News - bpca R package

1.5-0 (2026-05-25) - Faria, J. C.

Breaking changes

• var.rdf() now returns a structured list of class 'var.rdf' instead of a plain character data.frame. The three fields are: $display (character data.frame with '*', '', and '-' entries, for tabular display), $numeric (numeric matrix of absolute percentage differences), and $flagged (logical matrix, TRUE where the discrepancy exceeds limit). Code that accessed bp$var.rd as a data.frame directly must be updated to use bp$var.rd$display.
• summary.bpca() no longer accepts the presentation argument. The printing behaviour previously triggered by presentation = TRUE is now handled by the new print.summary.bpca() S3 method; calling print(summary(bp)) produces the same output.

New S3 methods

• print.var.rdf(): printing a var.rdf object (e.g. print(bp$var.rd)) automatically displays the character table ($display).
• print.summary.bpca(): separates computation from presentation following R’s S3 convention. summary.bpca() now only computes and returns the summary object; print.summary.bpca() handles console output.

Internal refactoring (no public API change)

• New file R/bpca-utils.R introduces four shared internal helpers that eliminate duplicated code across the package:
  • .center_scale(x, center, scale): centering and scaling logic previously duplicated between bpca.default() and dt.tools().
  • .cosine_matrix(m): pairwise cosine similarity between rows of a matrix, previously duplicated between var.rbf() and dt.tools().
  • .compute_var_factor(coobj, covar): automatic variable-scaling factor for biplots, previously duplicated between plot.bpca.2d() and plot.bpca.3d().
  • .pc_axis_labels(eigenvalues, dims): axis labels in "PC1 (38.5%)" format, previously duplicated between plot.bpca.2d() and plot.bpca.3d().
• plot.bpca.2d() decomposed from a single 634-line function into three files:
  • R/plot.bpca.2d.helpers.R: eight internal drawing functions (.draw_obj(), .draw_var(), .draw_var_seg(), .draw_circles(), .draw_axis_cross(), .proj_on_direction(), .solve_orthogonal_intersection(), .draw_circles_at()), extracted from closures that were recreated on every call.
  • R/plot.bpca.2d.types.R: ten internal type functions (.plot_type_bp() through .plot_type_rv()), one per switch branch, each independently readable and testable.
  • R/plot.bpca.2d.R: reduced to ~160 lines — validation, state preparation, context list (ctx) construction, and dispatch via switch().
• pc.names in bpca.default() is now generated once and reused for svdx.scal$v, g.scal, and hl.scal column names (previously generated twice).
• The fragile while loop in plot.bpca.2d(type = 'ww') — which relied on an NA sentinel at the end of chull() output — was replaced by a for loop with circular indexing over all convex-hull edges, including the closing edge.

Testing

• Test suite expanded from 3 to 45 tests. New coverage includes: all four factorization methods (hj, sqrt, jk, gh); all four centering modes (center = 0:3); all four internal helpers (.center_scale, .cosine_matrix, .compute_var_factor, .pc_axis_labels); var.rbf and var.rdf (including the new list structure); dt.tools; qbpca; summary.bpca and print.summary.bpca; all ten 2D plot types; 3D static plot; plot.qbpca; and bpca.prcomp.

1.4-3 (2026-05-11) - Faria, J. C.

Changes

• Cleaned core functions to improve readability for AI-assisted analysis.
• Manual improvements were made to some parts of the code that were refactored by AI.
• Refactored core computational functions for safer input handling and improved edge-case behavior (bpca.default, bpca.prcomp, dt.tools, qbpca, var.rbf, var.rdf).
• Refactored plotting internals (plot.bpca.2d, plot.bpca.3d, plot.qbpca) to reduce duplication and improve readability while preserving public API.
• Improved summary and table method internals (summary.bpca, xtable.bpca, print.xtable.bpca) and fixed minor string-handling issues.
• Enhanced 2D and 3D biplot diagnostics for improved visual clarity.
• Improved HTML table defaults in print.xtable.bpca for type = "html" while keeping LaTeX behavior unchanged.

Documentation

• Updated demo scripts across demo/ (2D/3D, static/dynamic, and utilities) to align examples with the refactored plotting code.
• Updated man/plot.Rd and man/qbpca.Rd to reflect the latest plotting behavior and usage.
• Expanded vignettes/bpca-overview.Rmd and added vignettes/latex-bpca.Rnw to support the updated guidance and examples.
• Documented print(x, type = "html") in man/print.xtable.Rd, the HTML overview vignette section, and README.md (use print() for S3 dispatch; results = 'asis' in R Markdown for HTML tables).
• Refined the qbpca plotting workflow to improve internal organization and keep graphical outputs consistent.
• print.xtable.bpca now supports type = "html" (via print(x, type = "html", ...)) for HTML table output, including column labels with eigenvalues; LaTeX layout is unchanged for the default type = "latex".
• Standardized and modernized package documentation across man/*.Rd.
• Updated package metadata files (DESCRIPTION, NAMESPACE, INDEX) for consistency with the current repository and dependency layout.
• Migrated the legacy NEWS file to NEWS.md for improved rendering on GitHub and pkgdown.
• Refactored vignettes/latex-bpca.Rnw for clearer didactic flow, improved visual layout, and updated examples.
• Updated vignettes/latex-bpca.pdf with the new vignette formatting.
• Simplified the HTML example in vignettes/bpca-overview.Rmd to use print(tbl, type = "html") directly.
• Regenerated vignettes/bpca-overview.html with the updated HTML table rendering.
• Removed prebuilt vignette artifacts from inst/doc/ to keep the repository clean.

Testing

• Added a new testthat suite under tests/testthat/ covering core bpca workflows, summary/plot smoke checks, and xtable output behavior for HTML and LaTeX.
• Updated package metadata to enable automated tests (Suggests: testthat (>= 3.0.0) and Config/testthat/edition: 3 in DESCRIPTION).

1.3-10 (2026-04-25) - Faria, J. C.

• Added support for vectorized var.pos in 2D and 3D plots, enabling precise manual label placement to reduce overlap.
• Fixed misaligned variable-to-object projections in plot.bpca.2d (type = "eo") by rewriting projection logic to properly account for scaling.

1.3-9 (2026-04-21) - Faria, J. C.

• Optimized plot.bpca.3d rendering performance when using rgl.
• Fixed an issue in plot.bpca.3d that prevented variable vectors from using distinct colors.
• Improved framing behavior in plot.bpca.2d and plot.bpca.3d, reducing the need for manual adjustments with var.factor, xlim, ylim, and zlim.
• Improved package and function documentation.

1.3-8 (2025-10-15) - Faria, J. C.

• Improved package and function documentation.

1.3-7 (2023-11-23) - Faria, J. C.

• Improved package and function documentation.

1.3-6 (2023-11-20) - Faria, J. C.

• Removed documentation notes as required by CRAN.

1.3-5 (2023-11-18) - Faria, J. C.

• Adjusted file encoding as required by CRAN.
• Performed substantial updates and improvements across package and function documentation.

1.3-4 (2021-03-23) - Faria, J. C.

• Completely redid the vignette to make it simpler, more direct, and more instructive.

1.3-3 (2021-03-19) - Allaman, I. B.

• Corrected a class-related bug in xtable.bpca.
• Fixed a bug in print.xtable.bpca; updated related commands and aux_com1 handling so sanitize.rownames.function works properly.

1.3-2 (2020-04-01) - Allaman, I. B.

• Created xtable.bpca and print.xtable.bpca.
• Deprecated and removed latex.bpca, print.latex.bpca, and summary.latex.bpca; corresponding .Rd files were removed.
• Updated NAMESPACE and DESCRIPTION accordingly.

1.3-1 (2018-06-16) - Allaman, I. B.

• Updated latex.bpca: changed footenotes default from "" to NULL.

1.3-0 (2018-06-07) - Allaman, I. B.

• Added stats, graphics, and grDevices imports in NAMESPACE to align with CRAN requirements.

1.2-2 (2013-11-23) - Faria, J. C.

• Added LaTeX table export for reduction summaries (latex.bpca).
• Improved parts of the source code.
• Added dataset marina.rda.
• Improved documentation.
• Removed unnecessary require calls for packages already attached via Depends (rgl and scatterplot3d).
• Released to CRAN.

1.2-1 (2012-12-12) - Faria, J. C.

• Added Ivan Bezerra Allaman as co-author in the project workflow.
• Added new plot options.
• Added new center options.
• Added new scale options.
• Added new summary options.
• Restricted release to testers.

1.2-0 (2012-10-06) - Faria, J. C.

• Improved parts of the source code.
• Removed var.position from the package; when needed, users can swap variable/object positions with bpca(t(dad)).
• Restricted release to testers.

1.0-10 (2012-02-20) - Faria, J. C.

• Applied cosmetic updates to plot.bpca.3d.

1.0-9 (2011-08-22) - Faria, J. C.

• Applied cosmetic updates to summary.

1.0-8 (2011-04-21) - Faria, J. C.

• Applied cosmetic updates to documentation.

1.0-7 (2011-04-20) - Faria, J. C.

• Improved summary method.
• Removed the comparison demo.

1.0-6 (2011-04-19) - Faria, J. C.

• Improved aliases for summary and plot methods in documentation.

1.0-5 (2011-04-09) - Faria, J. C.

• Fixed platform NOTE status in plot.bpca.3d (matrix(0, nc = 3) partial argument match of nc to ncol).

1.0-4 (2011-03-22) - Faria, J. C.

• Updated plot.bpca.2d and plot.bpca.3d to show, by default, the retained variation for each principal component on axis labels.
• Improved summary method.

1.0-3 (2009-06-10) - Faria, J. C.

• Updated plot.bpca.2d and plot.bpca.3d to accept xlim, ylim, zlim, xlab, ylab, and zlab.
• Reworked demos.
• Included PDF documentation in the package.

1.0-2 (2008-07-15) - Faria, J. C.

• Released to CRAN.
• Applied English corrections (by Clarice).
• Removed demo scripts using obj.identify = TRUE.

1.0-1 (2008-07-01) - Faria, J. C.

• First restricted release (testers only).