1294 add LCT SECIR model with two disease strains

[an-jung]

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

• added LCT SECIR Model for 2 DISEASES on the basis of the LCT SECIR model

If need be, add additional information and what the reviewer should look out for in particular:

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Closes #1294

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.33%. Comparing base (0fce556) to head (fa35096).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1340      +/-   ##
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+ Coverage   97.26%   97.33%   +0.07%     
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  Files         184      186       +2     
  Lines       15807    16320     +513     
==========================================
+ Hits        15374    15885     +511     
- Misses        433      435       +2     

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[jubicker]

I'm not sure whether the naming of the parameters and also of infection states is the best choice. Maybe we should use longer but more self-speaking names, like TimeExposedDisease1,... and for infection states something like: InfectedNoSymptomsDisease1Naive and InfectedNoSymptomsDisease1RecoveredDisease2? Or is that too long? @annawendler what do you think?

[annawendler]

I agree that the infection states are not that self-speaking but I also find the more explaining names really long and quite hard to read. I couldn't come up with a good compromise so I would go with the shorter names.

[annawendler]

Regarding names of infection states, I thought of renaming Recovered_a to Recovered_1a and Recovered_ab to recovered_2ab to make it more explicit how many infections the individuals have gone through.

[annawendler]

First part of review

[annawendler]

In a recent commit the use of floating point types was reworked to allow for automatic differentiation. This also affected the LCT-SECIR model, e.g. we now have an additional template parameter FP for the model class. Can you adapt your model accordingly so that the models are consistent? If you have any questions just let us know :)

[mknaranja]

@an-jung please use capitalization in github for shorthand notation such as LCT, SECIR, ...

[annawendler]

Remaining part of review. Looks good in general! The interact() function was a bit unclear to me, see questions below. Otherwise my comments are mainly regarding documentation

[annawendler]

Looks good to me! :) I only have minor comments regarding naming of some variables.

[annawendler]

Suggested change

	FP InfectedNoSymptoms_Group2_a = 0;
	FP infectedNoSymptoms_group2_a = 0;

Can you adjust the naming like this in the interact() function? According to our coding guidelines (https://memilio.readthedocs.io/en/latest/development.html#coding-guidelines) variables should use small letters. I know this isn't done 100% consistently throughout the code (such as N oder Ri_a) but here it also helps with consistency within the code of your model.

[annawendler]

Suggested change

	FP N_Group2 = pop.segment(first_index_group2, LctStateGroup2::Count).sum(); // Sum over all compartments.
	FP N_group2 = pop.segment(first_index_group2, LctStateGroup2::Count).sum(); // Sum over all compartments.

See above

[annawendler]

Suggested change

	const FP div_N_Group2 = (N_Group2 < Limits<FP>::zero_tolerance()) ? 0.0 : 1.0 / N_Group2;
	const FP div_N_group2 = (N_Group2 < Limits<FP>::zero_tolerance()) ? 0.0 : 1.0 / N_Group2;