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NEWS.md

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eppspectrum 0.1

  • Update to interface with epp v0.3 which implements ANC routine testing (ANC-RT) likelihood in EPP 2017.

eppspectrum 0.1.1

  • Add option to use .ep5 file inputs instead of .DP file when preparing fit from PJNZ file. (use_ep5=FALSE by default.)
  • update prepare_spec_fit() to not use popadjust if EPP projection has a single population.

eppspectrum 0.1.2

  • Parse Spectrum births in read_specdp_demog_param().
  • Add births from Spectrum to specfp object.
  • For epp regions, distribute number of births based on 15-44 population size and GFR.
  • Implement age 15 entrant prevalence and ART coverage inputs.

eppspectrum 0.1.3

  • EPP model setup occurs in fitmod()
  • Allow order of spline model penalty to vary (fp$rtpenord)
  • Allow number of knots to vary (fp$numKnots)
  • Return spline coefficients in fnCreateParam()

eppspectrum 0.1.5

  • Implemented O-spline model (penalized B-spline) using mgcv to construct
  • Added r0logiotaratio option to estimate ratio of r(t0) and log of initial seed, reduces correation. Not set as default.

eppspectrum 0.1.6

  • Bug fix: add check in ll_hhage_binom() that ldbinom() does not return NaN.
  • Bug fix: in create_spectrum_fixpar(), handle case where ART initiation starts in different years for men and women.

eppasm 0.3.0

  • Rename package eppasm.

  • Add IMIS function to eppasm package. In this version of IMIS, at each iteration a new mixture component is constructed either centered on input with greatest weight or based on optimizer. Allows optimizers to be run at arbitrary iterations, but doesn't implment multiple optimizers which might still be usful. Covariance for optimizer mixture component when Hessian is degenerate still needs further work.

  • Change from dependency to imports epp package.

  • Add ANC-RT data to aggregate national fits (prepare_national_fit() and create_aggr_input()).

  • Implement dsamp() to calculate density for initial IMIS samples. This allows different initial sampling density from prior distribution.

  • Specify knot locations for o-spline model

  • Estimate HIV+:HIV- FRR adjustment.

  • Specify knot locations for o-spline model

  • Add functions to read country and subnational region from Spectrum PJN file.

eppasm 0.3.2

  • Integrate random effects variance parameter out of likelihood.

  • Implement hybrid r-spline and RW model for r(t).

  • Implement logistic model for log r(t) (rlogistic), and version with random walk (rlogistic_rw).

  • Add optimization option to fitmod().

  • Add option to fit without site-level ANC data.

eppasm 0.3.3

  • Modularize code for calculating new infections.

  • Implement age 15 entrant prevalence and ART coverage inputs.

  • Implement logit transformation for sampling from uniform logiota prior distribution.

  • Set age IRR penalty variance at a fixed constant value (9003)

  • Implement piecewise-linear time-varying M:F incidence/transmission ratio and 15-24 incidence rate ratio. Knots fixed at 2002, 2007, and 2012.

  • Modularize code for incidence rate ratio parameterization, now in infections.R.

  • Updated default IRR priors to informative priors based on fits countries with several surveys.

  • Add function to generate summary model outputs

eppasm 0.3.4

  • Merge updates from v0.1.2 into v0.3.3

eppasm 0.4.0

  • Add annual direct incidence input option.

eppasm 0.5

eppasm 0.5.0

  • Implement age-specific prevalence among pregnant women.
  • Refactor age-specific prevalence function.
  • Add age-specific ART coverage function.

eppasm 0.5.1

  • Add tidy_output() function to generate long format of key output indicators.

eppasm 0.5.2

  • Use Beer's coefficients to graduate 5-year age IRRs to single year.
  • Add vignette to develop EPP-ASM to Spectrum workflow.

eppasm 0.5.3

  • More constrained prior for log(iota) ~ Unif(log(1e-13), log(0.0025)), matching EPP software.
  • Add posterior predictive outputs for site-level ANC data
  • Incorporate an effect of percentage circumcised on male HIV incidence rate.

eppasm 0.5.4

  • Updates for Spectrum v5.72:
  • Update fertility rate ratio input parameters to allow ART FRR by age.
  • Add time-varying mortality on ART

eppasm 0.5.5

  • Allow specification equilibrium prior standard deviation as a fixed prior parameter.
  • Revise logistic RW model to use fixed standard deviation.
  • Rename rlogistic_rw -> rhybrid
  • Add ANC site-level random effect estimates to tidy_output().
  • Add get_pointwise_ll() to calculate pointwise log-likelihood for data or new data inputs.
  • Add tidy_aggr() to generate summary outputs for aggregation of subnational fits.

eppasm 0.5.6

  • Re-implement r-hybrid model and incorporate smooth transition from logistic function to random walk.
  • Adjustable knot spacing for random walk component of r-hybrid model.
  • Implement Spectrum options for new ART patient allocation.
  • Implement option to scale mortality among untreated population by ART coverage (fp$scale_cd4_mort = 1)
  • Separate time time varying ART mortality trends for ART duration <12 months and > 12 months.

eppasm 0.5.7

  • ART dropout as part of gradient calculation at end of
  • Refactor ANC data model code and add option to input offset in regression equation.