newPop: Create new population

In AlphaSimR: Breeding Program Simulations

Create new population

Description

Creates an initial Pop-class from an object of MapPop-class or NamedMapPop-class. The function is intended for use with output from functions such as runMacs, newMapPop, or quickHaplo.

Usage

newPop(rawPop, simParam = NULL, ...)

Arguments

rawPop	an object of MapPop-class or NamedMapPop-class
simParam	an object of SimParam
...	additional arguments used internally

Details

Note that newPop takes genomes from the rawPop and uses them without recombination! Hence, if you call newPop(rawPop = founderGenomes) twice, you will get two sets of individuals with different id but the same genomes. To get genetically different sets of individuals you can subset the rawPop input, say first half for one set and the second half for the other set.

Value

Returns an object of Pop-class

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitA(10)

#Create population
pop = newPop(founderPop, simParam=SP)
isPop(pop)

#Misc
pop@misc$tmp1 = rnorm(n=2)
pop@misc$tmp2 = rnorm(n=2)

#MiscPop
pop@miscPop$tmp1 = sum(pop@misc$tmp1)
pop@miscPop$tmp2 = sum(pop@misc$tmp2)

AlphaSimR documentation built on Nov. 1, 2024, 5:07 p.m.