and plots (functions to print plots)

Arguments

n_pops: Number of populations
n_major_groups: Number of major groups
n_subgroups: Number of subgroups
model: One of "mixed", "geography", "genetics", or "custom"
geo_dims: Geographic dimensions (overrides default based on model if set)
isolation_factor: Geography-genetics balance (overrides default based on model if set)
genetic_dims: Genetic dimensions (overrides default based on model if set)
group_separation: Separation between major groups
subgroup_separation: Separation between subgroups (default: group_separation/3 when NULL)
pop_dispersion: Within-subgroup dispersion
admixture_prob: Proportion of admixed populations
bottleneck_prob: Proportion of bottlenecked populations
use_subgroups: Whether to create subgroups
use_genetic_dims: Whether to include genetic dimensions
use_admixture: Whether to include admixture
use_bottlenecks: Whether to include bottlenecks
use_isolation_by_distance: Whether to weight geographic distance
use_nonlinear: Whether to apply nonlinear transformation
use_noise: Whether to add noise
seed: Optional seed forwarded to simulate_genetic_distances()
output_file: Optional CSV file path to write the distance matrix
verbose: Print diagnostics