optiSel (version 1.0.0)

matings: Mate Allocation

Description

Males and females are allocated for mating such that all breeding animals have the desired number of offspring. The mean inbreeding coefficient in the offspring is minimized if matrix Kin contains pairwise kinships of the selection candidates.

Usage

matings(cand, Kin, N=2*sum(cand$Sex=="female"), alpha=1, 
    ub.nOff=NA, max=FALSE, solver="default", ...)

Arguments

cand

Data frame with optimum contributions (column oc), sexes (column Sex), and IDs (column Indiv) of the selection candidates. The data frame may also contain column herd containing the names of the herds to which the females belong (NA for males).

Kin

Kinship matrix (or an other similarity matrix) for selection candidates.

N

Desired number of offspring that should be available as selection candidates in the next generation.

alpha

If alpha<1 then the proportion of females mated with the same male is at most alpha in each herd. A value alpha<1 increases genetic connectedness between herds and enables to estimate more accurate breeding values.

ub.nOff

Maximum number of offspring per mating. Without this constraint (i.e. ub.nOff=NA), some superior animals may always be mated to the same inferior animal, so their offspring would likely not be suitable for breeding.

max

The default max=FALSE means that the objective function is minimized.

solver

Either solver="default", or solver=Rsymphony_solve_LP. The latter is possible only if package Rsymbhony is loaded, which is not available for all platforms.

...

Further optimization parameters. By default, they are passed to function ecos.control

Value

Data frame with columns Sire, Dam, nOff, and possibly herd, whereby column nOff contains the desired number of offspring from each mating, and column herd contains the herd of the dam.

The data frame has attributes objval with the value of the objective function (usually the mean inbreeding coefficient), and attribute info describing the solution as reported by the solver.

Details

Males and females are allocated for mating such that all breeding animals have the desired number of offspring. If Kin is a kinship matrix, then the mean inbreeding coefficient in the offspring is minimized. In general, the mean similarity of the parents is minimized.

The maximum number of offspring per mating can be constrained. For each herd, the proportion alpha of females mated with the same male can be constrained as well, but this increases computation time.

Note that the desired number of offspring per mating is the number of offspring that should be used as selection candidates in the next generation, which is not necessarily the total number of offspring.

Examples

# NOT RUN {
data("map")
data("Cattle")
dir   <- system.file("extdata", package = "optiSel")
files <- paste(dir, "/Chr", 1:2, ".phased", sep="")
sKin  <- segIBD(files, map, minSNP=20, minL=2.0)
Phen  <- Cattle[Cattle$Breed=="Angler", ]
cand  <- candes(phen=Phen, sKin = sKin)
con   <- list(ub.sKin = 0.057)
Offspring <- opticont("max.BV", cand, con, trace=FALSE)


#####  Minimize inbreeding   #####
Candidate <- Offspring$parent
Mating <- matings(Candidate, sKin, ub.nOff=5, maxit=50L)
Mating 
attributes(Mating)$objval
#[1] 0.007270397

# }
# NOT RUN {
## This is faster but not available on all platforms:
library("Rsymphony")
Mating <- matings(Candidate, sKin, ub.nOff=5, alpha=0.13, solver=Rsymphony_solve_LP)
Mating
attributes(Mating)$objval
#[1] 0.009648924

attributes(Mating)$info
#[1] "Optimum solution found"
# }
# NOT RUN {
# }
# NOT RUN {
# }