Hyper parameters are not estimated

[richelbilderbeek]

Hyper parameters are not estimated

[richelbilderbeek]

bjoelle has a point there: this has been implemented and tested only partially. First step is (in the commit above) is to have a failing assert when the implementation is incomplete.

[richelbilderbeek]

On the other hand, it is partially implemented! Should I throw away the partial implementation, and rebuild it when needed, or keep it, but fail fast?

[richelbilderbeek]

Nah, bjoelle is right: I should remove the illusion of having hyper priors from the interface.

[richelbilderbeek]

But also here: sometimes the interface is complete...

[richelbilderbeek]

I've removed the estimate = FALSE option from the interface. The partially complete back-end I leave intact.

There are some parameters that are estimate = TRUE by default, for the GTR site model. I just leave these be.

I consider this done.