Deprecate old analysis functions

[TobiasDijkhuis]

Deprecate/remove old analysis functions. They should not be used anymore, in favor of just model.get_dataframes to get the rate constants, and converting those to reaction rates, etc.

[GijsVermarien]

Yes, we should document this whole workflow like we do in notebook 4! Maybe some text based built-in functions would still be needed for those that like script based analysis?