multipleOutcomes 0.16

Breaking changes

• multipleOutcomes() and the legacy *MO() wrappers (coxphMO, glmMO, geeMO, logrankMO, kmMO, quantileMO) are removed. The package’s main entry point is now jointCovariance(), and each component model is specified through a constructor: glm_(), coxph_(), logrank_(), gee_(), mmrm_(), km_(), or quantile_(). pated() accepts the same spec constructors via ....
• Datasets supplied to jointCovariance() / pated() must now contain a column pid carrying subject identifiers. Records with the same pid across different data frames refer to the same subject.

New features

• mmrm_() adapter for mixed models with repeated measures.
• km_() adapter for Kaplan-Meier survival probabilities (bootstrap-only, since the empirical S(t) has no closed-form score).
• quantile_() adapter for between-arm quantile differences (bootstrap-only).
• gee_() adapter exposing a GEE fit’s per-cluster score and Hessian so it slots into the joint asymptotic covariance machinery alongside other engines.
• conf_type = "arcsin" is fully supported in km_() (previously silently fell back to logit transformation).

User-experience improvements

• data_index defaults to 1 in every spec constructor, and a single data frame is auto-wrapped, so jointCovariance(spec1(...), spec2(...), data = my_df) is the shortest valid call.
• Spec constructors validate data_index (must be a positive integer scalar); jointCovariance() adds an upfront bounds check naming the offending spec when data_index exceeds the number of supplied data frames.
• pated() emits a warning when the residual variance goes negative — typically a sign that a prognostic variable is collinear with the primary outcome or with another prognostic.

Bug fixes

• KMAdapter$fit_model() no longer strips the names off self$estimate, so id_map entries for KM models now carry the time_(strata)_(time) labels that pated()’s arm lookup relies on.
• parseTreatmentVariableFromCall() now walks the formula AST instead of regex-parsing the deparsed call, so formulas with nested parentheses (e.g., y ~ arm + us(visit | pid) for mmrm_) parse correctly.
• fitKMCurve() uses survival::summary(..., extend = TRUE) consistently, preventing NAs from leaking into the bootstrap covariance matrix when a resample’s stratum has no observations past a requested time.
• pated() no longer relies on is.null(family), which silently bound stats::family (a function) after the family argument was removed.

Documentation, testing, and tooling

• New testthat suite (52 tests / 245 expectations) covering every engine through both jointCovariance() and pated(). Tests are split into a fast tier (~4 s) and a Monte Carlo tier (~25 s, opt-in via MULTIPLEOUTCOMES_RUN_MC=1) that validates empirical vs. theoretical covariance for single-engine, cross-engine, partial-overlap, and kitchen-sink configurations.
• Regression fixture for the README example pinned to 1e-10 (file inst/testdata/readme_pated_reference.rds).
• GitHub Actions workflows for code coverage (codecov) and pkgdown.
• README example, vignette, and help-page examples migrated to the new spec-constructor API.

multipleOutcomes 0.15

• Initial support for Kaplan-Meier in the new spec-constructor interface via km_().
• pated() extended to handle KM time-stratum parameter vectors, including transformed-S(t) point estimates, pointwise confidence intervals, and KM-vs-PATED curve comparison plots.

multipleOutcomes 0.14 and earlier

• See git history.