nbsurv 0.5.1

CRAN resubmission

• DESCRIPTION: added method references to the Description field - Wolfson et al. (2015) doi:10.1002/sim.6526 for the censored naive Bayes model, and Gerds and Schumacher (2006) doi:10.1002/bimj.200610301 for the IPCW Brier score used in evaluation.
• man/nbsurv-class.Rd: added a \value section documenting the return values of the print() and plot() methods for "nbsurv" objects.

nbsurv 0.5.0

New features: kernel-smoothed horizons (time_smooth)

• New time_smooth = TRUE / bandwidth arguments to nbsurv()/ cv_nbsurv() (default FALSE, fully backward-compatible). The real remaining inefficiency identified after cov_structure = "full" (0.4.0): every horizon was fit completely independently, discarding the fact that class-conditional statistics should vary smoothly with time - costly right where one of the two horizon-defined classes (already failed vs. known to survive) is smallest, typically near the earliest or latest requested horizon. time_smooth = TRUE precomputes class- conditional statistics once at every point of time_grid at fit time, then combines them at predict() time via Nadaraya-Watson kernel regression across horizons (Gaussian kernel, width bandwidth) - borrowing strength from neighboring horizons while still allowing genuinely time-varying effects, unlike a proportional-hazards model that shares one coefficient across all of time. Because the combination is a convex (weight-normalized) average of already-valid per-grid-point statistics, smoothed covariance matrices stay positive semi-definite and smoothed categorical probabilities stay valid automatically - no PSD repair or renormalization needed. bandwidth is now a tunable column in tune_nbsurv()’s param_grid.
• Bug fix found and fixed during implementation: the first working version returned NA for every smoothed prediction. 0 * NA is still NA in R, so zero-weighting an invalid (all-NA) grid point before summing did not neutralize it; colSums() propagated the NA. Fixed by zeroing the invalid rows’ values, not just their weights, before summing. Regression test locks this in (tests/testthat/test-time-smooth.R).
• Empirical validation against coxph on lung (20 held-out 70/30 splits, age + sex + ph.ecog): a genuine, principled bias-variance tradeoff, confirmed rather than assumed. Concordance improves as bandwidth widens (0.60 at the default heuristic up to ~0.615-0.619 as bandwidth grows toward pooling most of the time range), closing roughly half to two-thirds of the gap to coxph’s 0.629 - but IPCW Brier score at the most extreme horizon tested (t=400) worsens monotonically as bandwidth widens (0.240 to 0.254), the expected cost of over-smoothing away genuine horizon-specific calibration. No single bandwidth wins on both metrics at every horizon; the default heuristic (one quarter of the fitted time range) is a reasonable balance, not a universally optimal choice - use tune_nbsurv()’s bandwidth grid column to tune it for a specific dataset, exactly as any other hyperparameter.
• Even at the best bandwidths tried, the lung benchmark gap to coxph narrows but does not fully close - reported honestly in the README rather than oversold. age/ph.ecog’s covariate effects are close to log-linear and non-interacting on this dataset, which is exactly what a correctly-specified Cox model is built to exploit; nbsurv’s value proposition is flexibility (genuinely time-varying, non-proportional effects a fixed-coefficient Cox model cannot represent), not raw accuracy dominance on every dataset.
• No C++ was added. Benchmarked at n=5000 (3270 distinct event times): time_smooth = TRUE fit time is ~2.5s vs ~0.03s without it - a real but tolerable one-time cost at realistic survival-analysis sample sizes, with predict() itself remaining fast (~17ms for 500 predictions) since it only does cheap kernel-weighted averaging over the precomputed grid. The existing time_grid argument already lets users pass a coarser custom grid to cut this cost further if needed. Rcpp would be unjustified complexity for a bottleneck that doesn’t clearly exist at the scale this package targets.

nbsurv 0.4.0

New features

• New cov_structure = c("diagonal", "full") argument to nbsurv()/ cv_nbsurv() (default "diagonal", fully backward-compatible). With "full", continuous predictors are modeled jointly as a single multivariate Gaussian per class (survivor/event), relaxing naive Bayes’s conditional-independence assumption between them, instead of the product of independent univariate Gaussians. The covariance matrix is shrunk toward its diagonal by the new shrinkage argument (default 0.2) for numerical stability at small sample sizes. Categorical predictors are unaffected and remain conditionally independent either way. With fewer than 2 continuous predictors, "full" is numerically identical to "diagonal" (verified by regression test).
• Empirical validation (see tests/testthat/test-cov-structure.R): on a synthetic case with two continuous predictors correlated at r=0.85, cov_structure = "full" gives a consistent ~5-6% relative improvement in held-out IPCW Brier score over "diagonal" at every horizon tested. Its effect on concordance is small and inconsistent even under strong correlation - concordance depends only on the ranking of risk scores, which a monotonic transform of the naive product often preserves even when the underlying probabilities are miscalibrated; Brier score, which scores the actual probability values, is the metric this correction reliably improves. On the real lung dataset (age/ph.ecog correlated at r=0.31, n=167), the improvement was smaller and mixed (Brier improved at 2 of 3 horizons tested, concordance improved at 2 of 3) - "full" is a genuine, validated improvement when continuous predictors are correlated, not a guaranteed win on every dataset, and did not close the gap to coxph on lung specifically (see README benchmark).

nbsurv 0.3.2

Bug fixes (scientific validity)

• evaluate_nbsurv()/cv_nbsurv()/tune_nbsurv() reported the complement of concordance (1 - true concordance), not concordance itself. concordance_at_horizon() calls survival::concordance(Surv(time, status) ~ risk), whose formula interface defaults to the opposite direction convention from a risk score (it expects higher risk to mean longer survival unless told otherwise). Since every internal caller passes a genuine risk-direction score (higher = more likely to fail), the returned value was systematically inverted - a model with a true C-index of 0.63 was reported as 0.37, making a genuinely discriminating model look worse than random. Fixed by adding reverse = TRUE to the survival::concordance() call. Verified against survival::concordance() on both a coxph linear predictor and an nbsurv fit (matches to full precision either way), and a new regression test on a clearly-separable synthetic case that would fail loudly if the direction ever flips back. Brier scores, predictions, and every other metric were unaffected - this only touched the concordance calculation.

nbsurv 0.3.1

Bug fixes

• plot.nbsurv() silently double-scaled continuous predictors before plotting, distorting every survival curve it drew. nbsurv() only ever stored the scaled training data on the fit object; plot.nbsurv() passed that already-scaled data into predict(), whose prepare_newdata() step scales its input again using the same stored means/sds. The result was visually “chunky” curves with implausible flat segments and near-zero collapses for some rows, especially past t=400 in the README example - not real model behavior, an artifact of predicting from twice-standardized covariates. Fixed by storing the raw (unscaled) training data separately (fit$training_data_raw) and having plot.nbsurv() use that instead. predict()/evaluate_nbsurv()/ cv_nbsurv()/tune_nbsurv()/varimp_nbsurv() were never affected - they operate on user-supplied newdata, which is only ever scaled once. New regression test locks plot.nbsurv()’s curves to match predict() called directly on the same raw rows.

nbsurv 0.3.0

New features

• New varimp_nbsurv(): permutation-based variable importance. For each predictor, its values are independently shuffled (n_repeats times), evaluate_nbsurv() is recomputed on the permuted data, and importance is the resulting degradation in the chosen metric ("brier" or "concordance"), averaged over the requested horizons and repeats. Returns a data.frame (class varimp_nbsurv) sorted by decreasing importance, with its own print() method.
• New base-graphics plot() methods: plot.varimp_nbsurv() (horizontal bar chart of importance), plot.cv_nbsurv() (mean cross-validation metric vs. horizon), and plot.tune_nbsurv() (mean tuning metric per candidate, best candidate highlighted).

nbsurv 0.2.0

New features

• evaluate_nbsurv() now computes the integrated Brier score (IBS) via the trapezoidal rule in addition to horizon-specific Brier scores and concordance.
• New calibration_plot_nbsurv() function for visual calibration assessment at a single prediction horizon.

Bug fixes and improvements

• Continuous predictor standard deviations are now bounded away from zero by min_sd in both the survivor and event classes, preventing numerical collapse in degenerate training subsets.
• predict.nbsurv() now enforces monotone survival curves via cumulative minimum across increasing horizons.
• Categorical likelihoods now use Laplace smoothing controlled by the laplace argument, with IPCW-weighted event-class counts.

nbsurv 0.1.0

• Initial release (prototype; class CNB, single-horizon prediction).