Genetic values

For some background, see Definitions.

class fwdpy11.DiploidGeneticValue

ABC for genetic value calculations for diploid members of fwdpy11.DiploidPopulation

property genetic_values

Return the list of genetic values.

New in version 0.3.0.

property maps_to_fitness

Returns True if object represents a mapping directly to fitness, and False otherwise.

New in version 0.7.0.

property maps_to_trait_value

Returns True if object represents a trait value, and False otherwise.

New in version 0.7.0.

property shape

Return the dimensions of the genetic values.

New in version 0.3.0.

class fwdpy11.Additive(scaling: float, gvalue_to_fitness: fwdpy11._fwdpy11.GeneticValueIsTrait = None, noise: fwdpy11._fwdpy11.GeneticValueNoise = None, ndemes: int = 1)

Additive effects on genetic values.

This class has the following attributes, whose names are also kwargs for intitialization. The attribute names also determine the order of positional arguments:

Parameters

When gvalue_to_fitness is None, then we are modeling additive effects on fitness.

For a model of fitness, the genetic value is 1, 1+e*h, 1+``scaling``*e for genotypes AA, Aa, and aa, respectively, where e and h are the effect size and dominance, respectively.

For a model of a trait (phenotype), meaning gvalue_to_fitness is not None, the values for the three genotypes are 0, e*h, and e, respectively.

Changed in version 0.8.0: Refactored to use attrs and inherit from low-level C++ class

asblack()

Return a string representation formatted with black

asdict()

Return dict representation

classmethod fromdict(d)

Build an instance from a dictionary

property genetic_values

Return the list of genetic values.

New in version 0.3.0.

property maps_to_fitness

Returns True if object represents a mapping directly to fitness, and False otherwise.

New in version 0.7.0.

property maps_to_trait_value

Returns True if object represents a trait value, and False otherwise.

New in version 0.7.0.

property shape

Return the dimensions of the genetic values.

New in version 0.3.0.

class fwdpy11.Multiplicative(scaling: float, gvalue_to_fitness: fwdpy11._fwdpy11.GeneticValueIsTrait = None, noise: fwdpy11._fwdpy11.GeneticValueNoise = None, ndemes: int = 1)

Multiplicative effects on genetic values.

This class has the following attributes, whose names are also kwargs for intitialization. The attribute names also determine the order of positional arguments:

Parameters

When gvalue_to_fitness is None, then we are modeling multiplicative effects on fitness.

For a model of fitness, the genetic value is 1, 1+e*h, 1+``scaling``*e for genotypes AA, Aa, and aa, respectively, where e and h are the effect size and dominance, respectively.

For a model of a trait (phenotype), meaning gvalue_to_fitness is not None, the values for the three genotypes are 0, e*h, and e, respectively.

Changed in version 0.8.0: Refactored to use attrs and inherit from low-level C++ class

asblack()

Return a string representation formatted with black

asdict()

Return dict representation

classmethod fromdict(d)

Build an instance from a dictionary

property genetic_values

Return the list of genetic values.

New in version 0.3.0.

property maps_to_fitness

Returns True if object represents a mapping directly to fitness, and False otherwise.

New in version 0.7.0.

property maps_to_trait_value

Returns True if object represents a trait value, and False otherwise.

New in version 0.7.0.

property shape

Return the dimensions of the genetic values.

New in version 0.3.0.

class fwdpy11.GBR(gvalue_to_fitness: object, noise: object = None)

The “gene-based recessive” trait model described in Thornton et al. 2013 http://dx.doi.org/10.1371/journal.pgen.1003258 and Sanjak et al. 2017 http://dx.doi.org/10.1371/journal.pgen.1006573.

The trait value is the geometric mean of the sum of effect sizes on each haplotype. It is undefined for the case where these sums are negative.

This class has the following attributes, whose names are also kwargs for intitialization. The attribute names also determine the order of positional arguments:

Parameters

Changed in version 0.8.0: Refactored to use attrs and inherit from low-level C++ class

asblack()

Return a string representation formatted with black

asdict()

Return dict representation

classmethod fromdict(d)

Build an instance from a dictionary

property genetic_values

Return the list of genetic values.

New in version 0.3.0.

property maps_to_fitness

Returns True if object represents a mapping directly to fitness, and False otherwise.

New in version 0.7.0.

property maps_to_trait_value

Returns True if object represents a trait value, and False otherwise.

New in version 0.7.0.

property shape

Return the dimensions of the genetic values.

New in version 0.3.0.

class fwdpy11.StrictAdditiveMultivariateEffects(ndimensions: int, focal_trait: int, gvalue_to_fitness: object, noise: object = None)

Multivariate trait values under strictly additive effects.

Calculate the trait value for a diploid in a fwdpy11.DiploidPopulation for a multidimensional trait.

This class is restricted to the case of simple additive effects, meaning that any dominance terms associated with mutations are ignored.

During a simulation, fwdpy11.DiploidMetadata.g is filled with the genetic value corresponding to a “focal” trait specified upon object construction. This class has the following attributes, whose names are also kwargs for intitialization. The attribute names also determine the order of positional arguments:

Parameters

Changed in version 0.8.0: Refactored to use attrs and inherit from low-level C++ class

asblack()

Return a string representation formatted with black

asdict()

Return dict representation

classmethod fromdict(d)

Build an instance from a dictionary

property genetic_values

Return the list of genetic values.

New in version 0.3.0.

property maps_to_fitness

Returns True if object represents a mapping directly to fitness, and False otherwise.

New in version 0.7.0.

property maps_to_trait_value

Returns True if object represents a trait value, and False otherwise.

New in version 0.7.0.

property shape

Return the dimensions of the genetic values.

New in version 0.3.0.