976 improve the documentation of the ide secir model

[lenaploetzke]

Changes and Information

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

• Documentation of the IDE-SECIR model has been extended.
• Added a diagram of possible transitions.

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

• We could add the model equations to make clear how the parameters are used (e.g. in the ODE-SECIR model this is clear because of the picture). However, we would then have to specify the full equations of the compartments and the transitions.

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)
• [x] 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)

• [x] Corresponding issue(s) is/are linked and addressed
• [x] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• [x] Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• [x] No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• [x] 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 #976.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 96.34%. Comparing base (8ddb863) to head (0424b55). Report is 7 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #1000 +/- ## ======================================= Coverage 96.34% 96.34% ======================================= Files 129 129 Lines 10056 10071 +15 ======================================= + Hits 9688 9703 +15 Misses 368 368 ```

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[lenaploetzke]

I also think the formulas would be misplaced in the README. We should publish the paper instead and link it here :D For now, I think it's fine as it is.

I think we can also merge the PR before #952, the link should work if it's merged. Then we have already finished this PR, #952 will be finished soon.

[annawendler]

This looks great and can be merged after PR #952 has been merged.