323 SECIRTS model with waning immunity

[HenrZu]

Changes and Information

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

• Added a new model including waning immunity and temporary immunity states build upon the secirvvs model
• New initialization method

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

• [x] Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
• [x] New code adheres to coding guidelines
• [x] No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• [x] Tests are added for new functionality and a local test run was successful (with and without OpenMP)
• [x] 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.)
• [ ] On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

closes #323

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 97.55773% with 55 lines in your changes missing coverage. Please review.

Project coverage is 96.35%. Comparing base (8f9a34c) to head (48dffed). Report is 3 commits behind head on main.

Files	Patch %	Lines
cpp/models/ode_secirts/parameters_io.h	97.00%	25 Missing :warning:
cpp/models/ode_secirts/parameters_io.cpp	89.28%	18 Missing :warning:
cpp/models/ode_secirts/parameters.h	98.96%	4 Missing :warning:
cpp/models/ode_secirts/model.h	99.40%	3 Missing :warning:
cpp/models/ode_secirts/parameter_space.h	97.50%	3 Missing :warning:
cpp/models/ode_secirvvs/model.h	75.00%	1 Missing :warning:
cpp/models/ode_secirvvs/parameters_io.h	87.50%	1 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #963      +/-   ##
==========================================
+ Coverage   96.23%   96.35%   +0.12%     
==========================================
  Files         128      134       +6     
  Lines       10852    13032    +2180     
==========================================
+ Hits        10443    12557    +2114     
- Misses        409      475      +66     

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