ogc.mobps: Breeding function

In MoBPS: Modular Breeding Program Simulator

Breeding function

Description

Function to simulate a step in a breeding scheme

Usage

ogc.mobps(
  population,
  animallist,
  relationship.matrix.ogc,
  depth.pedigree.ogc,
  bve.pedigree.error,
  ogc.target = "min.sKin",
  ogc.uniform = NULL,
  ogc.lb = NULL,
  ogc.ub = NULL,
  ogc.ub.sKin = NULL,
  ogc.lb.BV = NULL,
  ogc.ub.BV = NULL,
  ogc.eq.BV = NULL,
  ogc.ub.sKin.increase = NULL,
  ogc.lb.BV.increase = NULL,
  bve.p_i.list = NULL,
  miraculix = FALSE,
  miraculix.mult = FALSE,
  import.position.calculation = NULL,
  decodeOriginsU = decodeOriginsR,
  nbits = NULL,
  store.sparse = FALSE,
  verbose = TRUE,
  bit.storing = FALSE
)

Arguments

population	Population list
animallist	List of individuals to include in ogc
relationship.matrix.ogc	Method to calculate relationship matrix for OGC (Default: "pedigree", alt: "vanRaden", "CE", "non_stand", "CE2", "CM")
depth.pedigree.ogc	Depth of the pedigree in generations (default: 7)
bve.pedigree.error	Set to FALSE to ignore/correct for any pedigree errors
ogc.target	Target of OGC (default: "min.sKin" - minimize inbreeding; alt: "max.BV" / "min.BV" - maximize genetic gain; both under constrains selected below)
ogc.uniform	This corresponds to the uniform constrain in optiSel
ogc.lb	This corresponds to the lb constrain in optiSel
ogc.ub	This corresponds to the ub constrain in optiSel
ogc.ub.sKin	This corresponds to the ub.sKin constrain in optiSel
ogc.lb.BV	This corresponds to the lb.BV constrain in optiSel
ogc.ub.BV	This corresponds to the ub.BV constrain in optiSel
ogc.eq.BV	This corresponds to the eq.BV constrain in optiSel
ogc.ub.sKin.increase	This corresponds to the upper bound (current sKin + ogc.ub.sKin.increase) as ub.sKin in optiSel
ogc.lb.BV.increase	This corresponds to the lower bound (current BV + ogc.lb.BV.increase) as lb.BV in optiSel
bve.p_i.list	XXX
miraculix	XXX
miraculix.mult	XXX
import.position.calculation	XXX
decodeOriginsU	XXX
nbits	XXX
store.sparse	XXX
verbose	Set to FALSE to not display any prints
bit.storing	Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)

Value

contributions of each individual in selection

Examples

population <- creating.diploid(nsnp=1000, nindi=100, n.additive = 10)
population <- breeding.diploid(population, breeding.size=100, selection.size=c(25,25),
ogc = TRUE)

MoBPS documentation built on Nov. 5, 2025, 6:26 p.m.