Changelog

Source: NEWS.md

rhap 0.1.0

New features

  • fit_model() re-specified: linear year trend replaces year fixed effects, NMVOC dropped (non-significant under every specification/SE estimator tested), and Driscoll-Kraay standard errors are now computed and returned (vcov_dk), justified by confirmed serial correlation and cross-sectional dependence in the panel.
  • The country-level bias-correction term is now computed internally by fit_model() from the fitted model itself (bias_adder$bias.adder), replacing the static rhap::hia_adder dataset, which has been removed along with calc_hia_adder().
  • by_gr = TRUE in calc_hap_impacts() now reports within-country income-decile group shares of population, PM2.5+NOx exposure, and GDP (table + pie chart), instead of a fabricated group-level health-impact estimate. The regression model is fit on between-country variation only, so applying it to within-country decile inputs was an unvalidated extrapolation; shares of GCAM’s own group-level data carry no such risk.
  • fit_model()’s bias_adder now also returns reliability_ratio (and calc_hap_impacts()’s output a derived reliability “high”/“medium”/“low” label), flagging countries whose absolute-level prediction rests mostly on the bias correction rather than the regression’s own covariates – computed already, previously discarded.
  • calc_hap_impacts() gains a fit_result argument: pass a previously-computed fit_model(HIA_var) result to skip refitting the national regression (including its Driscoll-Kraay vcov) on every call, e.g. when comparing many GCAM scenarios for the same HIA_var.
  • Added a new “Validating the econometric model” vignette: a reproducible record of the panel/inference diagnostics, the (rejected) GDP x PM2.5 interaction test, the additive-vs-multiplicative bias-adder investigation, and the GBD real-data validation methodology.

Bug Fixes

  • Fixed the country-level bias correction silently clamping a negative “predicted” death/YLL/DALY rate to exactly 0 (occurred for ~12% of observations on the model’s own training data). It now floors at a small fraction of the naive, uncorrected prediction instead. (A multiplicative bias correction, which prevents negative values by construction, was also tried; it was rejected after validation against real GBD data showed it performing far worse than the additive form – see fit_model()’s documentation and the econometric-model vignette.)
  • Fixed fit_model(HIA_var = "yll"): valid input silently resolved to NULL due to a mismatched lookup key ("ylls" vs. "yll").
  • Fixed a rerun of calc_hap_impacts(map = TRUE) against a not-freshly-cleared output/ directory failing because the map-output file mover matched, and tried to rename, its own destination folder.
  • Fixed several .RData test snapshots (calc_hap_impacts, calc_ResidEm_grp x2, fit_model) being compared vacuously: load() injects an object under whatever name it was saved as, which for these files happened to match the local variable holding the freshly-computed test result (testOutput), silently overwriting it before expect_equal() ran – so the test was comparing the stale snapshot to itself, regardless of what the function under test actually returned. Also removed the now-redundant, structurally-brittle fit_model snapshot in favor of targeted structural/sign/parameter checks.

Package/performance

  • Removed dead code (flsp_pc_gr, flsp_pc_ctry_gr, gdp_pc_ctry_gr) left over from the by_gr redesign.
  • GCAM group-level queries (subregional population, subregional income) and their downstream processing now only run when by_gr = TRUE (the shares they feed are otherwise never consumed) – skips two extra GCAM queries and their processing on every default-mode (by_gr = FALSE) call.