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BreedingState

 BreedingState (population:__main__.Population, key:jax.Array,
                generation:int, next_id:int)

*The complete, self-contained state of a single simulation replicate at a point in time.

This object is the primary carrier passed between steps in the simulation.

Attributes: population (Population): The current population of individuals. key (jax.Array): The JAX pseudo-random number generator key. generation (int): The current generation number of the simulation.*

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Trait

 Trait (qtl_chromosome:jax.Array, qtl_position:jax.Array,
        qtl_effects:jax.Array, qtl_dominance_effects:jax.Array,
        intercept:jax.Array)

*Defines the genetic architecture of one or more traits.

This structure holds the information linking genotypes to phenotypes, based on an additive and dominance QTL model.

Attributes: qtl_chromosome (jnp.ndarray): Chromosome index for each QTL. Shape: (n_qtl,) qtl_position (jnp.ndarray): Locus index for each QTL within its chromosome. Shape: (n_qtl,) qtl_effects (jnp.ndarray): The additive effect of each QTL on each trait. Shape: (n_qtl, n_traits) qtl_dominance_effects (jnp.ndarray): The dominance effect of each QTL on each trait. Shape: (n_qtl, n_traits) intercept (jnp.ndarray): The base value for each trait. Shape: (n_traits,)*

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Population

 Population (geno:jax.Array, ibd:jax.Array, meta:jax.Array)

*Represents a collection of individuals within a breeding program.

Attributes: geno (jnp.ndarray): Genotypes. Shape: (n_individuals, n_chr, 2, n_loci) ibd (jnp.ndarray): Identity-by-descent tracking for founder alleles. Shape: (n_individuals, n_chr, 2, n_loci) meta (jnp.ndarray): Metadata [id, mother_id, father_id, birth_gen]. Shape: (n_individuals, 4)*

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GeneticMap

 GeneticMap (chromosome_lengths:jax.Array,
             locus_positions:List[jax.Array])

*Defines the genetic map of the organism.

Attributes: chromosome_lengths (jnp.ndarray): The genetic length of each chromosome in Morgans. Shape: (n_chr,) locus_positions (List[jnp.ndarray]): A list where each element is a JAX array containing the Morgan positions of loci for a single chromosome.*

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msprime_pop

 msprime_pop (key:jax.Array, n_ind:int, n_chr:int, n_loci_per_chr:int,
              ploidy:int=2, effective_population_size:int=15000,
              mutation_rate:float=1e-07,
              recombination_rate_per_chr:float=1e-08,
              maf_threshold:float=0.05, base_chr_length:int=500000,
              num_simulated_individuals:Optional[int]=None,
              enforce_founder_maf:bool=True)

*Simulate a founder population from an msprime ancestry model.

The output matches the lightweight Population/GeneticMap structures used by the workflow notebooks so it can plug straight into trait sampling, phenotype simulation, and selection routines.*

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quick_haplo

 quick_haplo (key:jax.Array, n_ind:int, n_chr:int, seg_sites:int,
              inbred:bool=False, chr_length:float=1.0)

Create a simple founder population and a uniform genetic map.

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add_trait

 add_trait (key:jax.Array, founder_pop:__main__.Population,
            n_qtl_per_chr:int, mean:jax.Array, var_a:jax.Array,
            var_d:jax.Array, sigma:jax.Array)

Sample QTLs and multi-trait effects for both additive and dominance components.

	Type	Details
key	Array
founder_pop	Population
n_qtl_per_chr	int
mean	Array	(n_traits,)
var_a	Array	Additive variance (n_traits,)
var_d	Array	Dominance variance (n_traits,)
sigma	Array	(n_traits, n_traits) PSD
Returns	Trait

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compute_dosage

 compute_dosage (population:__main__.Population)

*Computes the dosage of the ‘1’ allele for each individual at each locus.

Dosage is calculated as the sum of alleles across the two homologous chromosomes, resulting in values of 0, 1, or 2.

Args: population: A Population object.

Returns: A 3D array of dosages with shape (n_individuals, n_chr, n_loci).*

key = jax.random.PRNGKey(42)
founder_pop = quick_haplo(
key=key,
n_ind=10,
n_chr=3,
seg_sites=100,
inbred=False
 )