call by reference

Can you tell us what you want to do with 'pass/call by reference'?

If you want an R function to alter its argument then it is possible 
(KalmanLike is an example), but it should only be possible via C code.
And if you know enough to do that, you probably would not be asking (and 
definitely not be asking on R-help rather than R-devel).

Can anyone help me about pass by reference of arguments in R functions?

I have read about .Alias in base package however it is defunct and there 
is no replacement for it.

That's not a fair summary of the help entry for .Alias.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595