RecurrentSelectionBreedingProgram

class pybrops.breed.arch.RecurrentSelectionBreedingProgram.RecurrentSelectionBreedingProgram(initop, pselop, mateop, evalop, sselop, t_max, start_genome=None, start_geno=None, start_pheno=None, start_bval=None, start_gmod=None, **kwargs)

Bases: BreedingProgram

Class implementing recurrent selection. This class is very generic and highly modular to facilitate rapid prototyping.

Constructor for the concrete class RecurrentSelectionBreedingProgram.

This class simulates a recurrent selection breeding program.

Parameters:

• initop (InitializationOperator) –

• pselop (ParentSelectionOperator) –

• mateop (MatingOperator) –

• evalop (EvaluationOperator) –

• sselop (SurvivorSelectionOperator) –

• t_max (int) –

Methods

advance	Advance the breeding program by a specified number of generations.
evolve	Evolve the breeding program for a set number of replications and generations.
initialize	Initialize the breeding program with genotypes, phenotypes, and genomic models.
is_initialized	Return whether or not the BreedingProgram has been initialized with a starting set of conditions.
reset	Reset the evolution of the breeding program back to starting conditions.

Attributes

bval	Breeding values for individuals in the breeding program.
evalop	Evaluation operator.
geno	Genotypes for individuals in the breeding program.
genome	Genomes for individuals in the breeding program.
gmod	Genomic models for individuals in the breeding program.
initop	Initialization operator.
mateop	Mating operator.
pheno	Phenotypes for individuals in the breeding program.
pselop	Parent selection operator.
sselop	Survivor selection operator.
start_bval	Starting breeding values for individuals in the breeding program.
start_geno	Starting genotypes for individuals in the breeding program.
start_genome	Starting genomes for individuals in the breeding program.
start_gmod	Starting genomic models for individuals in the breeding program.
start_pheno	Starting phenotypes for individuals in the breeding program.
t_cur	Current time of the BreedingNode.
t_max	Maximum time of the BreedingNode.

advance(ngen, lbook, verbose=False, **kwargs)

Advance the breeding program by a specified number of generations.

Parameters:

• ngen (int) – Number of generations to advance the BreedingProgram.

• lbook (Logbook) – Logbook into which to write statistics.

• kwargs (dict) – Additional keyword arguments.

property bval: object

Breeding values for individuals in the breeding program.

property evalop: EvaluationOperator

Evaluation operator.

evolve(nrep, ngen, lbook, loginit=True, verbose=False, **kwargs)

Evolve the breeding program for a set number of replications and generations. The BreedingProgram is restarted using the starting geno, bval, gmod containers.

Parameters:

• nrep (int) – Number of evolution replicates.

• ngen (int, None) – Number of generations to evolve the population for each replicate. If None, use ‘t_max’. Note: if specified this does not modify ‘t_max’ which may affect operators that utilize ‘t_max’.

• lbook (Logbook) – Logbook into which to write statistics.

• loginit (bool) – Whether to log the initial state before main loop.

• verbose (bool) – Whether to print the rep number.

property geno: object

Genotypes for individuals in the breeding program.

property genome: object

Genomes for individuals in the breeding program.

property gmod: object

Genomic models for individuals in the breeding program.

initialize(**kwargs)

Initialize the breeding program with genotypes, phenotypes, and genomic models.

property initop: InitializationOperator

Initialization operator.

is_initialized(**kwargs)

Return whether or not the BreedingProgram has been initialized with a starting set of conditions.

Parameters:

kwargs (dict) – Additional keyword arguments.

Returns:

out – True if the BreedingProgram has been initialized. False if the BreedingProgram has not been initialized.

Return type:

boolean

property mateop: MatingOperator

Mating operator.

property pheno: object

Phenotypes for individuals in the breeding program.

property pselop: ParentSelectionOperator

Parent selection operator.

reset(**kwargs)

Reset the evolution of the breeding program back to starting conditions.

Parameters:

kwargs (dict) – Additional keyword arguments.

property sselop: SurvivorSelectionOperator

Survivor selection operator.

property start_bval: dict | None

Starting breeding values for individuals in the breeding program.

property start_geno: dict | None

Starting genotypes for individuals in the breeding program.

property start_genome: dict | None

Starting genomes for individuals in the breeding program.

property start_gmod: dict | None

Starting genomic models for individuals in the breeding program.

property start_pheno: dict | None

Starting phenotypes for individuals in the breeding program.

property t_cur: int

Current time of the BreedingNode.

property t_max: int

Maximum time of the BreedingNode.