kappaIbd() and inbred founder (grandparent-grandchild)

[hildekb]

kappaIbd() and inbred founder (grandparent-grandchild)

[magnusdv]

The IBD coefficients (kappa) are defined only for non-inbred individuals. In your example the grandfather is inbred, hence all kappas involving him come out as NA. As shown below, a warning about this is printed if you add verbose = T in the call. (Perhaps this should be the default behaviour!)

BTW, the function linearPed() is useful for creating (great)grandparent relationships. Also note that pedtools is loaded automatically with ribd.

library(ribd, warn = F)
#> Loading required package: pedtools

x = linearPed(2)
founderInbreeding(x, 1) = 0.1

# Undefined kappas since 1 in inbred
kappaIbd(x, ids = c(1, 5), verbose = T)
#> Warning: kappa coefficients are only defined for non-inbred individuals.
#> 1: f = 0.100000
#> [1] NA NA NA

# All pairs at once
kappaIbd(x)
#>    id1 id2 kappa0 kappa1 kappa2
#> 1    1   2     NA     NA     NA
#> 2    1   3     NA     NA     NA
#> 3    1   4     NA     NA     NA
#> 4    1   5     NA     NA     NA
#> 5    2   3    0.0    1.0      0
#> 6    2   4    1.0    0.0      0
#> 7    2   5    0.5    0.5      0
#> 8    3   4    1.0    0.0      0
#> 9    3   5    0.0    1.0      0
#> 10   4   5    0.0    1.0      0

^{Created on 2019-06-14 by the reprex package (v0.3.0)}