NEWS.md

In mrc-ide/first90release: The first90 model

first90 1.7.1

• Implement Spectrum adult ART adjustment by absolute count. This is a user input that adjust the number on ART count by an absolute value. It is intended to be used to account for clients receiving services in or from another region; typically with subnational Spectrum files.

If both absolute count and ratio adjustments are specified in the same year, the absolute count is applied first and then ratio is applied. If ART is specified as a percentage, then adjustments do not have any influence.

Previously entered ART adjustments were applied or not via a checkbox in Spectrum. The checkbox has been removed in Spectrum 6.38 beta 18. For backward compatability with previously simulated Spectrum outputs, if the checkbox flag exists in the .DP file, it is still used to determine application of the ratios; if the .DP file does not contain the checkbox flag, then the ratio is applied.

• Patch ART dropout implementation. Spectrum converts input ART dropout percent to an annual rate using [dropout rate] = -log(1.0 - [input percent]).

• Implement Spectrum ART allocation.

There has been a longstanding discrepancy betweeen EPP-ASM and Spectrum in ART allocation. For ART allocation by 'expected mortality', EPP-ASM allocated according to mortality by CD4 and age.

Spectrum allocates ART in a two step process: first, ART is allocated by CD4 category based on the 'expected mortality' and 'proportional to eligibility' weight. Second, within CD4 categories, ART is allocated by age solely proportional to number in each age group (propotional to eligibility).

This has modest overall difference, but was a source of numerical differences between Spectrum and EPP-ASM.

first90 1.7.0

• Update output plots and tables to 2024.

• Extend theta0 initial values for additional year random-walk parameters.

• 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

first90 1.6.12

• Update plots and tables to end in 2023.

first90 1.6.11

• Fix bug in R version of simmod() where new infections previously tested negative were subtracted from (instead of added to) the hiv positive. Implementation in C++ version was correct (thanks Andrey Kutsyh).

first90 1.6.10

• Implement recovery to next higher CD4 category following ART interruption for those on ART greater than one year.
• Qualify package names, fix some R CMD warnings and notes

first90 1.6.9

• Bug fix: account for end-year net migration in the ART population in the first year of ART start (implemented in v1.6.0).

first90 1.6.8

• Don't interpolate number aware outputs in Spectrum output table when using calendar year interpolation.

first90 1.6.7

• Update PJNZ extraction for adult ART need Dec 31 for 2023 PJNZ files. Previously child ART was note recorded in the .DP file tag <NeedARTDec31 MV>, and so it was fine to extract the total value. Now child ART is recorded, and so need to sum the adult age groups only.

first90 1.6.6

• Implement Spectrum Adult ART scalar adjustment. This is a user input that allows the input number on ART to be adjusted by a scalar to account for over/under-reporting of treatment numbers.

first90 1.6.5

• Exclude NA values to set max ylim in plot_prv_pos_yld(). This addresses issue with this plot not showing in interface and preventing plot downloads when data NA values are simulated.

first90 1.6.4

• Extend output plots and tables through 2022.

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.

first90 1.5.3

• Add missing @export tags to ensure README.Rmd runs

first90 1.5.2

• Update initial values to median of 2021 .shiny90 file final parameter estimates.

first90 1.5.1

• Update output tables and plots show results through 2021 (missed in v1.5.0 update)

first90 1.5.0

Updates for 2022 UNAIDS estimates:

• Extend output arrays, plots, and tables to output 2021 results.

• Extend theta0 initial values for additional year random-walk parameters.

• Intercalate new infections in each HIV time step. Equal number of infections are added in each time step. This is controlled by the option eppmod = "directinfections_hts".

• Option eppmod = "directinfections_hts" is specified as the default option in prepare_inputs(pjnz). Therefore, new package version will not reproduce simulations from a previous model fit. Simulating from a previous fit requires manually specifying fp$eppmod <- "directinfections" after calling prepare_inputs().

• extract_pjnz() reads whether custom population adjustment was used in the Spectrum file from the tag "<RegionalAdjustPopCBState MV>". This is used to set popadjust = TRUE automatically if a custom population was used in Spectrum.

first90 1.4.3

• Patch: in function add_ss_indices(), add argument type.convert(..., as.is = TRUE) to suppress R 4.0 warning.
• Bugfix: remove duplicate declaration of double incrate_g[NG]; in EPP_DIRECTINCID incidence option. This did not affect any results because this option is not used in Shiny90 application; new infections by sex and age group were directly specified (option EPP_DIRECTINFECTIONS).

first90 1.4.2

• Implement backward compatibility for simulating previous .shiny90 outputs.
• The updates for each year add an additional knot, which changes the length of the parameter vector. This update parses the knot definition based on the number of parameters.
• Function create_hts_param() will throw and error if an unexpected parameter vector length is identified.

first90 1.4.1

Updates for 2021 UNAIDS estimates:

• Extended arrays to output 2020 results.

• Changed prior for baseline testing rate to normal(log(0.005), sd = 0.25). (likelihood.R#138)

• Revise HIV retesting rate to increase log-linearly betwee 2005 and 2010. The implication of this is to reduce the retesting rate during the 2000s compared to the 2010s, which reduces implausibly high predictions for number of HIV tests conducted during the 2000s in the abscence of HTS programme data (Giguere et al 2020).

first90 1.3.5

• Updated the calculation of 'retests' among HIV positive adults to include HIV positive tests conducted amongst adults who had previously tested HIV negative. Previously new HIV diagnoses were excluded from the count of retests and only HIV positive adults who were previously diagnosed or on ART were counted as 'retests'. This should not change any of the standard displayed outputs because by convention the 'retest' figures have focused on retests among HIV negative adults while separate results have been reported for retesting among HIV positive results.

first90 1.3.4

• Add adjustment in Spectrum output CSV that the number aware of status is greater than the number on ART. This occurs in some cases when the 'internal' number on ART in Spectrum is greater than the input end of year numbers due to capping the number on ART below number of PLHIV within age/sex strata. This also means that if the number on ART in Spectrum is greater than the number of PLHIV, then the number aware will also be greater than the number of PLHIV. (This occurs seldomly, but can occur.)

first90 1.3.3

• Output the proportion of the undiagnosed population who were infected in the past year in the Spectrum outputs download.

first90 0.0.0.9000

• Added a NEWS.md file to track changes to the package.

mrc-ide/first90release documentation built on Nov. 22, 2024, 5:02 a.m.