Standard surveillance output

[seabbs]

I think we want to define some standard surveillance output for _make_epi_aware as this will help with postprocessing and be of general utility (given the aim of the tooling).

I think the way to we want to do this is to create a new abstract function in EpiAwareBase that is called in the return of _make_epi_aware and dispatches on the EpiInfModel type used. This is so that we can have a generic method that just uses the expected infections for its metrics and more specific methods that use the already computed reproduction number estimates and growth rate calculations.

Alternatively, we could consider this as a post-processing step for the model output (i.e it works with a for object) but I think its nice to make use of the struct information we have to provide custom solutions which I think favours doing this in model (albeit only as part of the generated quantities).

This would look like

struct SurveillanceMetrics
	growth_rate
    reproduction_number
    infections
end

surveillance_metrics(AbstractEpiInfModel, I_t, gen_y_t, inf_process_aux)
	growth_rate  = ...
    reproduction_number = ...
    ?

    return SurveillanceMetrics(growth_rate, reproduction_number, ?)
end

surveillanec_metrics(Renewal, ...)
	growth_rate .... 
    reproduction_number = inf_process_aux.Rt
    ?
   return SurveillanceMetrics(growth_rate, reproduction_number, ?)
end

I'm thinking about the return as a struct as then we can build postprocessing that interfaces with this w/ some guarantee of correctness. Not sure this really makes sense or is the right way to think about it so would appreciate thoughts @SamuelBrand1?

[SamuelBrand1]

I think this is a really good idea. Should be reasonable to achieve, we want or already have the functions to fill this in.

We can also add a pretty print to the struct so you get a lot of information (Unicode plots even?)

[seabbs]

We can also add a pretty print to the struct so you get a lot of information

I think we want more pretty printing of structs in general and wondered if there was a package out there. Can't find anything right now though

[seabbs]

Aside from structs are there any other data structures (and links please) we could be thinking about here to use to control dispatch?

[SamuelBrand1]

We can also add a pretty print to the struct so you get a lot of information

I think we want more pretty printing of structs in general and wondered if there was a package out there. Can't find anything right now though

I think the canonical way of doing this is overloading Base.show with a custom method

[seabbs]

Yeah I saw this and I was wondering if anyone had already done work on that for this kind of use case

[seabbs]

This kind of thing: https://github.com/MechanicalRabbit/PrettyPrinting.jl