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Changelog

Source: NEWS.md

spsurv 1.1.0

  • CRAN resubmission: Maintainer contact updated to rvpanaro@gmail.com; Authors@R roles reviewed (single maintainer; thesis advisors listed as ths, with rev for code review feedback); package Description citation updated to <doi:10.48550/arXiv.2003.10548>; set Config/rstantools/auto_config: FALSE and ship committed Stan C++ exports (no install-time configure/rstan_config(), avoiding Windows R-devel rstan.dll load failures); added RcppParallel and synced src/Makevars.win TBB flags with Unix Makevars; restored covr, rsample, and rsurv in Suggests for optional tests referenced in tests/.
  • Inference robustness: .spbp_gamma_information_diagnostics() no longer calls qr() on non-finite gamma information matrices; vcov()/survfit() return NA uncertainty with a warning when that block is unavailable.
  • tidymodels: parsnip engines spsurv (MLE) and spsurv_bayes for proportional_hazards(), new proportional_odds(), and survival_reg(); bp_survival_reg() convenience constructor; workflow / predict(type = "survival") support.
  • tidybayes: as_draws_df.spbp(), spread_surv_draws.spbp(), and S3 hooks for tidy_draws / spread_draws / gather_draws on Bayes fits; posterior draw indices (.chain, .iteration, .draw).
  • Prediction: censored-style predict.spbp() types (survival, time, linear_pred); augment.spbp().
  • Vignette: vignette("tidymodels").
  • Inference: vcov.spbp() no longer applies a diagonal ridge (polish removed); beta standard errors are unchanged when the Bernstein block is stable and no longer inflated when it is ill-conditioned.
  • Summary: summary.spbp() now includes a coef_interval component (Wald for MLE, HPD for Bayes) and prints it when show_intervals = TRUE.
  • Repository: paper workflow moved from inst/ to paper/ (excluded from the package tarball).
  • Dependencies: trimmed Suggests to packages used in vignettes, tests, or optional integrations; dev tools (devtools, roxygen2, covr) and unused tidymodels/rsurv entries removed (install transitively or only when needed locally).

spsurv 1.0.2

  • Vignettes: Expanded with EDA plots, visual checks, and decision guidance across all seven articles.
  • tidy/broom: tidy(), glance(), logLik(), AIC(), anova(), estimates(), and se() methods for spbp objects; bernstein() baseline specification.
  • Prediction: predict() and improved survfit() (tidy output, newdata covariates, Bayesian monotone bands).
  • Residuals: residuals() supports martingale, deviance, and Cox-Snell types; martingale diagnostics fixed in examples.
  • Handlers: Removed handlers.R; validation and setup logic inlined in spbp.default.
  • vcov: Block-wise inversion of the Hessian (regression vs Bernstein polynomial blocks) in vcov.spbp.
  • Stan: Slim transformed parameters (only alpha stored); pointwise log_lik moved to generated quantities; likelihood via bp_pointwise_log_lik() in the model block.
  • Stan (AFT): No clamping of u to avoid boundary bias; minimum feasible divisor (min_range) only when range is degenerate.
  • MLE: Initial values for the optimizer drawn from prior distributions; retries limited to 3 attempts.
  • spbp objects: Component degree on fits and in call$degree; default Bernstein degree ceiling(sqrt(n)) when omitted (documented in help, README, and vignettes).
  • anova.spbp: Pairwise and sequential analysis-of-deviance tables aligned with survival::survreg (Terms, Test, Df, Deviance, etc.).
  • bpph / bppo / bpaft: User-facing match.call() without unevaluated dist/baseline symbols; optional degree argument.
  • Documentation: Expanded spbp / spbp.default help (@details, return components, vignette links); README usage and model-comparison examples updated.
  • Examples: data("veteran", package = "survival") in docs and examples.
  • pkgdown: Reference index updated to match current package; Bootstrap 5 / default template; logo size and alt-text; README aligned with site style.
  • Repository: CRAN submission hygiene (.gitignore, .Rbuildignore, LICENSE).

spsurv 1.0.1

spsurv 1.0.0

CRAN release: 2020-03-31

  • This is the first release of spsurv.