Pedigree construction
Construct a pedigree yielding a prescribed set of IBD coefficients.
constructPedigree(kappa, describe = TRUE, verbose = FALSE)
kappa |
A probability vector of length 3; (κ_0, κ_1, κ_2). |
describe |
A logical. If TRUE, a textual description of the resulting relationship is printed. |
verbose |
A logical. If TRUE, various details about the calculations are printed. |
The construction follows the method and formulae given in Vigeland (2020).
A ped object containing a pair of double half cousins with inbred
founders. (In corner cases the relationship collapses into siblings.)
M. D. Vigeland (2020). Relatedness coefficients in pedigrees with inbred founders. Journal of mathematical biology. doi: 10.1007/s00285-020-01505-x
# Full siblings x = constructPedigree(kappa = c(0.25, 0.5, 0.25)) kappaIBD(x, leaves(x)) # A relationship halfway between parent-child and full sibs kap = c(1/8, 6/8, 1/8) showInTriangle(kap, label = " (1/8, 1/8)", pos = 4) y = constructPedigree(kappa = kap) plot(y) stopifnot(all.equal(kappaIBD(y, leaves(y)), kap)) # kappa = (0,1,0) does not give a parent-child relationship, # but half siblings whose shared parent is completely inbred. z = constructPedigree(kappa = c(0,1,0)) plot(z)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.