11 Model object

The TMB core model object is the object returned by MakeADFun(). A number of options can be passed to MakeADFun to control the model. The current section walks you through all the options. Additionally we demonstrate some of the methods that can be applied to a fitted model object. We shall see how to:

  • Fix and collect parameters using the map argument.
  • Switch parameters back and forth between the inner and outer optimization problem using the arguments random and profile.
  • Set options for the inner optimization problem.
  • sdreporting a fitted object.
  • Bias correction if random effect estimates.
  • Likelihood profiling a fitted object.