Hi Anita
You need to create an NY-by-NY-by-P matrix, where NY is the number of variables in the VAR, and P is the order of the VAR (this is a transition matrix), and enter either an NaN for all coefficients that are to be freely estimated, or a particular number for those that are to be fixed.
In your example, let's say you want to restrict the coefficients A(1,2,1) and A(1,2,2) to zero, i.e. the effect of PI{-1} and PI{-2} on R.
You create the A matrix as follows
A = nan(3,3,2);
A(1,2,1) = 0;
A(1,2,2) = 0;
and call the estimate command as follows
[v,vdata] = estimate(v,d,{'R','PI','Y'},Inf,'order=',2,'A=',A);
Let me know whether this is clear enough...
Best
Jaromir