A simple way to calculate the effective dielectric constant of a transmission line is to use the unwrapped phse of the S21. The phase of S21 is electrical length of the transmission line in degree. So, you can plot the effective dielectric constant versus frequencies by adding an expression of the output variable as shown below.
θ=(2*pi/λ)*L where L=physical length of the transmission line, θ=unwrapped phase of S21.
=(2*pi*√(er_eff)/λ0)*L
Er_eff=(θ*c/(2*pi*f*L))^2;
Actually, the expression for the effective dielectric consatnt is more complex, but for general transmission lines such as microstrip lines and CPWs, you can use this express.