initialize.multilocus: Initialize multilocus simulations

In MarcoAndrello/MetaPopGen-2.0: Simulation of metapopulation genetics

Description

Function used to initialize multilocus simulations.

Usage

initialize.multilocus(allele_vec,
                      r,
                      mu=rep(0,length(allele_vec)),
                      n,
                      z,
                      kappa0,
                      init.state="fixed",
                      sexuality=NULL)

Arguments

allele_vec	Vector giving the number of alleles at each locus.
r	Recombination rate. A single value between 0 and 0.5. For more than two loci, recombination rate must be set to 0.5.
mu	Vector giving the mutation rate for each locus, i.e. the probability that an allele mutate to a different allele.
n	Number of demes.
z	Number of age classes.
kappa0	Initial number of individuals per deme. This is used to assign individuals to genotype and age-classes in each deme according to the criterion defined in "init.state". Because the assignment involves rounding, the realized number of individuals might be different than the one set by the user.
init.state	String defining the genetic composition of the initial population. If "fixed", all genotypes and age-classes will have the same number of individuals. If "random", numbers of individuals will be assigned randomly.
sexuality	One of "monoecious" or "dioecious", defining the sexuality of the modelled species.

Value

A list with the following items:

r	The recombination rate input by the user
mu	The vector of mutation rates input by the user
m	The number of multilocus genotypes
n	The number of demes input by the user
z	The number of age-classes input by the user
kappa0	The initial number of individuals per deme given by the user
index_matr	The index of the multilocus genotypes given by the function genotype.index.multilocus
meiosis_matrix	A matrix giving the probabilities of producing multilocus gametes (rows) for each multilocus genotype (columns)
mat_geno_to_index_mapping	A square matrix giving the genotype index for each combination of female (rows) and male (columns) multilocus gametes
N1	The initial composition of the population as a 3D array giving the number of individuals of each genotype (first dimension) in each deme (second dimension) in each age-class (third dimension)

Author(s)

Marco Andrello

Examples

## Not run: 
allele_vec <- c(2,2)
init.par <- initialize.multilocus(allele_vec=allele_vec,
                                  r=0.5,
                                  mu=c(0.01,0.01),
                                  n=3,
                                  z=1,
                                  kappa0=100,
                                  sexuality="monoecious")


## End(Not run)

MarcoAndrello/MetaPopGen-2.0 documentation built on Nov. 25, 2020, 11:20 p.m.