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exametrika v1.13.0

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@kosugitti kosugitti released this 17 May 07:54
· 113 commits to main since this release
v1.13.0
5fa6142

Highlights

This release rolls up the development changes from 1.12.0–1.12.2 (never published to CRAN) together with new 1.13.0 features.

New features (1.13.0)

  • Graphical Lasso (Glasso): Sparse precision matrix estimation from ordinal item response data. Uses polychoric correlations + block coordinate descent (Friedman, Hastie & Tibshirani 2008) with EBIC-based lambda selection (Foygel & Drton 2010) and warm-starting across the lambda grid.
  • Chatterjee's xi correlation: chatterjee_xi() (single-shot), xi_stable(B = 1000) (tie-stabilized via averaging), chatterjee_matrix() (p x p asymmetric pairwise matrix). The asymmetry between xi(j, k) and xi(k, j) is exploitable for direction detection in graphical-model construction.
  • print.exametrika Glasso method for tidy summaries (lambda, EBIC, edges, precision matrix).

Rolled-up changes from 1.12.0–1.12.2

  • C++ IRM Gibbs sampler (src/irm_gibbs_core.cpp): roughly 4x speedup on the inner Gibbs loop (J20S600 nominal 82 to 20 ms/iter; J35S500 ordinal 76 to 19 ms/iter). R reference implementation preserved behind use_cpp = FALSE. Bit-identical for the first iterations; diverges sub-LSB on real data but targets the same posterior (Wilcoxon p = 0.56 / 0.81 on 50 seeds).
  • Class-side Confirmatory Biclustering: new conf_class argument fixes class memberships during EM (companion to existing conf for fields). Available for binary / ordinal / nominal / rated.
  • Vectorized EM hot path in Biclustering.ordinal().
  • Bug fixes: confirmatory Biclustering across binary/ordinal/nominal (matrix-form conf was silently dropped; NCOL(U) validation was wrong; ordinal fldmemb was being overwritten); GRM() fit indices NaN for >= 8 items; GRM() degrees of freedom; GRM() non-1..K coded ordinal responses; GridSearch() per-cell error tolerance; Biclustering.ordinal() maxiter honoring; Biclustering EM stability for empty fields/classes; dataFormat(response.type = "rated") now warns instead of erroring when a CA category is unobserved.

Documentation and check cleanup

  • Roxygen Markdown bracket expressions (`[0, 1]`, `[j, k]`, `Q[i, j]`) backticked so they are not rewritten as \link{} cross-references.
  • Glasso() ... documented; determinant(..., logarithm = TRUE) to clear partial-match NOTE.

Test suite

  • 4,844 tests across 28 files, all passing.
  • R CMD check: 0 errors | 0 warnings | 0 notes (local --as-cran, win-devel, R-hub linux / macos-arm64 / windows).

See NEWS.md for the full changelog.

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