Initialization

class InitSex

class InitSex

This operator initializes sex of individuals, either randomly or use a list of sexes.

InitSex(maleFreq=0.5, maleProp=-1, sex=[], begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create an operator that initializes individual sex to MALE or FEMALE. By default, it assigns sex to individuals randomly, with equal probability of having a male or a female. This probabability can be adjusted through parameter maleFreq or be made to exact proportions by specifying parameter maleProp. Alternatively, a fixed sequence of sexes can be assigned. For example, if sex=[MALE, FEMALE], individuals will be assigned MALE and FEMALE successively. Parameter maleFreq or maleProp are ignored if sex is given. If a list of (virtual) subpopulation is specified in parameter subPop, only individuals in these subpopulations will be initialized. Note that the sex sequence, if used, is assigned repeatedly regardless of (virtual) subpopulation boundaries so that you can assign sex to all individuals in a population.

class InitInfo

class InitInfo

This operator initializes given information fields with a sequence of values, or a user-provided function such as random.random.

InitInfo(values, begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create an operator that initialize individual information fields infoFields using a sequence of values or a user-defined function. If a list of values are given, it will be used sequentially for all individuals. The values will be reused if its length is less than the number of individuals. The values will be assigned repeatedly regardless of subpopulation boundaries. If a Python function is given, it will be called, without any argument, whenever a value is needed. If a list of (virtual) subpopulation is specified in parameter subPop, only individuals in these subpopulations will be initialized.

class InitGenotype

class InitGenotype

This operator assigns alleles at all or part of loci with given allele frequencies, proportions or values. This operator initializes all chromosomes, including unused genotype locations and customized chromosomes.

InitGenotype(freq=[], genotype=[], prop=[], haplotypes=[], genotypes=[], loci=ALL_AVAIL, ploidy=ALL_AVAIL, begin=0, end=1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

This function creates an initializer that initializes individual genotypes with random alleles, genotypes, or haplotypes with specified frequencies (parameter freq) or proportions (parameter prop). If parameter genotypes or haplotypes is not specified, freq specifies the allele frequencies of alleles 0, 1, 2… respectively. Alternatively, you can use parameter prop to specified the exact proportions of alleles 0, 1, …, although alleles with small proportions might not be assigned at all.

Values of parameter prob or prop should add up to 1. In addition to a vector, parameter prob and prop can also be a function that accepts optional parameters loc, subPop or vsp and returns a list of requencies for alleles 0, 1, etc, or a number for frequency of allele 0 as a speciail case for each locus, subpopulation (parameter subPop), or virtual subpopulations (parameter vsp, pass as a tuple).

If parameter genotypes is specified, it should contain a list of genotypes (alleles on different strand of chromosomes) with length equal to population ploidy. Parameter prob and prop then specifies frequencies or proportions of each genotype, which can vary for each subpopulation but not each locus if the function form of parameters is used.

If parameter haplotypes is specified, it should contain a list of haplotypes (alleles on the same strand of chromosome) and parameter prob or prop specifies frequencies or proportions of each haplotype.

If loci, ploidy and/or subPop are specified, only specified loci, ploidy, and individuals in these (virtual) subpopulations will be initialized. Parameter loci can be a list of loci indexes, names or ALL_AVAIL. If the length of a haplotype is not enough to fill all loci, the haplotype will be reused. If a list (or a single) haplotypes are specified without freq or prop, they are used with equal probability.

In the last case, if a sequence of genotype is specified through parameter genotype (not genotypes), it will be used repeatedly to initialize all alleles sequentially. This works similar to function Population.setGenotype() except that you can limit the initialization to certain loci and ploidy.

class InitLineage

class InitLineage

This operator assigns lineages at all or part of loci with given values. This operator initializes all chromosomes, including unused lineage locations and customized chromosomes.

InitLineage(lineage=[], mode=PER_ALLELE, loci=ALL_AVAIL, ploidy=ALL_AVAIL, begin=0, end=1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=["ind_id"])

This function creates an initializer that initializes lineages with either a specified set of values or from the field infoFields (default to ind_id), whose value will be saved as the lineage of modified alleles. If a list of values is specified in parameter lineage, each value in this list is applied to one or more alleles so that each allele (PER_ALLELE, default mode), alleles on each chromosome (PER_CHROMOSOME), on chromosomes of each ploidy (PER_PLOIDY), or for each individual (PER_INDIVIDUAL) have the same lineage. A single value is allowed and values in lineage will be re-used if not enough values are provided. If an empty list is provided, values 1, 2, 3, .. will be used to provide an unique identify for each allele, genotype, chromosome, etc. If a valid field is specified (default to ind_id), the value of this field will be used for all alleles of each individual if mode is set to FROM_INFO, or be adjusted to produce positive values for alleles on the frist ploidy, and negative values for the second ploidy (and so on) if mode equals to FROM_INFO_SIGNED. If loci, ploidy and/or subPops are specified, only specified loci, ploidy, and individuals in these (virtual) subpopulations will be initialized.