DiseasyModel

[RasmusSkytte]

Intent

This PR adds the DiseasyModel class (fixing #26)

Approach

Exported from NGC and adapted.

This class (now fully documented) forms the basis for all model templates in diseasy.

To do this, it includes the ability to contain instances of functional modules (presently, DiseasySeason, DiseasyActivity and DiseasyObservables).

These can be added either in the constructor of through the $load_module() function (implemented in DiseasyBaseModule not DiseasyModel).

Beyond containing these instances of functional modules, DiseasyModel defines the "API" for the model templates to use.
That is, it provides the functions:

• $get_results()
• $get_training_data()

and it implements the $parameters list of parameters for the model.

The implementation of $load_module() in DiseasyBaseModule is also refactored and generalized to load arbitrary modules and not just DiseasyObservables.
Now, if any class includes the private field $.Diseasy<Module> then $load_module() can populate this field if the provided module has the class "<Module>" (e.g. DiseasyObservables).

Known issues

The tests for DiseasySeason and DiseasyObservables are failing.
This is due to the tests being run across all diseasystores which as introduced errors.
This is being fixed in a different PR:

• Disable test across all diseasystores #99

The R-CMD-Check without dependencies is failing.
This is being fixed in a different PR

• Gracefeully handle missing suggests #102

We may want to wait for #101 and #111 to be merged before merging this PR.
This way, we can add these new functional modules to DiseasyModel.

• New DiseasyImmunity module and waning function #101
• DiseasyVariant #111

Checklist

• The PR passes all local unit tests
• I have documented any new features introduced
• If the PR adds a new feature, please add an entry in NEWS.md
• A reviewer is assigned to this PR

[codecov]

Codecov Report

Attention: Patch coverage is 61.36364% with 17 lines in your changes missing coverage. Please review.

Project coverage is 85.79%. Comparing base (0e01449) to head (d5fa480).
Report is 29 commits behind head on main.

❗ Current head d5fa480 differs from pull request most recent head 0b866fd

Please upload reports for the commit 0b866fd to get more accurate results.

Files	Patch %	Lines
R/DiseasyModel.R	61.36%	17 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #36      +/-   ##
==========================================
- Coverage   87.19%   85.79%   -1.41%     
==========================================
  Files           8        9       +1     
  Lines         914      929      +15     
==========================================
  Hits          797      797              
- Misses        117      132      +15     

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[LasseEngboChr]

Please have a look at suggestions and comments