rcpp_recombo_segregate_expo: rcpp version of function that does recombination and...

In eriqande/gids: Genomic Landscape of Divergence Simulation

rcpp version of function that does recombination and segregation with exponential crossovers

Description

In this version, we have to have a position for each locus (an integer less than 2^31) and then we have crossing over points exponentially distributed as a Poisson process. but that could be changed so that crossovers happen at a variable rate. Note that this is hard-wired for diploidy.

Usage

rcpp_recombo_segregate_expo(G, dims, pos, chromo_length, cross)

Arguments

G	the structure giving the genotypes of the indviduals. Actually a 3-D array indexed by indiv, locus, gene copy
dims	the dimensions of the 3-D array G for internal use.
pos	vector of positions of the loci. This is an integer vector. Has to be in sorted order (ascending)
chromo_length	total chromoome length in base pairs
cross	per base-pair rate of recombination. For example, 1 cM per megabase equates to 1e-08.

Value

The return value is a long vector that can be squished into a matrix as appropriate to put it into the genotype struct.

eriqande/gids documentation built on Jan. 5, 2024, 12:31 a.m.