2025 update -- non-AIDS excess mortality

[jeffeaton]

• Implement new excess non-AIDS mortality among PLHIV implemented in
  Spectrum 6.38 for 2025 UNAIDS HIV estimates.

  Spectrum 6.38 implements rates of non-AIDS excess mortality by sex,
  age group, CD4 category and ART status. By default these mortality rates
  are applied in concentrated epidemic countries and defaulted to zero in
  African HIV epidemic settings.

  Spectrum outputs for non-AIDS deaths among PLHIV in AIM include non-AIDS
  excess deaths. EPP-ASM deaths outputs are updated accordingly.

  To ensure backward compatibility, excess non-AIDS mortality are initialized
  to 0.0 and replaced with values read from Spectrum if the relevant values
  exist in the .DP file.

  simmod() updated to incorporate excess non-AIDS mortality among PLHIV.
  Internally new model parameters arrays cd4_nonaids_excess_mort and
  art_nonaids_excess_mort follow the same dimensions and stratification
  of cd4_mort and art_mort arrays. These represent expansions of the
  arrays saved in Spectrum-AIM, to all age groups and ART duration categories,
  consistent with handling of the cd4_mort and art_mort arrays.

• Fix bug in R version for end-year net migration in first year of ART eligibility

[m-maheu-giroux]

Thanks for updating this. I looked at the excess non-AIDS mortality and seems straightforward as it is not affected by testing history or KOS status.

[m-maheu-giroux]

The 2025-update branch has version number 1.7.0 whereas the master has 1.16.11. Should I edid the master to 1.7.0 to match the update? @jeffeaton

[jeffeaton]

The 2025-update branch has version number 1.7.0 whereas the master has 1.16.11. Should I edid the master to 1.7.0 to match the update? @jeffeaton

Thanks for spotting that. I have pulled the master branch and fixed the merge conflicts, that should be good for now.

Please hold on merging this for a moment; I want to share with Guy to see the changes.