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first90 v1.6.3
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@jeffeaton jeffeaton released this 02 Dec 12:49
· 1 commit to update-2023-theta0 since this release
v1.6.3
c666eb9

This release implements updates for 2023 UNAIDS estimates.

In addition to typical extension of arrays for additional year, this release changes the projection period to calendar year instead of mid-year for PJNZ files saved with Spectrum v6.2 or later.

Shiny90 has also been implemented as part of Spectrum in Spectrum v6.2.

first90 1.6.3

  • Correct initial theta0 value for 2023 extended parameters.

first90 1.6.2

  • Use vroom::vroom() to read PJNZ files; much faster for reading .DP file.
  • Handle Spectrum version numbers saved on Francophone locale devices: e.g. 6,13 instead of 6.13.
  • In read_specdp_demog_param(), ensure no zero totals when normalising age-specific fertility
    distribution and net-migration age distribution.
  • Fix calculation for target number on treatment during transition from number to percent input.

first90 1.6.1

Updates for 2023 UNAIDS estimates:

  • Extend output arrays, plots, and tables to output 2022 results.
  • Extend theta0 initial values for additional year random-walk parameters.

Other:

  • Remove data.table dependency.

first90 1.6.0

Updates for Spectrum transition from mid-year projection period to calendar year
projection period. Implemented in Spectrum 6.2 in November 2022.

Previous mid-year interpolation is still available in code by using argument
create_fp(..., projection_period = "midyear"). The default argument
projection_period = NULL will choose the projection period based on the
Spectrum inputs version number. For versions 6.19 and earlier,
projection_period = "midyear". For versions 6.2 and later, projection_period = "calendar".

  • Normalise asfd and netmigagedist to sum to exactly 1.0 before distributing
    to age groups.

  • Disaggregate under-5 net migration proportional to paediatric survival probabilities
    in the base year.

  • Net-migrations added at end of projection step, consistent with WPP 2022. No longer
    (1) adjust net migration for half-period survival, nor (2) adjust net migration to
    be half in current age group and half in next age group.

  • End-year ART input interpolation adjusted to reflect calendar year projection period,
    such that ART input aligns to end of projection year.
    Note: since net migration is applied after ART initiations, the number on ART will
    be scaled by the net migration proportions. Therefore the model output for number on
    ART will not exactly match the ART inputs.

  • In likelihood calculations for household survey proportion ever tested, interopolate
    model outputs to mid-year. This affects ll_evertest(). Likelihood for annual
    HIV tests and diagnoses (ll_prgdat()) is unaffected.

first90 1.5.5

  • Patch to eppmod = "directinfections_hts" option (v1.5.0) to avoid referencing
    uninitialised memory.
  • Fix error in ART deaths calculation in R version of simulation code. ART mortality time trend
    was omitted from deaths removed from total HIV population.

first90 1.5.4

  • Update time to diagnosis functions to account for CD4 at seroconversion in categories below 350.
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