IoTs and WSNs utilize their connectivity to enable solutions supporting a spectrum of industries in different and volatile environments. To effectively enhance the security and quality of service of networks, empirical research should take into account a variety of factors and be structured in a replicable manner. This will not only ensure scalability but also enable verification of conclusions, leading to more constructive outcomes. Cooja offers limited performance analysis capabilities of simulations, which are often extracted and calculated manually. In this paper, we introduce a framework and a toolkit that enable researchers to conduct structured and conclusive experiments considering different factors and metrics, experiment design to results analysis. Besides, this tool summarizes multiple network metrics and allows multiple scenarios. As proof of concept, this paper studies the flooding attacks on IoT and illustrates their impact on the network, leveraging the proposed framework and tools.