Use per-capita contacts in contact_basis

[RasmusSkytte]

Intent

Currently we perform the age group remapping from the contact matrix age groups to the model age groups in DiseasyActivity.

However, since the population is now primarily being handled in DiseasyPopulation which has access to both the model demography and model age groups, this is a more fitting place for this age handling to occur.

To migrate the age handling from DiseasyActivity to DiseasyPopulation, the first step is to make the contact matrices in DiseasyActivity agnostic to the original demography used to compute the matrices.

Approach

Contact matrices now saved as the per-capita contact rates ("C" domain) instead of the current mean contact rate ("M" domain).

This removes the need to store the original demography used to compute the contact matrices.

This data is still kept, but it paves the way to fully remove this demography when we migrate age handling to DiseasyPopulation.

Contacts returned from DiseasyActivity$get_scenario_contacts() are now also per-capita, and DiseasyActivity$rescale_rates_to_counts() is modified so the output is still C*N.

Known issues

N/A

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

❌ Patch coverage is 73.56322% with 23 lines in your changes missing coverage. Please review.
✅ Project coverage is 64.22%. Comparing base (50d7d25) to head (aef4e1d).
⚠️ Report is 13 commits behind head on main.

Files with missing lines	Patch %	Lines
R/DiseasyActivity.R	76.11%	16 Missing ⚠️
R/generate_contact_basis.R	0.00%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #283      +/-   ##
==========================================
- Coverage   66.09%   64.22%   -1.88%     
==========================================
  Files          28       28              
  Lines        4643     9586    +4943     
==========================================
+ Hits         3069     6157    +3088     
- Misses       1574     3429    +1855     

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