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:

Merge Request - Guideline Checklist

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Checks by code author

• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
• New code adheres to coding guidelines
• No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• Tests are added for new functionality and a local test run was successful (with and without OpenMP)
• Appropriate documentation within the code (Doxygen) for new functionality has been added in the code
• Appropriate external documentation (ReadTheDocs) for new functionality has been added to the online documentation
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• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Checks by code reviewer(s)

• Corresponding issue(s) is/are linked and addressed
• Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
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Closes #1294

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.38%. Comparing base (564fbf1) to head (cd61b69).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1340      +/-   ##
==========================================
+ Coverage   97.31%   97.38%   +0.07%     
==========================================
  Files         187      189       +2     
  Lines       16019    16532     +513     
==========================================
+ Hits        15589    16100     +511     
- Misses        430      432       +2     

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[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.