Prototyping is the gathering of information. “Information gathered in the prototyping phase allows the analyst to set priorities and redirect plans inexpensively, with a minimum of disruption” (Kendall & Kendall, 2011, p. 156). The prototyping helps to determine the basic requirement of input and output information, user interfaces, and customers and end users feedback. The advantage of prototyping can help the system analyst to stop development if the system is unworkable or potential changes to the system in the early developing stage. The disadvantage of prototyping for a system analyst can be an incomplete prototype and thinking it is a complete system.
Rapid Application Development (RAD) is a software development methodology, which focuses on building applications in a small amount of time. RAD has three phases that help both users and analyst to design, assess, and implement. The first phase is a requirement planning phase, which the user and analyst will meet to identify objectives and information of the application or system. The second phase is RAD design workshop, which is design and refine phase that helps the analyst and user to design based on feedback. The last phase is the implementation phase, which comes from the analyst working with the users on the planning phase and design workshop phase that will help to determine if the system is compatible with the old system before implementation. The advantage of the RAD is that it is flexible and can adapt to change. The disadvantage of RAD is, not all application might be compatible with RAD.
Agile Modeling, “A systems development approach which has values, principles, and practices useful for systems analysts who desire a flexible, interactive, and participative approach”( Kendall & Kendall, 2011, p.557). One advantage of Agile modeling is, “daily face to face conversation is key point in agile testing. This is most efficient & effective way of communication” (Periyasamy, 2009). One disadvantage of Agile modeling is, if the customer is not clear of what they want then the project can get off track.
Each methodology will assure the system analyst that they have a complete system and that the outcome of the project will be a success. Each methodology will help everyone that is involved with the project to get a good understanding of the direction that the project is heading toward, and the outcome of the project.

References:
Kendall, K. E., & Kendall, J. E. (2011). Systems Analysis and Design (8th ed.). Upper Saddle, NJ: Prentice Hall
Periyasamy, J (2009). Define Agile Model and its Advantages. Retrieved fromhttp://www.jobsnewstoday.com/2013/06/define-agile-model-and-its-advantages.html