Feature - Sub-compartments

[Quantalabs]

Is your feature request related to a problem? Please describe. Currently, sub-compartments in models are not supported. This prevents users from having more advanced models, perhaps a SIR model with an asymptomatic and symptomatic sub-compartments for the infected compartment, or even two sub-compartments for recorded and actual case data.

Describe the solution you'd like Adding a simple way to include sub-compartments in a model, which will allow users to include more complex models like the examples above.

Describe alternatives you've considered Users could instead create two separate compartments for each sub-compartment, however now if #83 is implemented, plotting will plot those as separate compartments, so in stacked charts, the plots will have an infected category, and then a symptomatic category, and asymptomatic category, all plotted separately.

Additional context This feature should most likely be implemented before #83, or otherwise the issue will be reopened once finished.

[Quantalabs]

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[Quantalabs]

My proposal for this is we make comp a submodule of a larger comp module (yes this is a breaking change, but we already are planning to release v3, see #115) and create another submodule called sub in comp for submodules. The submodules will be like compartments, but can only be a percentage of the larger compartment. The model will look like the following (when exported into JSON):

{
  "compartments": {
    "S": {
      "equation": "S-(B*S*I/p)"
    },
    "I": {
      "equation": "I+(B*S*I/p)-(u*I)",
      "compartments": {
        "Asymptomatic": {
          "percent": 10,
        },
       "Symptomatic": {
          "percent": 90,
        }
      }
    },
    "R": {
      "equation": "R+(u*I)"
    }
  },
  "key": {
    "S": 10000,
    "B": 0.3,
    "I": 100,
    "R": 0,
    "p": 10100,
    "u": 0.2
  }
}

[Quantalabs]

I've decided to disregard the idea to have a sub-compartment, but instead add a method in the compartment classes called .addSub(). The JSON structure will stay.

[Quantalabs]

With 88cb0c23de2b27857715dcb741df8b49282cb571 we have the initial code for subcompartments.

[Quantalabs]

Sub compartments are now officially implemented with f8e2399f2bd43bbe12334ff4b403487d9c47a632, which will be merged into master soon.