LD R-Squared Compute squared linkage disequilibrium r2 = D^2 / (p(A) * (1 - p(A)) * p(B) * (1 - p(B))). Description Compute squared linkage disequilibrium r2 = D^2 / (p(A) * (1 - p(A)) * p(B) * (1 - p(B))).