Hi Laura,
All questions are opportunities to provide clarifying responses.
You believe that initial equilibrium catch is very small, but SS does not know that because you have set the lambda on that small catch to zero. Therefore the estimated value of initial equilibrium F will not be influenced by the low value of initial equilibrium catch. Instead, the value of initial equilibrium F will be influenced by other data in your model. What kinds of other data would cause SS to fit best with a high initial F value? One situation is when the early years of age or size composition data show a paucity of old/large fish, causing SS to try to have a high Z in early years to reduced the expected value for proportion old/large fish. The other situation is when the CPUE trend is increasing. CPUE can only be expected to increase when the stock is rebounding from an earlier depletion (e.g. from high initial F), or when there is a sequence of higher than average productivity.
My recommendation is to profile on the value of initial F to see what type of data shows improved -logL when initial F is high.
Rick
