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run_simulation_cycles

 run_simulation_cycles (initial_state:chewc.structs.BreedingState,
                        trait:chewc.structs.Trait,
                        genetic_map:chewc.structs.GeneticMap,
                        heritabilities:jax.Array, n_cycles:int,
                        n_select:int, n_offspring:int, max_crossovers:int)

*Runs the entire multi-cycle simulation using lax.scan for high performance.

Args: initial_state (BreedingState): Starting state of the simulation. trait (Trait): Trait architecture. genetic_map (GeneticMap): Genetic map. heritabilities (jnp.ndarray): Heritability values. n_cycles (int): Number of selection cycles to run. n_select (int): Number of parents to select per cycle. n_offspring (int): Number of offspring to produce per cycle. max_crossovers (int): Maximum crossovers per chromosome.

Returns: final_state (BreedingState): The state after the last cycle. history (jnp.ndarray): Array of shape (n_cycles, 2) containing [mean_tbv, mean_phenotype] for each generation.*

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phenotypic_selection_step

 phenotypic_selection_step (carry:chewc.structs.BreedingState, _,
                            trait:chewc.structs.Trait,
                            genetic_map:chewc.structs.GeneticMap,
                            heritabilities:jax.Array, n_select:int,
                            n_offspring:int, max_crossovers:int)

*Executes one full cycle of phenotypic selection and breeding.

This function performs the following steps: 1. Phenotyping: Calculates phenotypes and True Breeding Values (TBVs). 2. Selection: Selects top n_select parents based on the first trait (index 0). 3. Mating: Generates a random mating plan. 4. Crossing: Simulates meiosis and crossover to create the next generation. 5. Update: Updates the simulation state (generation, IDs, pedigree).

Args: carry (BreedingState): Current simulation state. _ (Any): Ignored loop iterator from lax.scan. trait (Trait): Trait architecture. genetic_map (GeneticMap): Genetic map for recombination. heritabilities (jnp.ndarray): Heritability values for phenotypes. n_select (int): Number of parents to select. n_offspring (int): Number of offspring to generate. max_crossovers (int): Maximum crossovers per chromosome.

Returns: next_state (BreedingState): The updated simulation state. metrics (jnp.ndarray): Array [mean_tbv, mean_phenotype] for the first trait.*

	Type	Details
carry	BreedingState
_		Placeholder for lax.scan’s iteration number
trait	Trait
genetic_map	GeneticMap
heritabilities	Array
n_select	int
n_offspring	int
max_crossovers	int
Returns	Tuple