I have conducted the preparation phase and now wish to write an R01 application. Should I propose to complete both the optimization and evaluation phases, or only the optimization phase?

In general, we recommend applying for funding to complete only the optimization phase, and making it clear in the application that you intend to apply for funding to support a subsequent evaluation of the optimized intervention (assuming this is what you plan to do).  There are two reasons for this.

First, depending on the exact situation, it can be difficult to conduct both an evaluation and an optimization trial in a single five-year funding cycle (see How can I estimate how long my trials will take?)

Second, imagine you have applied for funding to conduct an optimization trial to examine an array of candidate intervention components, followed by an RCT to evaluate the optimized intervention.  A reviewer could (justly) point out that you don’t know whether you will find enough candidate components with detectable effects to assemble an intervention that is worth evaluation.  An alternative would be to apply for a 3- or 4-year R01 to conduct only the optimization trial.