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Changelog

Source: NEWS.md

cfrnow (development version)

  • pp_check_cfr() runs a posterior-predictive check on a fit: it draws replicate line-list outcomes from the posterior, replays the real-time truncation, and compares the observed death counts (plus recoveries in a two-outcome fit) and the observed onset-to-death delays against the replicates (#14).
  • summary() gains an ascertainment_ratio argument that corrects the CFR for outcome-dependent case ascertainment (fatal and non-fatal cases entering the line list at different rates). The ratio is supplied, defaulting to 1.
  • fit_cfr() accepts intercept-free CFR formulas (e.g. cfr ~ 0 + group, one estimated logit-CFR per group): the cfr_prior is placed on those coefficients rather than a non-existent intercept, so the fit no longer fails brms prior validation.
  • summary() reports a CFR per group for a cfr ~ group fit (one cfr[<group>] row per group), rather than erroring or silently reporting only the reference level.

cfrnow 0.1.0

First release.

  • fit_cfr() estimates a real-time case fatality ratio from line-list data with a Bayesian mixture-cure survival model. It is registered as an epidist model type, so the CFR and the onset-to-death delay both take brms formulas.
  • prepare_cfr_data() turns a line list into model inputs. It sorts each case, at a chosen observation cut-off, into an observed death, a resolved non-death, or a right-censored survivor.
  • The onset-to-death delay (LogNormal or Gamma) can be co-estimated or held fixed. Hold it fixed and you get the Ghani/Nishiura estimator.
  • Pass a recovery_date column and a two-outcome fit also times recoveries.
  • Put a brms formula on the CFR or the delay for covariates or a time-varying CFR.
  • simulate_linelist() builds line lists for testing and examples.
  • summary() and print() report the corrected CFR, the delay moments, convergence diagnostics, and a flag for when the CFR is only weakly identified.