R-DAT allows the user to create and maintain multiple project databases for the purpose of storing and organizing data, analyses, and analysis results. Project databases contain all information related to the project, including data sets, analyses and associated documentation.

Within each project, the storage of data and analyses can be organized using the project hierarchy, which acts in a similar way as a file directory structure. The hierarchy can be freely defined, and is not limited in terms of the number of levels, or the number of items within each level. A typical example of the hierarchy consists of a structural breakdown of the system into its subsystems and components, or of a classification of the various types of components in the system.

Projects can be viewed and edited in the Project Navigator, which allows the user to quickly navigate the project hierarchy and to access data and analysis stored within the project. Multiple project databases may open at the same time, and all data sets and data sets can be copied between these projects.