We can construct a mask to get the non-repeated elements of A. Then, cumsum(mask) will effectively give a phase number for each "new" (i.e. non-repeated) entry in A, which we can use to accumulate B:
A=[9 9 8 7 6 6 6 7 9 9 10 9]
B=[1 1 2 3 1 2 3 2 3 2 4 5]
mask = [true, diff(A) ~= 0];
Anew = A(mask)
Bnew = accumarray(cumsum(mask).', B, [], @mean).'
output:
Anew =
9 8 7 6 7 9 10 9
Bnew =
1.0000 2.0000 3.0000 2.0000 2.0000 2.5000 4.0000 5.0000
Please accept this answer if it helps, or let me know in the comments if I've missed something.
