NEWS.md

In cifmodeling: Visualization and Polytomous Modeling of Survival and Competing Risks

cifmodeling 1.2.3

• tidy.polyreg() accepts the default arguments forwarded by modelsummary::msummary(), so tables can display exponentiated coefficients and confidence intervals at the requested level.
• polyreg() validates the active event codes and requires both event types by the analysis time for fixed-time competing-risk models. IPCW uses the specified censoring code, supports character strata, and accounts for estimating the censoring distribution within each stratum in the fixed-time sandwich variance.
• Multilevel binomial models use the generalized log odds product to fit separate exposure contrasts against the reference level. Proportional models use the requested level for normal bootstrap intervals and compute BCa intervals separately for the reported coefficients.
• cifcurve() computes delta and Aalen variances using all event times up to each reported time. The legacy engine reports risk sets immediately before each time and accepts unweighted data or positive weights that are constant within each stratum. Confidence limits and one-sided p-values are missing beyond each stratum's positive-weight follow-up.
• Time-to-event analyses reject unsupported Surv() response types. Explicit competing-risk analyses retain their selected outcome type when a cause is absent, subject to the event requirements of each estimator. The joint Gray covariance in ciftest_mdir() respects custom event codes.

cifmodeling 1.2.2

• Added direct optional gtsummary::tbl_regression() support for polyreg, including event selection, reference rows and event-specific RR/OR/SHR headings. tidy.polyreg() supports exponentiate and the standard logical conf.int/numeric conf.level interface while retaining legacy numeric conf.int. Stored intervals are retained when inference settings are unchanged.
• Corrected survival-summary SE scaling and unstratified curve compatibility. cifcurve() now returns a subclass of survfit; its summary and stratum-subsetting methods keep saved inference aligned and prevent interval extrapolation past positive-weight follow-up. Reporting adapters preserve the fitted statistical results.
• Added reporting articles for CIF curves/tests and event-specific regression, with gtsummary formatting and Word/HTML export examples.

• Fixed unweighted cifplot() calls being treated as weighted when NULL weights were forwarded internally. Unweighted plots now honor error = "aalen" and "delta", and retain the unweighted default variance choice. Actual supplied weights retain the existing weighted-inference rules.

• Added pointwise IF-t, FG-normal and FG-t intervals to cifcurve() for independent observations with no weights or known fixed weights. Select conf.dist = "t" for Student critical values, or error = "fay" for the FG sandwich correction. Existing default method choices are retained.

• IF-t supports df.method = "deletion" (FG-type allocation, default) or "equal" (equal-allocation working Satterthwaite degrees of freedom). FG-t uses deletion allocation. Results record time-specific degrees of freedom, critical values and interval availability reasons. These are approximations, not exact t distributions or uniform coverage guarantees.
• Supplied weights, including externally estimated IPTW, are treated as fixed. Propensity-score estimation and its full IF contribution remain outside this API. IF/FG limits beyond positive-weight follow-up, or with invalid interior variance/df, are missing rather than silently replaced by a normal interval; valid boundary singletons are retained.
• Corrected the C++ IF recursion to differentiate the actual KM/AJ product limit, including tied jumps. IF standard errors can consequently differ from earlier versions. FG contributions share that recursion. Also fixed zero cause-1 CIFs when only competing events are observed.

cifmodeling 1.2.0

• Added ciftest() for standard and weighted log-rank/Gray tests and closed-form augmented competing-risk score tests with separately specified censoring and competing-risk nuisance strata.

• Redesigned the public ciftest() selector around test = "auto", "logrank", "gray", "score", or "augmented"; "early" and "late" select outcome-specific Fleming--Harrington presets. Survival outcomes now default to log-rank and competing-risk outcomes to the augmented score. Added "L", "LR", and "log-rank" aliases for log-rank, "G" for Gray, and "A", "aug", and "augmentation" for the augmented score test. Added a null robust score option, individual score-contribution matrices, two-sided multigroup omnibus tests, and survdiff compatibility for the ordinary unweighted log-rank result.

• Renamed the public analysis-stratification argument from strata.event to strata. strata.censor is formally available for the competing-risk null score, while strata.competing.risk remains specific to augmentation.

• Added prob.truncation for derivative-aware probability lower truncation of censoring KM and working AJ survival denominators. Raw probabilities continue to determine structural positivity failures; raw and used minima and truncation counts are returned in diagnostics.

• Added ciftest_mdir() to combine user-selected unweighted, early, late, or custom Fleming--Harrington directions in a Ditzhaus--Friedrich quadratic score test with rank-adaptive asymptotic chi-square calibration. Classical log-rank directions use a joint finite-population-corrected hypergeometric covariance, while classical Gray directions use the bilinear extension of Gray's event, competing-event, and censoring covariance. Consequently, linearly dependent FH directions do not change the quadratic test. ciftest(test = "multiple") and its "multi" and "m" aliases use the linearly independent default directions (2, 0), (0, 2), and (0, 0); the single-direction early and late presets remain (1, 0) and (0, 1).

• Added analysis stratification to ciftest() independently of strata.censor and strata.competing.risk. Log-rank and Gray scores/covariances, Fine--Gray risk sets, and FH weight processes are constructed within event strata and then summed. Closed-form augmentation uses event-by-exposure-by-competing-risk-by-censoring computational cells; positive fixed-point iterations remain restricted to pooled models. All three strata arguments accept one or more column names; multiple columns define their observed interaction and share one complete-case filter.

• Added finite Scheike fixed-point refinement to ciftest(). The single iteration argument selects the closed-form augmented score at zero and a fixed number of iterated time-weighted Fine--Gray updates at positive integers, with subject-level scores and residual diagnostics returned. Appendix-E iteration now evaluates the working competing-risk ratio with the coherent Aalen--Johansen survival and enforces positivity only where a future cause-1 score contribution is active; censoring times beyond the last cause-1 event are excluded from the correction map and reported in diagnostics$iteration.support.

• Anchored positive finite iterations and the internal direct fixed-point reference at the closed-form augmented score using closed-form + AIPWCC(value) - AIPWCC(seed). This preserves the zeroth-step identity in each observed sample while retaining the raw AIPWCC(seed) as a batch-only diagnostic. Anchoring discrepancies are returned under diagnostics$iteration.anchor.

• Added an internal batched ciftest engine for simulation studies. It reuses censoring Kaplan--Meier and working Aalen--Johansen nuisance fits within one data set, preserves scalar ciftest() result objects, and moves the nested Fine--Gray score-IID and closed-form augmentation loops to Rcpp kernels. Fixed Fleming--Harrington weights with a common nuisance specification are evaluated together in a multiweight traversal.

• Replaced the default Fine--Gray score-IID traversal with an internal sort-plus-prefix/reverse-suffix C++ kernel. Risk moments, the base IID, censoring derivative, and censoring-martingale IID are evaluated without the former event-by-censoring-time-by-subject loop. The independent legacy kernel remains available through options(cifmodeling.ciftest.fg.engine = "legacy"); "check" evaluates both kernels and stops if their numerical outputs differ beyond tolerance.

• Added a cell-aggregated prefix C++ kernel for closed-form augmentation. Reverse at-risk sums replace the censoring-time-by-subject centering loop, and cell-specific censoring-hazard prefixes replace the subject-level martingale traversal. The legacy implementation remains available through options(cifmodeling.ciftest.augmentation.engine = "legacy"); "check" evaluates both implementations and verifies all returned IID and diagnostic quantities.

• Added a batch-only direct Appendix-E fixed-point reference solver. It builds the affine iteration operator, reuses one QR factorization across FH weights, and reports residual, spectral-radius, and conditioning diagnostics. Finite iteration and the public scalar ciftest() interface remain unchanged. A direct solution is now marked converged only when its algebraic residual meets tolerance and the empirical operator has spectral radius below one; solving a non-contractive linear system is retained as a diagnostic result.

• Added a batch-only Fine--Gray score-IID reference for simulation comparisons. It uses the Fine--Gray influence-function cross-product as its test variance and is kept separate from the public standard Gray test.

• Added diagnostics$fh.weight.process to ciftest() results so the exact event-time FH process and its pooled-AJ or native-Gray construction can be audited and compared with independent implementations.

cifmodeling 1.0.0

• Third CRAN release.

• Added cifflowchart() for lightweight flowchart summaries of exclusions, groups, and outcome status.

• Added one-sided normal approximation tests in cifcurve() via time.point and null.hypothesis.
• Improved handling of risk-set display and event coding options.
• Updated documentation, examples, vignettes, and pkgdown site.
• Fixed bugs and expanded test coverage.

cifmodeling 0.9.8

• Second CRAN release.

cifmodeling 0.9.7

• Added n.risk.type to cifcurve() to optionally display weighted, unweighted, or Kish ESS risk set sizes without changing estimates or SEs.
• Modified the risk table of cifplot() to display integer values.
• Simplified the special-case handling for cloglog by unifying axis-application logic, improving maintainability without changing user-facing results.
• Added/strengthened robust tests for axis limits and breaks behavior.

cifmodeling 0.9.6

• Documentation and tests were polished for CRAN submission.
• Fixed GCC r-devel warning (-Wstringop-overread) triggered in calculateAJ_Rcpp (no change to user-facing results).

cifmodeling 0.9.5

• First CRAN release.
• Documentation and tests were polished for CRAN submission.

cifmodeling 0.9.4

• Sixth CRAN submission.

Invalid DESCRIPTION file, software names were single quoted. Rebuilt and resubmitted.

cifmodeling 0.9.3

• Fifth CRAN submission.

Addressed CRAN feedback regarding file-system and environment management. Removed development-time scripts under tools/ that performed bulk renaming and wrote to the package directory or the current working directory. These files are no longer included in the source tarball. Eliminated the remaining use of .GlobalEnv in internal helpers. panel_as_formula_global() now evaluates formulas in the calling environment (parent.frame()) instead of .GlobalEnv, fully complying with the “no modification of the .GlobalEnv” CRAN policy. No user-visible changes; only internal cleanup for CRAN compliance.

cifmodeling 0.9.2

• Fourth CRAN submission.
• Invalid file URLs (articles/gallery.html, articles/polyreg.html, articles/formulas.html) were replaced by URLs in the web and verified using urlchecker::url_check(). Rebuilt and resubmitted.

cifmodeling 0.9.1

• Third CRAN submission.
• The DOI reported by CRAN (10.21105/joss.00510) does not appear to be present in the package source. Verified using recursive search and a freshly created tarball. Rebuilt and resubmitted.

cifmodeling 0.9.0

• Second CRAN submission.

cifmodeling 0.8.2

• Bug fixes
• README.Rmd, Vignettes and site were updated.
• Cumulative hazard and log-log plots were implemented

cifmodeling 0.8.1

• README.Rmd, Vignettes and site were updated.
• polyreg S3 methods were implemented

cifmodeling 0.8.0

• Breaking change: cifplot() and cifpanel() now return structured objects with explicit plot/list.plot and patchwork elements, metadata, and printing handled via new S3 methods. Automatic printing is limited to interactive sessions, and panel outputs store engine metadata in print.info$engine.

• Standardized outcome.type canonical values to lowercase; legacy uppercase and short aliases remain accepted. Internals now use tolower().

cifmodeling 0.7.0

• Bug fixes
• README.Rmd, Vignettes and site were updated.

cifmodeling 0.6.0

• Initial CRAN submission.

cifmodeling 0.5.0

• Bug fixes

cifmodeling 0.4.0

• Bug fixes

cifmodeling 0.3.0

• cifpanel() and panel mode of * cifplot() were developed.

cifmodeling 0.2.0

• Bug fixes

cifmodeling 0.1.0

• cifcurve(), cifplot() and polyreg() were developed.

cifmodeling documentation built on Nov. 11, 2026, 9:06 a.m.