Subpopulation: Subpopulation

In rdinnager/slimrlang: Write SLiM Population Genetics Simulation Scripts in R

Description

Documentation for Subpopulation class from SLiM

Usage

Subpopulation

Format

An object of class list of length 43.

Details

This class has the following methods (functions):

• addCloned

• addCrossed

• addEmpty

• addRecombinant

• addSelfed

• cachedFitness

• configureDisplay

• defineSpatialMap

• getValue

• outputMSSample

• outputSample

• outputVCFSample

• pointInBounds

• pointPeriodic

• pointReflected

• pointStopped

• pointUniform

• removeSubpopulation

• sampleIndividuals

• setCloningRate

• setMigrationRates

• setSelfingRate

• setSexRatio

• setSpatialBounds

• setSubpopulationSize

• setValue

• spatialMapColor

• spatialMapValue

• subsetIndividuals

• takeMigrants

This class has the following properties:

cloningRate

A property of type float. This property is a constant, so it is not modifiable. Property Description: The fraction of children in the next generation that will be produced by cloning (as opposed to biparental mating). In non-sexual (i.e. hermaphroditic) simulations, this property is a singleton float representing the overall subpopulation cloning rate. In sexual simulations, this property is a float vector with two values: the cloning rate for females (at index 0) and for males (at index 1).

firstMaleIndex

A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The index of the first male individual in the subpopulation. The genomes vector is sorted into females first and males second; firstMaleIndex gives the position of the boundary between those sections. Note, however, that there are two genomes per diploid individual, and the firstMaleIndex is not premultiplied by 2; you must multiply it by 2 before using it to decide whether a given index into genomes is a genome for a male or a female. The firstMaleIndex property is also the number of females in the subpopulation, given this design. For non-sexual (i.e. hermaphroditic) simulations, this property has an undefined value and should not be used.

fitnessScaling

A property of type float. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A float scaling factor applied to the fitness of all individuals in this subpopulation (i.e., the fitness value computed for each individual will be multiplied by this value). This is primarily of use in nonWF models, where fitness is absolute, rather than in WF models, where fitness is relative (and thus a constant factor multiplied into the fitness of every individual will make no difference); however, it may be used in either type of model. This provides a simple, fast way to modify the fitness of all individuals in a subpopulation; conceptually it is similar to returning the same fitness effect for all individuals in the subpopulation from a fitness(NULL) callback, but without the complexity and performance overhead of implementing such a callback. To scale the fitness of individuals by different (individual-specific) factors, see the fitnessScaling property of Individual. The value of fitnessScaling is reset to 1.0 every generation, so that any scaling factor set lasts for only a single generation. This reset occurs immediately after fitness values are calculated, in both WF and nonWF models.

genomes

A property of type Genome object. This property is a constant, so it is not modifiable. Property Description: All of the genomes contained by the subpopulation; there are two genomes per diploid individual.

id

A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The identifier for this subpopulation; for subpopulation p3, for example, this is 3.

immigrantSubpopFractions

A property of type float. This property is a constant, so it is not modifiable. Property Description: The expected value of the fraction of children in the next generation that are immigrants arriving from particular subpopulations.

immigrantSubpopIDs

A property of type integer. This property is a constant, so it is not modifiable. Property Description: The identifiers of the particular subpopulations from which immigrants will arrive in the next generation.

individualCount

A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The number of individuals in the subpopulation; one-half of the number of genomes.

individuals

A property of type Individual object. This property is a constant, so it is not modifiable. Property Description: All of the individuals contained by the subpopulation. Each individual is diploid and thus contains two Genome objects. See the sampleIndividuals() and subsetIndividuals() for fast ways to get a subset of the individuals in a subpopulation.

selfingRate

A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The expected value of the fraction of children in the next generation that will be produced by selfing (as opposed to biparental mating). Selfing is only possible in non-sexual (i.e. hermaphroditic) simulations; for sexual simulations this property always has a value of 0.0.

sexRatio

A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: For sexual simulations, the sex ratio for the subpopulation. This is defined, in SLiM, as the fraction of the subpopulation that is male; in other words, it is actually the M:(M+F) ratio. For non-sexual (i.e. hermaphroditic) simulations, this property has an undefined value and should not be used.

spatialBounds

A property of type float. This property is a constant, so it is not modifiable. Property Description: The spatial boundaries of the subpopulation. The length of the spatialBounds property depends upon the spatial dimensionality declared with initializeSLiMOptions(). If the spatial dimensionality is zero (as it is by default), the value of this property is float(0) (a zero-length float vector). Otherwise, minimums are supplied for each coordinate used by the dimensionality of the simulation, followed by maximums for each. In other words, if the declared dimensionality is "xy", the spatialBounds property will contain values (x0, y0, x1, y1); bounds for the z coordinate will not be included in that case, since that coordinate is not used in the simulation’s dimensionality. This property cannot be set, but the setSpatialBounds() method may be used to achieve the same thing.

tag

A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined integer value. The value of tag is initially undefined, and it is an error to try to read it; if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code. The value of tag is not used by SLiM; it is free for you to use. See also the getValue() and setValue() methods, for another way of attaching state to subpopulations.

rdinnager/slimrlang documentation built on June 20, 2020, 8:17 p.m.