NEWS.md

In s20x: Functions for University of Auckland Course STATS 201/208 Data Analysis

s20x development news

Purpose

s20x 3.3.0

• Prepared s20x 3.3.0 as a CRAN-facing release after optional plotting engine polish and the tslm() calling-environment compatibility fix.
• Removed obsolete deprecated diagnostics methods that triggered roxygen warnings during documentation regeneration.
• Updated diagnostic API tests so modcheck.lm removal is treated as deliberate while modelcheck remains the supported model diagnostic helper.
• Removed stale roxygen argument tags for deleted diagnostics methods so regenerated Rd usage sections pass CRAN checks.
• Replaced non-standard DESCRIPTION contributor roles with CRAN-standard ctb roles.
• Rendered casestudy() files in a fresh environment with globalenv() as the parent instead of passing .GlobalEnv directly.
• Validated with strict tests, local as-CRAN checks, and external CRAN preflight submissions.

s20x 3.2.325

• Added regression tests comparing tslm() calling-environment fits with explicit data-frame fits.
• Covered both ordinary lm-backed fits and AR gls-backed fits using the existing beer.df and airpass.df teaching datasets.
• Preserved the Stage 21.1 tslm() implementation while locking in the new data-optional behaviour before CRAN submission.
• Kept tests offline, deterministic, and focused on user-visible teaching workflows.
• Validated by the standard s20x stage workflow.

s20x 3.2.323

• Updated tslm() so formulas can be evaluated from the calling environment when data is omitted, matching the familiar lm() and glm() workflow.
• Preserved explicit data-frame use for tslm() while using model-frame-based data handling for safer internal evaluation.
• Added deterministic tests covering omitted data and explicit data for ordinary tslm() fits.
• Kept the change small and backward compatible for the Stage 21.1 CRAN-preparation workflow.
• Validated by the standard s20x stage workflow.

s20x 3.2.320

• Added final release-polish wording for optional plotting engines, with base graphics remaining the default.
• Confirmed Stage 20.1 is limited to dependency-safety and release-note polish rather than new plotting functionality.
• Preserved compatibility by treating ggplot2 and GGally as optional engines rather than required plotting dependencies.
• Used the stage workflow's validation-mode detection so only changed files trigger package checks.

s20x 3.2.319

• Added final release-polish wording for optional plotting engines, with base graphics remaining the default.
• Confirmed Stage 20.1 is limited to dependency-safety and release-note polish rather than new plotting functionality.
• Preserved compatibility by treating ggplot2 and GGally as optional engines rather than required plotting dependencies.
• Used the stage workflow's validation-mode detection so only changed files trigger package checks.

s20x 3.2.318

• Adjusted pairs20x() ggplot2 diagonal histogram panels so the y-limits reserve base-like headroom for variable labels.
• Moved diagonal labels above the histogram bars rather than inside the plotted counts.
• Added a regression test for the ggplot2 histogram panel y-limit contract.
• Preserved the base graphics engine as the default and kept ggplot2/GGally optional.
• Validated by the standard s20x stage workflow.

s20x 3.2.317

• Added the missing ggplot2 geom_segment() import used by the base-like modelcheck() Cook's distance panel.
• Set the returned pairs20x() GGally matrix axisLabels field to document the outside-axis contract used by the optional ggplot2 engine.
• Preserved the Stage 19.7 pairs20x() visual-parity changes and the base graphics default.
• Validated by the standard s20x stage workflow.

s20x 3.2.315

• Added the missing ggplot2 geom_text import used by the modelcheck() Cook's distance labels.
• Kept the Stage 19.6.3 base-like ggplot2 modelcheck layout and Cook's distance display unchanged.
• Preserved the base graphics engine as the default and kept ggplot2 optional.
• Validated by the standard s20x stage workflow.

s20x 3.2.313

• Changed the optional eovcheck() ggplot2 smoother example to use the peru.fit regression model rather than the oyster one-way ANOVA-style fit.
• Kept the oyster example for the ggplot2 object-return and Levene/two-standard-deviation demonstrations where it remains appropriate.
• Avoided loess singularity warnings in the documented smoother example while preserving package behaviour.
• Validated by the standard s20x stage workflow.

s20x 3.2.312

• Added an explicit loess formula to the optional modelcheck() ggplot2 smoother so printing the diagnostic plot object is silent.
• Preserved the Stage 19.6 base-like ggplot2 diagnostic styling and Cook's distance vertical-line display.
• Kept the base graphics engine as the default and preserved the optional ggplot2 object-return paths.
• Validated by the standard s20x stage workflow.

s20x 3.2.310

• Polished the optional ggplot2 eovcheck output so the two-standard-deviation reference lines remain visible.
• Included the plus/minus two-standard-deviation limits in the plotted y-range and matched the base plot line weight more closely.
• Removed the default grey ggplot2 panel styling from the optional eovcheck engine to keep the teaching plot closer to base graphics.
• Kept the base graphics engine as the default and preserved the optional ggplot2 object-return path.
• Validated by the standard s20x stage workflow.

s20x 3.2.309

• Extended the optional normcheck() ggplot2 histogram density curve across the full displayed x-axis range.
• Kept the histogram as a native ggplot2 geom_histogram() layer while replacing stat_function() with explicit density data.
• Preserved base graphics defaults and existing normcheck() return behaviour.
• Documented the Stage 19.5 normcheck density-curve polish notes.
• Validated by the standard s20x stage workflow.

s20x 3.2.308

• Polished the optional ggplot2/GGally engine for pairs20x() while preserving base graphics as the default.
• Renamed internal pairs20x ggplot2 helpers to use clearer *_ggplot2 names.
• Kept the existing ggplot2/GGally example and return-class tests for the optional plot matrix path.
• Documented the Stage 19.4 pairs20x plotting-engine review notes.
• Validated by the standard s20x stage workflow.

s20x 3.2.307

• Polished the optional ggplot2 engine for modelcheck() while preserving base graphics as the default.
• Renamed internal modelcheck ggplot2 helpers and list classes to use clearer *_ggplot2 names.
• Reworked ggplot2 aesthetic mappings to use data-column pronouns and avoid external-vector warnings.
• Added a print method for multiple ggplot2 modelcheck plots and ggplot2-engine examples for individual diagnostics.
• Added offline regression tests for the renamed class and clean plot printing.
• Validated by the standard s20x stage workflow.

s20x 3.2.306

• Polished the optional ggplot2 engine for eovcheck() while preserving base graphics as the default.
• Renamed internal eovcheck ggplot2 helpers to use clearer *_ggplot2 names.
• Reworked ggplot2 aesthetic mappings to use data-column pronouns and avoid external-vector warnings.
• Added ggplot2-engine examples and an offline regression test for clean plot printing.
• Validated by the standard s20x stage workflow.

s20x 3.2.305

• Restored the documented s20xNormcheckGgplot2 return class while retaining the clearer internal s20xNormcheck_ggplot2 class alias.
• Preserved the Stage 19.1 ggplot2 normcheck plotting fixes, examples, and naming cleanup.
• Fixed compatibility with existing diagnostic plotting tests after the internal class-name cleanup.
• Preserved base graphics as the default plotting engine and kept ggplot2 optional.
• Validated by the standard s20x stage workflow.

s20x 3.2.303

• Added regression tests that scan controlled R and test files for namespace operators in executable code.
• Added regression tests that scan controlled R and test files for dynamic namespace lookup helpers.
• Reworked the internal-test helper to avoid getFromNamespace() while preserving access to unexported helpers during tests.
• Preserved the Stage 18.6 import-based plotting cleanup and base graphics defaults.
• Validated by the standard s20x stage workflow.

s20x 3.2.302

• Replaced dynamic ggplot2 and GGally plotting function lookups with direct calls backed by roxygen import declarations.
• Moved ggplot2 and GGally into Imports so their functions can be declared through NAMESPACE.
• Removed namespace operator usage from controlled package and test code by using imported functions and a shared internal-test helper.
• Preserved base graphics as the default plotting engine.
• Validated by the standard s20x stage workflow.

s20x 3.2.301

• Refactored normcheck ggplot2 Q-Q and histogram builders to use grouped optional plotting function lookups.
• Refactored the eovcheck ggplot2 diagnostic builder to use grouped optional plotting function lookups.
• Preserved base graphics as the default engine and kept ggplot2 optional.
• Validated by the standard s20x stage workflow.

s20x 3.2.300

• Added a grouped optional plotting function lookup helper for ggplot2 implementations.
• Refactored modelcheck ggplot2 residual and Cook distance builders to use grouped helper lookups.
• Preserved base graphics as the default engine and kept ggplot2 optional.
• Validated by the standard s20x stage workflow.

s20x 3.2.299

• Centralised optional plotting function lookup behind the internal getPlottingFunction() helper.
• Replaced repeated direct getExportedValue() calls in the ggplot2 and GGally plotting implementations.
• Preserved base graphics as the default engine and kept ggplot2/GGally optional.
• Validated by the standard s20x stage workflow.

s20x 3.2.298

• Added matchPlottingEngine() as a shared internal helper for plotting engine argument matching.
• Replaced repeated match.arg(engine) calls in normcheck(), eovcheck(), modelcheck(), and pairs20x().
• Added a Stage 18.2 plotting engine dispatch note for the cleanup and deferred candidates.
• Ignored the local .s20x_validation_mode file so R CMD check tarballs do not include validation state.
• Preserved base graphics defaults, optional ggplot2/GGally behavior, and teaching-oriented plotting output.

This file records user-facing and developer-facing changes for s20x. It is a release-note summary, not a commit-by-commit history.

s20x 3.2.297

• Added a shared internal helper for optional plotting package availability checks.
• Replaced duplicated ggplot2 and GGally engine checks in normcheck(), eovcheck(), modelcheck(), and pairs20x().
• Added a Stage 18.1 plotting audit note to record remaining cleanup candidates.
• Preserved base graphics defaults, optional ggplot2/GGally behavior, and teaching-oriented plotting output.

s20x 3.2.295

Modernisation

• Completed a final consistency pass over README and package-level plotting-engine documentation.
• Clarified optional ggplot2 and GGally requirements for diagnostic plotting helpers.
• Ignored stage-runner validation scratch files in package builds so strict checks do not report them as hidden-file notes.
• No plotting behaviour or public API changed.

s20x 3.2.294

Modernisation

• Clarified README guidance for choosing between base and ggplot2 diagnostic plotting engines.
• Added package-level documentation describing stable teaching defaults and optional plotting engines.
• No plotting behaviour or public API changed.

s20x 3.2.293

Modernisation

• Added a README-level explanation of the optional diagnostic plotting engines while preserving base graphics as the default teaching workflow.
• Added a Stage 17.4 developer note recording the documentation-only scope and optional-dependency guard pattern.
• No plotting behaviour or public API changed.

s20x 3.2.288

Development notes

• Archived the Stage 16 plotting modernisation developer note under Completed.
• Recorded that pairs20x(), normcheck(), eovcheck(), and modelcheck() now have optional ggplot2 engines with base graphics preserved as the default.
• Kept this as a documentation wrap-up stage with no intended plotting behavior changes.

s20x 3.2.287

Modernisation

• Refined the optional ggplot2/GGally panels in pairs20x() with a base-like white theme.
• Preserved the original base graphics output as the default teaching path.
• Kept GGally and ggplot2 as optional dependencies for the modern plotting engine.

s20x 3.2.286

Modernisation

• Added an optional ggplot2 engine to modelcheck() while preserving the original base graphics output as the default.
• Returned a ggplot object for the optional residual-versus-fitted model checking diagnostic when ggplot2 is installed.

s20x 3.2.285

Modernisation

• Added an optional ggplot2 engine to eovcheck() while preserving the original base graphics output as the default.
• Returned a ggplot object for the optional residual-versus-fitted equality-of-variance diagnostic when ggplot2 is installed.

s20x 3.2.280

Modernisation

• Added an optional ggplot2 engine to normcheck() while preserving the original base graphics output as the default.
• Returned ggplot objects for optional normal Q-Q and residual histogram diagnostics when ggplot2 is installed.

s20x 3.2.278

Modernisation

• Added an optional ggplot2/GGally engine to pairs20x() while preserving the original base graphics output as the default.

s20x 3.2.276

Data

• Store nzarrivals.df$month as a factor with levels ordered by month.abb and update the dataset documentation accordingly.

s20x 3.2.274

Data

• Add nzarrivals.df, a monthly Stats NZ Infoshare arrivals data set, and fix the Stage 14 colors() import so note-level checks remain strict.

s20x 3.2.273

• Document remaining Stage 14 internal helper functions with roxygen2 comments.

s20x 3.2.272

• Document internal prediction helper functions with roxygen2 comments.

s20x 3.2.271

Modernisation

• Removed qualified namespace calls from R source files by adding roxygen imports, broadened internal helper documentation, and hardened the Stage 14 style-compliance regression test.

s20x 3.2.270

Modernisation

• Consolidated residual and fitted-value extraction for targeted diagnostic plotting internals without changing plotting output or public APIs.

s20x 3.2.269

Modernisation

• Added a small internal graphics-parameter save/restore helper and used it in targeted diagnostic plotting code paths without changing plotting output.

s20x 3.2.268

Modernisation

• Deprecated legacy diagnostic plotting helpers modelcheck(), modcheck(), boxqq(), stripqq(), and the autocor.plot() alias, and removed them from the exported API while keeping their internal compatibility definitions.

s20x 3.2.267

Modernisation

• Added prediction-wrapper regression coverage for multi-row return shapes, binomial-logit predictGLM() output, and wrapper-level quasi interval multiplier behaviour without changing prediction internals.

s20x 3.2.264

Modernisation

• Standardised predictGLM() return shape to a data frame with stable fit, lwr, and upr columns, while preserving link/response scale calculations and legacy fallback to link-scale output for unsupported type values.

s20x 3.2.263

Modernisation

• Consolidated internal prediction interval output formatting for linear-model and GLM teaching wrappers while preserving legacy return shapes, column names, rounding, and scale handling.

s20x 3.2.262

Modernisation

• Consolidated prediction-wrapper newdata data-frame validation into a shared internal helper and removed duplicated validation from predictGLM() without changing prediction output or error text.

s20x 3.2.261

Modernisation

• Added the Stage 13 prediction-wrapper internal audit note, identifying narrow maintenance targets for prediction internals while deferring public API and behaviour changes.

s20x 3.2.260

Modernisation

• Finalised the Stage 12 documentation-coherence developer note, summarising completed documentation improvements and deferring deeper API or behavioural refactors to later stages.

s20x 3.2.259

Modernisation

• Audited exported help examples for strict-check suitability, confirmed remaining synthetic examples are deterministic or guarded, and tightened freq1way() documentation wording without changing behaviour.

s20x 3.2.258

Modernisation

• Standardised diagnostic help wording for model checking, residuals versus fitted values, Q-Q plots, and plotting side effects without changing package behaviour.

s20x 3.2.257

Modernisation

• Guarded the displayPairs() help example so it only runs the optional emmeans workflow when emmeans is available, keeping examples suitable for strict checks without changing package behaviour.

s20x 3.2.256

Modernisation

• Clarified prediction helper and AR-error model documentation so teaching wrappers are distinguished from ordinary predict() and independent-error ANOVA behaviour without changing package behaviour.

s20x 3.2.255

Modernisation

• Replaced the artificial summary1way() help example with computer.df, made the summaryStats() matrix example dataset-based, and tightened summary-helper documentation wording without changing behaviour.

s20x 3.2.254

Modernisation

• Applied a strict NZ English and grammar documentation pass and accepted "normalised" as a package-owned alias for "normalized" residual diagnostics while preserving compatibility.

s20x 3.2.253

Modernisation

• Made diagnostic helper examples deterministic or dataset-based and corrected small documentation spelling and grammar issues without changing diagnostic behaviour.

s20x 3.2.252

Modernisation

• Replaced the interactionPlots() help examples with the arousal.df teaching dataset and clarified the deprecated vector-form example wording without changing plotting behaviour.

s20x 3.2.251

Modernisation

• Added a Stage 12 documentation audit covering help examples, teaching datasets, time-series examples, R CMD check suitability, and NZ English spelling and grammar notes without changing package behaviour.

s20x 3.2.250

Modernisation

• Added a Stage 11 completion plan summarising completed API-consistency work and deferring larger documentation and internal refactor items to later stages.

s20x 3.2.249

Modernisation

• Documented diagnostic plotting helper return conventions and added regression tests for current validation behaviour without changing plotting behaviour.

s20x 3.2.248

Modernisation

• Documented and tested crosstabs() and rowdistr() printed-output and invisible-return conventions without changing behaviour.

s20x 3.2.247

Modernisation

• Documented and tested summary2way() printed-output and invisible-return conventions without changing behaviour.

s20x 3.2.246

Modernisation

• Documented and tested summary1way() printed-output and invisible-return conventions without changing behaviour.

s20x 3.2.245

Modernisation

• Documented and tested summaryStats() printed-output and invisible-return conventions without changing behaviour.

s20x 3.2.244

Modernisation

• Added a Stage 11 return-convention modernisation plan to guide future low-risk API updates without changing public behaviour.

s20x 3.2.243

Modernisation

• Added a Stage 11 audit of printed-output and invisible-return conventions without changing public behaviour.

s20x 3.2.242

Modernisation

• Standardised legacy-helper documentation wording without changing public behaviour.

s20x 3.2.241

Modernisation

• Added regression tests documenting current prediction interval semantics before further API changes.

s20x 3.2.240

Modernisation

• Consolidated shared confidence-interval arithmetic for prediction teaching wrappers without changing public prediction behaviour.

Modernisation

• Extracted shared internal prediction helpers for linear-model and GLM teaching wrappers without changing public prediction behaviour.

Modernisation

• Added a deeper Stage 11 legacy API audit focused on outdated teaching wrappers, deprecation candidates, and future modernisation priorities.

Modernisation

• Added a camelCase outputDir alias for rendered case-study helpers while preserving output_dir compatibility.
• Clarified prediction helper documentation so their teaching-wrapper roles and return values are explicit.
• Added a Stage 11 API consistency audit for prediction helpers before changing public interfaces.
• Completed the Stage 10 style-normalisation sweep for remaining legacy helpers without changing public interfaces.
• Normalised style in Cook's distance plotting helpers without changing their public interface.
• Normalised style in count prediction helpers without changing their public interface.
• Normalised style in row distribution helpers without changing their public interface.
• Normalised style in residual diagnostic plotting helpers without changing their public interface.
• Normalised style in autocorrelation plotting helpers without changing their public interface.
• Normalised style in trend scatter plotting helpers without changing their public interface.
• Normalised style in two-way ANOVA summary helpers without changing their public interface.
• Normalised style in summary statistics helpers without changing their public interface.
• Normalised style in the deprecated one-way frequency table helper without changing its public interface.
• Normalised style in the one-way ANOVA summary helper without changing its public interface.
• Normalised style in package version and skewness utility helpers without changing their public interface.
• Normalised style in regression confidence interval helpers without changing their public interface.
• Normalised style in generalised linear model prediction helpers without changing their public interface.
• Normalised style in one-way comparison helper functions without changing their public interface.
• Normalised style in case study helper functions without changing their public interface.
• Normalised style in deprecated grouped QQ plotting helpers.
• Normalised style in small utility files as part of the staged modernisation work.
• Added package infrastructure for automated R CMD check runs.
• Updated package build ignores for repository-only infrastructure files.

s20x 3.2.296

• Clarified README guidance for ggplot2 diagnostic return values.
• Added tests that pin named-list return contracts for multi-plot ggplot2 diagnostics.
• Confirmed single selected diagnostics still return individual ggplot objects where appropriate.
• Preserved base graphics as the default plotting engine.

s20x 3.2.292

• Removed no-op examplesIf blocks from deprecated, unexported legacy helper documentation.
• Clarified the deprecated boxqq(), stripqq(), and modcheck() descriptions without restoring exported examples.
• Preserved legacy helper behavior while reducing CRAN-facing example clutter in generated Rd files.
• Regenerated documentation should be produced by devtools::document() during the stage runner.

s20x 3.2.291

• Refreshed legacy helper documentation so deprecated, unexported functions no longer show direct internal-call examples.
• Replaced older case-study dontrun examples with interactive examples for CRAN-facing documentation hygiene.
• Preserved case-study and deprecated-helper behavior while making the examples clearer for current teaching material.
• Regenerated documentation should be produced by devtools::document() during the stage runner.

s20x 3.2.290

• Clarified that the default base plotting engine preserves direct teaching graphics while optional ggplot2 engines return reusable plot objects.
• Added guarded examples for optional ggplot2 and GGally plotting engines in normcheck(), eovcheck(), modelcheck(), and pairs20x().
• Kept ggplot2 and GGally usage behind requireNamespace() guards so examples remain compatible when optional packages are unavailable.
• Regenerated documentation should be produced by devtools::document() during the stage runner.

s20x documentation built on July 1, 2026, 9:06 a.m.