[R] covar

[rex.dwyer at syngenta.com]

I hate to sound like David "Have You Read The Posting Guide?" Winsemius, but there's no way for anyone to know what you are trying to accomplish here without a lot more information.  You don't show us the output you expect and the output you got.  I would expected "relatedness" to be on a scale from 0 to 1, but it's clear that you'll get values >1 in this program.
To use R effectively, you need to rephrase your computation as a matrix computation.  People generally use R at least partly to avoid debugging index computations in for-loops.  For-loops are also much slower than the corresponding matrix operations in R.  If you want to use for-loops, you can always put in some prints and trace what's going on, just like the old days!

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Val
Sent: Wednesday, February 16, 2011 3:14 PM
To: r-help at stat.math.ethz.ch
Subject: [R] covar

Hi all,

I want to construct relatedness among individuals and have a look at the
following script.

#########################
rm(list=ls())

N=5
id   = c(1:N)
dad = c(0,0,0,3,3)
mom  = c(0,0,2,1,1)
sex  = c(2,2,1,2,2) # 1= M and 2=F

   A=diag(nrow = N)
   for(i in 1:N)    {
      for(j in i:N)      {
         ss = dad[j]
         dd = mom[j]
         sx = sex[j]
          if( ss > 0 && dd > 0 )
            {
              if(i == j)
                   { A[i,i] = 1 + 0.5*A[ss,dd] }
                 else
                  { A[i,j] = A[i,ss] + 0.5*(A[i,dd])
                    A[j,i] = A[i,j] }
            }

      } #inner for loop
     } # outer for loop
  A

If the sex is male ( sex=1)  then I want to set A[i,i]=0.5*A[ss,dd]
If it is female ( sex=2) then A[i,i] = 1 + 0.5*A[ss,dd]


How do I do it ?

I tried several cases but it did not work from me. Your assistance is
highly  appreciated  in advance

Thanks

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