Adding a new SEIR model that simulates Infectious Diseases

[mgharamti]

Description:

Added a new model to DART. The model simulates the spread of infectious diseases for example COVID-19. The model has 7 state variables and 10 other parameters. This version of the code can be used for state estimation only. Future versions may also include parameter estimation capabilities. The model makes use of identity observations such as: number of people recovered, number of those who died or the number of people who got vaccinated.

Fixes issue

NA

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] Documentation update

Documentation changes needed?

• [x] My change requires a change to the documentation.
  • [ ] I have updated the documentation accordingly.

Tests

Ran model_mod_check, perfect_model_obs, filter with different obs_seq files.

Checklist for merging

• [ ] Updated changelog entry
• [ ] Documentation updated
• [ ] Update conf.py

Checklist for release

• [x] Merge into main
• [ ] Create release from the main branch with appropriate tag
• [ ] Delete feature-branch

Testing Datasets

• [ ] Dataset needed for testing available upon request
• [x] Dataset example is included
• [ ] No dataset needed

[hkershaw-brown]

Hi Moha, this looks really good. Quick question before I review this: At the moment this pull request is into NCAR:seir from mgharamti:seir. Do you want to do the pull request into NCAR:main and release this model_mod as part of dart?

[mgharamti]

Opps, didn't realize that the PR wasn't made into main. Yes, the intention is to push this model to the main public dart code. Do you want me to cancel and do the PR again?

[hkershaw-brown]

no problem I switched to be be into main. Cheers, Helen

[hkershaw-brown]

d86fdc5effc177ab36dcc9f50d5fc070ba33beeb swapped :raw-math: for :math: since readthedocs not rendering the :raw-math:

[mgharamti]

Helen, thanks for all the great suggestions especially for the location and perturbation. For the check to initialized modules, I'm also ok either way. I just felt it's a simple model and wanted to keep the code volume minimal but happy to change if needed. As far as the science go, I think it should be ok. I compared the equations to the original work I did with my collaborators and the code that Shaniah left us with. It should be ok.