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In this paper we develop a generic hierarchical model for performance analysis of intrusion detection techniques as applied to a cyber-physical system (CPS) consisting of mobile nodes with navigation, manipulation, sensing and actuating capability. We develop two intrusion detection techniques, namely, positional discontinuity and enviroconsistency, for intrusion detection of malicious attackers in a CPS. We utilize the hierarchical model developed to analyze the performance characteristics of these two techniques and identify optimal design settings under which the reliability of the CPS may be maximized. The analysis reveals design tradeoffs in security assurance and energy consumption, and suggests that enviroconsistency be used over positional discontinuity for reliability maximization. Numerical results with physical interpretations are given to demonstrate the effectiveness of our approach.