optiSel (version 2.0.7)

matings: Mate Allocation

Description

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

Usage

matings(phen, Kin,  alpha=1, 
    ub.n=NA, max=FALSE, solver="default", ...)

Value

Data frame with columns Sire, Dam, n, and possibly herd, whereby column n contains the desired number of matings, 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.

Arguments

phen

Data frame with desired number of matings (column n), 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.

alpha

If alpha<1 then the proportion of matings 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.n

Maximum number of matings of the same individuals. Without this constraint (i.e. ub.n=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

.

Author

Robin Wellmann

Details

Males and females are allocated for mating such that all breeding animals have the desired number of matings. 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 matings of the same individuals can be constrained. For each herd, the proportion alpha of matings with the same male can be constrained as well, but this increases computation time.

Examples

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", ]

cont  <- data.frame(
  age   = c(   1,    2,    3,    4,    5,    6), 
  male  = c(0.11, 0.11, 0.10, 0.08, 0.06, 0.04),
  female= c(0.11, 0.11, 0.10, 0.08, 0.06, 0.04))

cand  <- candes(phen=Phen, sKin = sKin, cont=cont)
con   <- list(uniform="female", ub.sKin = 0.047)
Offspring <- opticont("max.BV", cand, con, trace=FALSE)


#####  Minimize inbreeding   #####
Candidate   <- Offspring$parent
Candidate$n <- noffspring(Candidate, N=20)$nOff
Mating      <- matings(Candidate, sKin)
Mating 
attributes(Mating)$objval


if (FALSE) {
## This is faster but not available on all platforms:
library("Rsymphony")
Mating <- matings(Candidate, sKin, alpha=0.30, solver=Rsymphony_solve_LP)
Mating
attributes(Mating)$objval

attributes(Mating)$info
#[1] "Optimum solution found"
}