1032 implementation of stochastic two variant seir model

[nijawa]

Changes and Information

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

• Added stochastic two variant seir model
• Added example for this 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 for new functionality has been added (Doxygen in the code and Markdown files if necessary)
• Proper attention to licenses, especially no new third-party software with conflicting license has been added
• (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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[nijawa]

Hey @reneSchm magst du dir das mal anschauen? Sollte im Grunde einfach nur ein neues Modell sein, die meisten Sachen sind quasi "copy and paste"

[reneSchm]

There are several issues caused by the copy/paste that need to be fixed.

Please merge the main branch as soon as possible.

Please add tests for the new model. You can look at the other SDE model tests, e.g. cpp/tests/test_sde_sirs.cpp. Note that the parameters for those tests are chosen such that a the derivative can be easily computed by hand, but is not trivial.

[codecov]

Codecov Report

Attention: Patch coverage is 96.87500% with 6 lines in your changes missing coverage. Please review.

Project coverage is 96.43%. Comparing base (8889b81) to head (caf756e).
Report is 2 commits behind head on main.

Files	Patch %	Lines
cpp/models/sde_seirvv/simulation.h	84.21%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1047      +/-   ##
==========================================
+ Coverage   96.14%   96.43%   +0.29%     
==========================================
  Files         131      135       +4     
  Lines       11049    11253     +204     
==========================================
+ Hits        10623    10852     +229     
+ Misses        426      401      -25     

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[reneSchm]

There are still some remnants of copy-pasting code, and some comments from my previous review were not addressed.

[mknaranja]

I think most and important points have been addressed through @reneSchm 's reviews, I just have some minor comments, mostly on documentation. Thank you @nijawa.

[reneSchm]

The example needs a little bit more polish, but I think this can be merged soon.

[reneSchm]

Okay, I'd say this is looking good now. Thank you @nijawa for implementing this model!