Currently (i.e. after #136), ContactNetwork accepts transition rates for KineticModel; however, transition rates for MasterEquationEnsemble are set separately. This creates confusion, so it's better to either
set transition rates inside KineticModel without ever touching ContactNetwork (through a factory method), or
set true transition rates on ContactNetwork, and then let the ensemble read those that are needed, and pass distributions for those that have to be inferred via EAKF.
Besides, generate_diagram_indep and generate_diagram_neigh methods are inside ContactNetwork simply because of the names of weight labels; they don't really belong there. This can be fixed via a Glossary class which would hold all parameter names.
Currently (i.e. after #136),
ContactNetworkaccepts transition rates forKineticModel; however, transition rates forMasterEquationEnsembleare set separately. This creates confusion, so it's better to eitherKineticModelwithout ever touchingContactNetwork(through a factory method), orContactNetwork, and then let the ensemble read those that are needed, and pass distributions for those that have to be inferred via EAKF.Besides,
generate_diagram_indepandgenerate_diagram_neighmethods are insideContactNetworksimply because of the names of weight labels; they don't really belong there. This can be fixed via aGlossaryclass which would hold all parameter names.