Internet of Things (IoT) systems are ubiquitous, highly complex and dynamic event-based systems. These characteristics make their security analysis challenging. Security in IoT requires domain-specific methodologies and tools. The proposed methodologies need to be able to capture information from software and hardware constructs to security and social constructs. In this paper, in addition to refining the modeling language of the Apparatus Framework, we propose a class-based notation of the modeling language and a structured approach to transition between different models. Apparatus is a security framework developed to facilitate security analysis in IoT systems. We demonstrate the application of the framework by analyzing the security of smart public transport system. The security analysis and visualization of the system are facilitated by a software application that is developed as part of the Apparatus Framework.