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- Add bcanon() function and documentation (nonparametric BCa) - Bump version 0.2-3 -> 0.3 - Modernize package doc to use _PACKAGE sentinel - Update RoxygenNote to 7.3.2 - Fix .Rbuildignore and .gitignore patterns - Add CLAUDE.md with cleanup notes
- Add mathematical annotations with citations (Efron 1987, DiCiccio-Efron 1992, Efron-Narasimhan 2020) - Unify return value structure: standardized lims columns (bca/jacksd/std/pct), stats columns (theta/sdboot/z0/a), always include call+seed - Fix bcajack2(B=Blist) bug where m=nrow(x) evaluated eagerly - Fix bcapar lims column ordering to match bcajack/bcajack2 - Eliminate dollar-sign partial matching in bcapar accessing bca() returns - Rename cryptic variables: t.->jack_infl, ty.->reg_infl, ooo->bca_idx, vl->result, etc. - Delete dead code: o1, Limsd, I=diag(p) - Extract shared helpers: compute_bca_limits(), compute_kl_distance() in bca_core.R - Modernize bcanon: replace rou/catj/sw with verbose/txtProgressBar, remove internal rounding - Fix bcaplot: replace magic numbers with name-based row/column detection, remove partial matching - Add m>n guard (else stop) in bcajack, bcajack2, bcanon - Add singular covariance guard in abcpar - Add mr unused-parameter warning in bcajack2 - R idiom sweep: seq_len/seq_along, numeric(), scale(center=TRUE,scale=FALSE) - Add tinytest regression tests with baseline fixtures - R CMD check --as-cran passes with Status: OK
Factor out duplicated code from bcajack, bcajack2, bcanon, bcapar: - expand_alpha: alpha expansion pattern (was in all 4 functions) - bootstrap_resample: bootstrap loop + count matrix (bcajack2/bcanon) - jackknife_accel: classical delete-one/group jackknife (bcajack) - regression_accel: KL-regression acceleration (bcajack2/bcanon qbca2) - compute_ustats: bias-corrected estimator (bcajack/bcajack2) All 14 regression tests pass with identical results.
- new_bcaboot(): canonical constructor with consistent structure (limits, stats, B_mean, ustats, method, accel, plus optional diagnostic/abc/conf_density/accel_matrix/sese) - print.bcaboot(): formatted summary with confidence limits table and diagnostics instead of raw list dump - Handles both old-style ($lims) and new-style ($limits) objects for smooth transition during rewrite
- bca_nonpar(): consolidated nonparametric BCa replacing bcajack/bcajack2/bcanon - accel="regression"|"jackknife" for acceleration method - conf.level instead of alpha (broom convention) - Descriptive parameter names (n_groups, kl_fraction, n_jack, etc.) - gbca diagnostic always computed for regression method - boot_data parameter instead of overloading B - bca_par(): parametric BCa replacing bcapar - Same conf.level/parameter naming conventions - Remaps internal bca() return to canonical structure - deprecated.R: lifecycle-based wrappers for bcajack, bcajack2, bcapar, bcaplot - Translate old parameter names to new API - Once-per-session deprecation warnings - Removed: R/bcajack.R, R/bcajack2.R, R/bcanon.R, R/bcapar.R, R/bcaplot.R (logic migrated to new files + bca_core.R helpers) - All new functions return canonical bcaboot objects via new_bcaboot() with consistent $limits (9x4), $stats (2x5), $B_mean, $ustats
- tidy.bcaboot(): returns tibble with one row per (conf.level, method) following broom conventions (conf.level, method, estimate, conf.low, conf.high, jacksd.low, jacksd.high) - glance.bcaboot(): returns one-row tibble with method, accel, theta, sdboot, z0, a, sdjack, B, boot_mean - autoplot.bcaboot(): ggplot2 visualization using tidy() output - Colored vertical segments for BCa intervals per coverage level - Grey dashed segments for standard intervals (offset to avoid overlap) - Red error bars for jackknife internal SE - Theta reference line with annotation - ggplot2 in Suggests: conditional s3_register in .onLoad (R/zzz.R)
- Bump version to 0.4.0 - Add tibble, generics, lifecycle to Imports - Add ggplot2 to Suggests - Export bca_nonpar, bca_par, tidy, glance - Keep deprecated exports (bcajack, bcajack2, bcapar, bcaplot) Tests: 34 (up from 14) - Adapter tests proving numerical equivalence against old fixtures for all 4 original functions via the new API - Structure tests: canonical return format (9x4 limits, 2x5 stats) - tidy/glance output shape and column name tests - autoplot returns ggplot object test Fix: element_blank() -> ggplot2::element_blank() in autoplot
- NEWS.md: documents all breaking changes, deprecations, new features
- Vignette rewritten to use bca_nonpar/bca_par throughout
- Demonstrates tidy(), glance(), autoplot() workflow
- New "Migration from pre-1.0 API" section with function/parameter
mapping tables and deprecation timeline
- Version bumped to 1.0 (lifecycle deprecation messages updated)
- README.Rmd/README.md: updated with logo, new API examples (bca_nonpar, tidy, autoplot), installation instructions - Logo appears in pkgdown navbar and og:image metadata - Regenerated full pkgdown site
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Tidy version