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

• 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.)
• 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]

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files

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  Coverage   96.34%   96.34%           
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  Files         129      129           
  Lines       10056    10071   +15     
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+ Hits         9688     9703   +15     
  Misses        368      368           

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[annawendler]

I liked the description and also the picture :) I made some suggestions.

I'm actually unsure whether I would add the formulas for the compartments and transitions here. I'm not sure if the readme gets too long and overwhelming with the formulas. By looking at the table we still know which parameters play a role in our model. On the other hand, without the formulas it is somehow incomplete as it is not clear where exactly the parameters go into the model as you mentioned. What is your opinion?

We should remember to only merge this PR after PR #952 so that the links work correctly.

[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]

I agree :D

I would still only merge after the other PR, I will look at it soon!

[annawendler]

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

[annawendler]

Looks good!