spsurv 1.1.0
- CRAN resubmission: Maintainer contact updated to
rvpanaro@gmail.com; license is GPL-3 (removed
the bundled LICENSE copy of the GPL);
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.
devtools and roxygen2 are not listed in
Suggests.
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
- This is the first release of spsurv.