pid= PIDTune[(TransferFunctionModel[(1/((0.4s+1)(((0.5s+1))^2))), ]),"PID","PIDData"];

d=SquareWave[t];
yres1=OutputResponse[pid["DisturbanceOutput"],d,{t,0,5}];
ures1=OutputResponse[pid["DisturbanceControl"],d,{t,0,5}];

{Plot[yres1,{t,0,5},PlotRange->All],Plot[ures1,{t,0,5},PlotRange->All]}

r=UnitBox[t];
yres2=OutputResponse[pid["ReferenceOutput"],r,{t,0,5}];
ures2=OutputResponse[pid["ReferenceControl"],r,{t,0,5}];

{Plot[yres2,{t,0,5},PlotRange->All],Plot[ures2,{t,0,5},PlotRange->All]}

m=0.2t;
yres3=OutputResponse[pid["SensorOutput"],m,{t,0,5}];
ures3=OutputResponse[pid["SensorControl"],m,{t,0,5}];

{Plot[yres3,{t,0,5},PlotRange->All],Plot[ures3,{t,0,5},PlotRange->All]}