Updates to vaccination

[ruthmccabe]

Please can I ask that you both review this just to be safe? I am extra concerned about vaccination due to all of the problems we've had

As discussed in the meeting on 8/1, this PR attempts to correct the following issues:

• renamed children_ind_raw to is_child
• adult_ind_raw is now binned and is replaced with (1 - is_child)
• renamed coverage_achieved_X with coverage_target_X to hopefully make more sense
• simplified target_met_children_t to be a vector rather than a matrix as only giving 1 dose
• create indicator give_doseX, X = {1_children,1_adults,2_adults}, based on 1) eligbility 2) prioritisation and 3) if target for the group has been met. This is a vector of 0s and 1s to indicate which groups vaccines can go to
• eligibility vector is now updated to Y_denom, Y = {children_dose1,adults_dose1,adults_dose2} by multiplying the sum of the relevant compartments within groups by the irelevant indicator give_doseX
• doses are given by (e.g. for compartment S): (doses * S[i,2]/sum(give_dose_X * Y_denom)) * give_dose_X - to me because the give_dose_X in the denom is within a sum, I don't think it will cancel with the numerator? Happy to discuss but some kind of restriction on the denominator is needed because otherwise the denominator will refer to all individuals in the model, not just those who can get the model, and then only a tiny fraction of the vaccines to be given out will be.

[codecov]

Codecov Report

Attention: Patch coverage is 99.37500% with 1 line in your changes missing coverage. Please review.

Project coverage is 88.38%. Comparing base (53a7305) to head (2e55d33).
Report is 30 commits behind head on main.

Files with missing lines	Patch %	Lines
src/model-targeted-vax.cpp	99.37%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #59      +/-   ##
==========================================
+ Coverage   88.28%   88.38%   +0.10%     
==========================================
  Files           8        8              
  Lines        1647     1653       +6     
==========================================
+ Hits         1454     1461       +7     
+ Misses        193      192       -1     

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[ruthmccabe]

before you both review I'll merge Lilith's PR in to avoid any more hiccups

[lwhittles]

Nice! Very minor suggestion about using one of the new objects you define rather than repeating the calc, but otherwise looks good to me, and next checking steps are probably best done graphically