I am working on the adaptive control of quadrotor UAV in MATLAB/Simulink environment. I prepared some trajectories for the UAV to follow in $x$, $y$ and $z$ directions. I would like to implement these trajectories by using a commercial pilot joystick whose blocks are available on Simulink. What I am quite unclear is the selection of these inputs through the joystick.
In flight control systems, one can give roll, pitch and yaw rates ($p$, $q$ and $r$) as inputs to be followed by the UAV. In a conference paper I came across an example where the roll angle ($\phi$), the pitch angle ($\theta$) and the yaw rate ($\dot{\psi}$) are given from the joystick.
My question is the following: What is the general selection for the UAV inputs through a joystick? I watched some videos on Youtube, where some people are controlling the UAVs with joysticks. Do they directly provide the desired $p$, $q$ and $r$ ?