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In this paper we analyze the effect of intrusion detection and response on the reliability of a cyber physical system (CPS) comprising sensors, actuators, control units, and physical objects for controlling and protecting a physical infrastructure. We develop a probability model based on stochastic Petri nets to describe the behavior of the CPS in the presence of both malicious nodes exhibiting a range of attacker behaviors, and an intrusion detection and response system (IDRS) for detecting and responding to malicious events at runtime. Our results indicate that adjusting detection and response strength in response to attacker strength and behavior detected can significantly improve the reliability of the CPS. We report numerical data for a CPS subject to persistent, random and insidious attacks with physical interpretations given.