NEWS

msma 4.0

Added opt-in supervised sparse soft-structured PCA through 'msma()' using 'structure.method', 'gammaX', 'history.method', and 'niterS4'.
Added hard-exclusive structured PCA with 'structure.method = "exclusive"'.
Added 's4pca_reconstruct()' for training-data and new-data reconstruction.
Added 's4pca_conformal_select()' for repeated split reconstruction-based selection of 'lambdaX', 'gammaX', and 'comp', with an optional overlap constraint and full-data refitting.
Added 'overlap_all', 'overlap_selected', convergence diagnostics, and stored preprocessing information to structured-PCA results.

Calls that do not request structured PCA retain the Version 3.2 dispatcher and computational paths.
The manuscript-generating S4PCA code is retained as a frozen numerical reference. The refactored engine is tested against it at tolerance 1e-12.
Unsupported combinations, including multiblock structured PCA, PLS, multi-column Z, and NMF-based super-level structured analysis, fail with explicit messages rather than silently changing interpretation.

Added input-validation, diagnostics, public-API, reconstruction, model-selection, reproducibility, and Version 3.2 regression tests.
Added a soft-structured PCA vignette and documentation for the two new public helper functions.
Corrected UTF-8 metadata handling during documentation generation.

Made reduced-dimension simulation fixtures safe for variable counts below the manuscript template size.
Avoided use of the reserved R keyword 'repeat' with '$' indexing.

Added sparse non-negative matrix factorization at the super level through sprmethod = "sNMF".
Z can now contain multiple supervision variables in separate columns.
Added con4spv to specify weights for combining multiple columns of Z.

Calls using only version 3.1 functionality are dispatched to the preserved version 3.1 computational engine.
The extended computational engine is used only when NMF, sNMF, multivariate Z, or con4spv is explicitly requested.

A one-column matrix supplied to Z is now normalized to a vector before the preserved version 3.1 engine is called. This makes Z = z and Z = cbind(z) produce identical numerical results and returned objects.

Renamed the internal legacy and extended computational engines so that they are not interpreted as unregistered S3 methods of the msma generic.
Added the internal '.s4pca_fit_reference()' candidate engine and the first regression suite against the frozen manuscript-generating implementation.
Added a validated internal S4PCA interface and diagnostic metadata while retaining the reference-compatible numerical engine unchanged.
Added strict validation for data, supervision, tuning, iteration, and seed inputs.
Fixed reduced-dimension S4PCA test fixtures and ensured the canonical UTF-8 DESCRIPTION is installed before roxygen2 documentation generation.

Added opt-in S4PCA through 'msma()' using 'structure.method', 'gammaX', 'history.method', and 'niterS4'.
Added public contract tests and a soft-structured PCA vignette.

Added 's4pca_reconstruct()' for training and new-data reconstruction.
Added 's4pca_conformal_select()' for repeated split reconstruction-based selection of 'lambdaX', 'gammaX', and 'comp', with an overlap constraint.
Updated the Version 3.2 versus Version 4.0 compatibility validation document.
Fixed parsing of the repeated-split identifier by using bracket indexing for the reserved R keyword 'repeat'.

Added reproducible scripts for the independent Version 3.2 compatibility audit, the 'mand' reverse-dependency check, and release-manifest generation.
Reload the newly installed namespace after the build so interactive post-build tests see the current Version 4.0 exports generated by roxygen2.
Removed a redundant source-tree NAMESPACE inspection test. Export status is already verified against the installed namespace, avoiding a context-only skip when tests are run from the development tree.
Fixed the Milestone 6 compatibility runner to use absolute input, reference, source, and output paths when rendering from the validation directory.
Corrected the 'mand' reverse-dependency audit to install msma 4.0 into a genuinely isolated library and to separate compatibility checks from CRAN incoming same-version warnings.
Made the 'mand.Rcheck' log discovery robust to the Windows R front end, which may create the check directory in the development root even when the command is launched after changing to the reverse-dependency work directory.