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a guest Aug 14th, 2019 42 Never
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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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