relationshipAdditive {GeneticsPed} | R Documentation

## Additive relationship matrix and its inverse

### Description

`relationshipAdditive` creates additive relationship matrix, while `inverseAdditive` creates its inverse directly from a pedigree. `kinship` is another definition of relationship and is equal to half of additive relationship.

### Usage

    relationshipAdditive(x, sort=TRUE, names=TRUE, ...)
    inverseAdditive(x, sort=TRUE, names=TRUE, ...)
    kinship(x, sort=TRUE, names=TRUE, ...)

### Arguments

`x` | Pedigree
`sort` | logical, for the computation the pedigree needs to be sorted, but results are sorted back to original sorting (sort=TRUE) or not (sort=FALSE)
`names` | logical, should returned matrix have row/colnames; this can be used to get leaner matrix
`...` | arguments for other methods

### Details

Additive or numerator relationship matrix is symetric and contains 1 + F_i on diagonal, where F_i is an inbreeding coefficients (see `inbreeding`) for subject i. Off-diagonal elements represent numerator or relationship coefficient bewteen subjects i and j as defined by Wright (1922). Henderson (1976) showed a way to setup inverse of relationship matrix directly. Mrode (2005) has a very nice introduction to these concepts.

Take care with `sort=FALSE, names=FALSE`. It is your own responsibility to assure proper handling in this case.

### Value

A matrix of n * n dimension, where n is number of subjects in `x`

### Author(s)

Gregor Gorjanc and Dave A. Henderson

### References

Henderson, C. R. (1976) A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32(1):69-83

Mrode, R. A. (2005) Linear models for the prediction of animal breeding values. 2nd edition. CAB International. ISBN 0-85199-000-2 http://www.amazon.com/gp/product/0851990002

Wright, S. (1922) Coefficients of inbreeding and relationship. American Naturalist 56:330-338

### See Also

`Pedigree`, `inbreeding` and `geneFlowT`

### Examples

      data(Mrode2.1)
      Mrode2.1$dtB <- as.Date(Mrode2.1$dtB)
      x2.1 <- Pedigree(x=Mrode2.1, subject="sub", ascendant=c("fat", "mot"),
                       ascendantSex=c("M", "F"), family="fam", sex="sex",
                       generation="gen", dtBirth="dtB")

      (A <- relationshipAdditive(x2.1))
      fractions(A)
      solve(A)
      inverseAdditive(x2.1)
      relationshipAdditive(x2.1[3:6, ])

      ## Compare the speed
      ped <- generatePedigree(nId=10, nGeneration=3, nFather=1, nMother=2)
      system.time(solve(relationshipAdditive(ped)))
      system.time(inverseAdditive(ped))

[Package GeneticsPed version 1.48.0 Index]