Setting up genomic intervals¶

class
fwdpy11.
Region
(beg: float, end: float, weight: float, coupled: bool = True, label: int = 0)¶ A genomic region, defined by halfopen interval [beg, end)
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
coupled (bool) – if True, the weight is converted to (endbeg)*weight
label (numpy.uint16) – Not relevant to recombining regions. Otherwise, this value will be used to fill
fwdpy11.Mutation.label
.
When coupled is True, the “weight” may be interpreted as a “per base pair” (or per unit, generally speaking) term.
Changed in version 0.3.0: Refactored from a pure Python class to a C++/pybind11 class
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
Sregion
¶ Representation of a “region” in a simulation with a dominance term.
This class is an ABC.
Changed in version 0.13.a2: Added “scaling” attribute.
Changed in version 0.3.0: Refactored from a pure Python class to a C++/pybind11 class
Changed in version 0.8.0: C++ version of class API minimized in favor of attrs.
This class is an ABC derived from
fwdpy11.Region

class
fwdpy11.
ConstantS
(beg: float, end: float, weight: float, s: float, h: float = 1.0, coupled: bool = True, label: int = 0, scaling: float = 1.0)¶ Mutations with fixed effect sizes
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
s (float) – the selection coefficient
h (float) – the dominance
coupled (bool) – if True, the weight is converted to (endbeg)*weight
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.scaling (float) – The scaling of the DFE
When coupled is True, the “weight” may be interpreted as a “per base pair” (or per unit, generally speaking) term.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
UniformS
(beg: float, end: float, weight: float, lo: float, hi: float, h: float = 1.0, coupled: bool = True, label: int = 0, scaling: float = 1.0)¶ Uniform distrubution of effect sizes
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
lo (float) – lower bound on s
hi (float) – upper bound on s
h (float) – the dominance
coupled (bool) – if True, the weight is converted to (endbeg)*weight
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.scaling (float) – The scaling of the DFE
When coupled is True, the “weight” may be interpreted as a “per base pair” (or per unit, generally speaking) term.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
ExpS
(beg: float, end: float, weight: float, mean: float, h: float = 1.0, coupled: bool = True, label: int = 0, scaling: float = 1.0)¶ Exponential distribution of effect sizes
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
mean – the mean selection coefficient
h (float) – the dominance
coupled (bool) – if True, the weight is converted to (endbeg)*weight
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.scaling (float) – The scaling of the DFE
When coupled is True, the “weight” may be interpreted as a “per base pair” (or per unit, generally speaking) term.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
GammaS
(beg: float, end: float, weight: float, mean: float, shape_parameter: float, h: float = 1.0, coupled: bool = True, label: int = 0, scaling: float = 1.0)¶ Gamma distribution of effect sizes
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
mean (float) – the mean selection coefficient
shape (float) – the shape parameter of the distribution
h (float) – the dominance
coupled (bool) – if True, the weight is converted to (endbeg)*weight
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.scaling (float) – The scaling of the DFE
When coupled is True, the “weight” may be interpreted as a “per base pair” (or per unit, generally speaking) term.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
GaussianS
(beg: float, end: float, weight: float, sd: float, h: float = 1.0, coupled: bool = True, label: int = 0, scaling: float = 1.0)¶ Gaussian distribution of effect sizes
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
sd (float) – standard deviation of effect sizes
h (float) – the dominance
coupled (bool) – if True, the weight is converted to (endbeg)*weight
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.scaling (float) – The scaling of the DFE
When coupled is True, the “weight” may be interpreted as a “per base pair” (or per unit, generally speaking) term.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
MultivariateGaussianEffects
(beg: float, end: float, weight: float, cov_matrix: numpy.ndarray, fixed_effect: float = 0.0, h: float = 1.0, coupled: bool = True, label: int = 0)¶ Pleiotropic effects via a multivariate Gaussian distribution.
This class can be used to generate mutations with both vectors of effect sizes as well as a separate fixed effect.
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – Beginning of the region
end (float) – End of the region
weight (float) – Weight on the region
matrix (numpy.ndarray) – Variancecovariance matrix
fixed_effect (float) – Fixed effect size. Defaults to 0.0.
h (float) – Dominance. Defaults to 1.0
coupled (bool) – Specify if weight is function of endbeg or not. Defaults to True
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.
The input matrix must be square and semipositive definite. If either of these conditions are not met, ValueError will be raised. ValueError will also be raised if the input matrix contains any nonfinite values.
Note
The dominance parameter (h) applies to both the fixed effect and those drawn from a multivariate normal.
New in version 0.3.0.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
LogNormalS
(beg: float, end: float, weight: float, zeta: Optional[float], sigma: Optional[float], h: float = 1.0, coupled: bool = True, label: int = 0, scaling: float = 1.0)¶ Lognormal distribution of effect sizes.
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
zeta (float) – the zeta parameter
sigma (float) – the sigma parameter
h (float) – the dominance
coupled – if True, the weight is converted to(endbeg)*weight
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.scaling (float) – The scaling of the DFE
When coupled is True, the “weight” may be interpreted as a “per base pair” (or per unit, generally speaking) term.
New in version 0.7.0.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

classmethod
mv
(beg: float, end: float, weight: float, h: float = 1.0, coupled: bool = True, label: int = 0, scaling: float = 1.0)¶ Factory method to create an instance compatible with
fwdpy11.mvDES
. See Different effect sizes of mutations in different demes for details. Parameters
beg (float) – the beginning of the region
end (float) – the end of the region
weight (float) – the weight to assign
h (float) – the dominance
coupled (bool) – if True, the weight is converted to(endbeg)*weight
label (numpy.uint16) – Fill
fwdpy11.Mutation.label
with this value.scaling (float) – The scaling of the DFE

class
fwdpy11.
mvDES
(des: object, means: object, matrix: Optional = None)¶ General multivariate distribution of effect sizes.
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
des (list) – Distributions of effect sizes
means (numpy.ndarray) – means marginal gaussian Distributions
matrix (numpy.ndarray) – Variance/covariance matrix
New in version 0.7.0.
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class

class
fwdpy11.
GeneticMapUnit
¶ ABC for components of genetic maps
New in version 0.3.0.
Changed in version 0.5.0: Refactored backend to be based on fwdpp types

class
fwdpy11.
PoissonInterval
(beg: float, end: float, mean: float)¶ Generate poisson number of crossover breakpoints.
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
New in version 0.3.0.
Changed in version 0.5.0: Refactored backend to be based on fwdpp types
Changed in version 0.7.1: Add __repr__
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class
This class inherits from
fwdpy11.GeneticMapUnit

class
fwdpy11.
PoissonPoint
(position: float, mean: float)¶ Generate a recombination breakpoint at a fixed position if the number of crossover events is odd.
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
New in version 0.3.0.
Changed in version 0.5.0: Refactored backend to be based on fwdpp types
Changed in version 0.7.1: Add __repr__
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class
This class inherits from
fwdpy11.GeneticMapUnit

class
fwdpy11.
BinomialPoint
(position: float, probability: float)¶ Generate a crossover breakpoint at a fixed position with a fixed probability. This class represents genetic distance as centiMorgans/100.
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
New in version 0.3.0.
Changed in version 0.5.0: Refactored backend to be based on fwdpp types
Changed in version 0.7.1: Add __repr__
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class
This class inherits from
fwdpy11.GeneticMapUnit

class
fwdpy11.
FixedCrossovers
(beg: float, end: float, num_xovers: int)¶ Generate a fixed number of crossover breakpoints.
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
New in version 0.3.0.
Changed in version 0.5.0: Refactored backend to be based on fwdpp types
Changed in version 0.7.1: Add __repr__
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class
This class inherits from
fwdpy11.GeneticMapUnit

class
fwdpy11.
BinomialInterval
(beg: float, end: float, probability: float)¶ Generate exactly one crossover with a given probability
This class has the following attributes, whose names are also
kwargs
for intitialization. The attribute names also determine the order of positional arguments: Parameters
New in version 0.5.2.
Changed in version 0.7.1: Add __repr__
Changed in version 0.8.0: Refactored to use attrs and inherit from lowlevel C++ class
This class inherits from
fwdpy11.GeneticMapUnit