For non-trivial problems in any domain, Systems Engineering provides a starting framework for identifying problems, assessing possible solutions, implementing those solutions, measuring the performance of the efforts to deliver the solutions and the effectiveness of those solutions. Here's the collective wisdom of Systems Engineering from Mitre.
This book has many resources for a variety of problems in many domains, including agile development. This text speaks to managing in the presence of uncertainty and the processes needed to make decisions including estimating.
Systems engineering and policy analysis must account for costs and affordability. An elegant engineering solution that the customer cannot afford is useless; so too is a policy option that would make many people happy, but at a prohibitive cost. Therefore, careful efforts to estimate the cost of a particular option and the risk that the actual cost may exceed the estimate are necessary for systems engineering and policy analysis. Engineers who design products for commercial sale are familiar with the concept of “price points,” and a manufacturer may wish to produce several products with similar purposes, each of which is optimal for its own selling price. In the case of systems engineering for the government, it may be necessary to conduct a policy analysis to determine how much the government is willing to spend, before conducting a systems engineering analysis to arrive at the technically “best” solution at that cost level.