Calculating the lag phases in growth curves by minimizing sum of squared errors

I studied '1471-2180-11-140-s1.m', a matlab script that can estimate lag phases from growth curves. This program can 'align' growth curves using the matlab optimization procedures.  I used Octave 3.8.0 with GUI and found it useful.

My plan to is to use R optim() to minimize the sum of errors.  The differences of lag phases are the indices in the vectors.   So, somehow, I need to re-index the vectors.  Maybe I can use the a small threshold and put NA to very small values.  I will then have two vectors, X1 and X2.  The sum of errors can be defined as
  SumOfErrors = sum( (X1[1:lengthOfX2] - X2[delta:END2] )^2 )

20140316:
This is basically the global alignment problems in sequence alignment.


Reference:
1471-2180-11-140-s1.m  from the Xavier group.