Simulates a pedigree for the “double first cousin” mating design (Fairbairn and Roff 2006).
simPedDFC(U, gpn = 4, fsn = 4, s = 2, fws = 2, prefix = NULL)A data.frame with columns corresponding to: id, dam, sire,
and sex. Sex is M for males and F for females.
An integer number of units or blocks for the design
Number of grandparent pairs in the generation 0 (GP) (must be >= 2). Equals the number of full-sib families in generation 1 (P).
Number of offspring in each full-sib family of generations 1 and 2 (P and F1 - must be an even number >= 4).
Number of sires per full-sib family in generation 1 (P - must be >=2)
Number of generation 1 (P) families with sires. Together, with
s, sets up how cousins and double first cousins are produced
Optional prefix to add to every identity
This is an adaption to a half-sib breeding design which also produces first cousins and double first cousins. Double first cousins are produced by mating two brothers to two sisters (the offspring of the resulting two families are double first cousins with one another). This is described in Fairbairn and Roff (2006) as being particularly effective for separating autosomal additive genetic variance from sex chromosomal additive genetic variance. It is also amenable to estimating dominance variance, however, it still has difficulty separating dominance variance from common maternal environmental variance (Meyer 2008).
For a given unit of the design (U total), 2*gpn 0-generation
(grandparental or GP) individuals are created and paired to make gpn
full-sib families. Then the first fws families are each allocated
s males/sires and s*(fws-1) females/dams in the 1 (parental or P)
generation. The remaining (gpn-fws) families (only when:
gpn > fws) are assigned s*fws females/dams. If
fsn > (s*fws), the remaining generation 1 (P) individuals in each
full-sib family (fsn - (s*fws)) are allocated to each family with
equal numbers of females and males [this allows for more individuals to be
phenotyped in generation 1 (P) than are used to produce generation 2 (F1)].
Generation 2 (F1) is then assigned, based on the mating design in Fairbairn
and Roff (2006) - essentially each sire [of the s per full-sib family
in generation 1 (P)] is mated to a female from each of the other gpn-1
full-sib families to produce fsn offspring (with equal numbers of
females and males).
Fairbairn, D.J. and D.A. Roff. 2006. The quantitative genetics of sexual dimorphism: assessing the importance of sex-linkage. Heredity 97:319-328.
Meyer, K. 2008. Likelihood calculations to evaluate experimental designs to estimate genetic variances. Heredity 101:212-221.
simPedHS, warcolak
DFC1 <- simPedDFC(U = 1, gpn = 2, fsn = 4, s = 2, fws = 2)
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