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Aug 14th, 2019
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  1. fam <- structure(list(ID = c(1L, 2L, 3L, 4L, 6L, 5L, 7L), dad = c(0L,
  2. 0L, 1L, 1L, 1L, 3L, 5L), mum = c(0L, 0L, 0L, 2L, 4L, 4L, 6L),
  3. GEN = c(1L, 1L, 2L, 2L, 3L, 3L, 4L)), class = "data.frame", row.names = c(NA,
  4. -7L))
  5.  
  6. library(Matrix)
  7.  
  8. hom = function(fam) {
  9. t1 <- min(which.max(fam$dad > 0), which.max(fam$mum > 0))
  10. t2 <- max(fam[["ID"]])
  11.  
  12. A<-Matrix(0, nrow=t2,ncol=t2, sparse=TRUE)
  13. diag(A) <- 2-0.5^(fam[["GEN"]]-1)
  14.  
  15. for (t in t1:t2) {
  16. A[t,t]<- sum(c(A[t,t], 0.5^(fam[t,"GEN"])*A[fam[t,"dad"],fam[t,"mum"]]))
  17. for(j in 1:(t-1)) {
  18. A[t,j]<- 0.5 * sum(c(A[j,fam[t,"dad"]],A[j,fam[t,"mum"]]))
  19. A <- tril(A) + t(tril(A, -1))
  20. }
  21. }
  22. A
  23. }
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