It seems like the order in which this loop runs does matter, as you might change Rate_array(i+1) on one iteration, thereby changing the result of Rate_array(i) > ChainLengths(i) on the next iteration. Therefore, vectorizing this code may leave you with incomplete results. You could solve the issue by rerunning the code until you know you're done, demonstrated below using sample A and B vectors:
A = randi(10,10,1);
B = randi(10,10,1);
i = A>B;
while any(i)
sg = A-B;
A(i) = B(i);
A([false; i(1:end-1)]) = A([false; i(1:end-1)]) + sg([i(1:end-1); false]);
i = A>B;
end
There may be a better way. This at least shows how you can "reference the next/previous value in a vector without using a for loop."
