DiseasyActivity: Use non-informative activity by default

[RasmusSkytte]

Intent

This PR expands DiseasyActivity to provide non-informative activity information by default.

That way, a new instance created with DiseasyActivity$new() can directly be used to generate contact matrices and openness.

Approach

$get_scenario_openness() and $get_scenario_contacts() now checks if a scenario is loaded.

If no scenario is loaded, it will provided non-informative activity information.

If the contact_basis is set, it will use the age groups from here by default.
If not, it will only have the "0+" age group.

Non-informative activity information means:

• Openness is always 1
• The contact matrices are uniform and, when summed, the largest eigenvalue is 1

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

[LasseEngboChr]

Wouldn't it be smarter to make the initializer so that this is resolved?

[RasmusSkytte]

Wouldn't it be smarter to make the initializer so that this is resolved?

I am not sure this would be easier.

As far as I could tell, to achieve unit scenario_openness, we would then do the following.

• By default, set the scenario_matrix to have an acitivity which corresponds the unit activity

• Set the default activity_units with a unit corresponding to unit activity.

• Both of these would have to respect the value of direction to ensure that we get unit values when we compute the openess.

• Set a default risk_matrix

This would give us a openness that we could use in the remaining computation and which should hopefully resolve to a unit openness.

This would however also be fragile in principle.
That is, if a user changes the activity units but does not configure a full scenario (using $change_activity), it would fail.

The current solution keeps a unit scenario until a new scenario is fully configured.

The steps to achieve unit scenario_contacts would be similar but there may be more pitfalls here.