1208 implement endemic IDE model

[hatrit]

Changes and Information

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

added an endemic SECIR-type IDE model, meaning we allow for natural birth and death.
-All in all the structure is similar to the ide_secir model and similar functionalities are implemented. One big difference besides the birth and death rate is that in this case another approach for the initialization is used. We just assume to know the sizes of the compartments at start time 0.

• Added the folder ide_endemic_secir in the folder models
• In the foler are the following files:

• infection_state.h: Definition of infection states and transitions

• parameters.h: all the given parameters are defined here

• computed_parameters.h: Contains the class CompParameter, where we compute all the model parameters, we can compute before the start of the iteration.

• model.h/model.cpp: Functions needed in the iteration. two different schemes are implemented, as there a two ways to implement the compartments, everything computed with the update scheme is names _update

• normalized_model.h/normalized_model.cpp: Againg Functions needed in the iteration are implemented. But in this case we model a normalized SECIR-type IDE model.

• Added the example ide_endemic_secir.cpp in the examples folder.

-No tests yet!

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

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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
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• 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.)
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Closes#1208

[annawendler]

Review of computed_parameters.h

[annawendler]

Remaining review of ide_endemic_secir folder