Logbook

class pybrops.breed.op.log.Logbook.Logbook

Bases: object

Abstract class defining interfaces for logging statistics about an entire breeding program.

The purpose of this abstract class is to provide functionality for:

1. Logging data on an entire breeding program.

Methods

log_evaluate	Record information directly after 'EvaluationOperator.evaluate' is called.
log_initialize	Record information directly after 'InitializationOperator.initialize' is called.
log_mate	Record information directly after 'MatingOperator.mate' is called.
log_pselect	Record information directly after 'ParentSelectionOperator.pselect' is called.
log_sselect	Record information directly after 'SurvivorSelectionOperator.sselect' is called.
reset	Reset Logbook internals.
write	Write Logbook to file

Attributes

data	Logbook data.
rep	Replicate number.

abstract property data: object

Logbook data.

abstract log_evaluate(genome, geno, pheno, bval, gmod, t_cur, t_max, **kwargs)

Record information directly after ‘EvaluationOperator.evaluate’ is called.

Parameters:

• genome (dict) – Dictionary of genomes for the breeding program.

• geno (dict) – Dictionary of genotypes for the breeding program.

• pheno (dict) – Dictionary of phenotypes for the breeding program.

• bval (dict) – Dictionary of breeding values for the breeding program.

• gmod (dict) – Dictionary of genomic models for the breeding program.

• t_cur (int) – Current time in the breeding program.

• t_max (int) – Deadline time for the breeding program.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract log_initialize(genome, geno, pheno, bval, gmod, t_cur, t_max, **kwargs)

Record information directly after ‘InitializationOperator.initialize’ is called.

Parameters:

• genome (dict) – Dictionary of genomes for the breeding program.

• geno (dict) – Dictionary of genotypes for the breeding program.

• pheno (dict) – Dictionary of phenotypes for the breeding program.

• bval (dict) – Dictionary of breeding values for the breeding program.

• gmod (dict) – Dictionary of genomic models for the breeding program.

• t_cur (int) – Current time in the breeding program.

• t_max (int) – Deadline time for the breeding program.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract log_mate(genome, geno, pheno, bval, gmod, t_cur, t_max, **kwargs)

Record information directly after ‘MatingOperator.mate’ is called.

Parameters:

• genome (dict) – Dictionary of genomes for the breeding program.

• geno (dict) – Dictionary of genotypes for the breeding program.

• pheno (dict) – Dictionary of phenotypes for the breeding program.

• bval (dict) – Dictionary of breeding values for the breeding program.

• gmod (dict) – Dictionary of genomic models for the breeding program.

• t_cur (int) – Current time in the breeding program.

• t_max (int) – Deadline time for the breeding program.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract log_pselect(mcfg, genome, geno, pheno, bval, gmod, t_cur, t_max, **kwargs)

Record information directly after ‘ParentSelectionOperator.pselect’ is called.

Parameters:

• mcfg (dict) – Dictionary of mating configurations for the breeding program.

• genome (dict) – Dictionary of genomes for the breeding program.

• geno (dict) – Dictionary of genotypes for the breeding program.

• pheno (dict) – Dictionary of phenotypes for the breeding program.

• bval (dict) – Dictionary of breeding values for the breeding program.

• gmod (dict) – Dictionary of genomic models for the breeding program.

• t_cur (int) – Current time in the breeding program.

• t_max (int) – Deadline time for the breeding program.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract log_sselect(genome, geno, pheno, bval, gmod, t_cur, t_max, **kwargs)

Record information directly after ‘SurvivorSelectionOperator.sselect’ is called.

Parameters:

• genome (dict) – Dictionary of genomes for the breeding program.

• geno (dict) – Dictionary of genotypes for the breeding program.

• pheno (dict) – Dictionary of phenotypes for the breeding program.

• bval (dict) – Dictionary of breeding values for the breeding program.

• gmod (dict) – Dictionary of genomic models for the breeding program.

• t_cur (int) – Current time in the breeding program.

• t_max (int) – Deadline time for the breeding program.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract property rep: int

Replicate number.

abstract reset()

Reset Logbook internals.

Return type:

None

abstract write(filename)

Write Logbook to file

Parameters:

filename (str) – File name to which to write file.

Return type:

None