NEWS

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colleyRstats 0.1.0 (2026-06-11)

NEW FEATURES

• analyze_and_report(): one-call pipeline per dependent variable -- assumption checks with a ready-made methods sentence, the matching ggstatsplot figure (automatic parametric/non-parametric selection), the omnibus result, and post-hoc comparisons.
• report_all(): runs analyze_and_report() over many dependent variables (e.g., all questionnaire scales of a study), returns a summary table with Holm-adjusted omnibus p-values across the DVs, and a combined figure when patchwork is installed.
• latex_preamble(): prints (or writes to a file) the complete set of LaTeX \newcommand definitions required by the report functions -- no more hunting through individual help pages.
• All report functions accept sink_to to write their output to a .tex file, so manuscripts can \input{} the results and stay up to date when the analysis is re-run. They all also invisibly return their text for programmatic use (e.g., inline in Quarto/R Markdown).
• save_paper_figure(): saves plots with publication presets (ACM-style single-column 3.33 in / full-width 7 in, Cairo PDF with embedded fonts).
• assumption_methods_text(): turns the Shapiro-Wilk (and optionally Levene) checks into the methods-section justification sentence reviewers expect, including the test statistics. check_normality_by_group() and check_homogeneity_by_group() now attach their test statistics as attributes.
• cite_methods(): prints methods boilerplate plus the BibTeX entries for the packages behind the analyses (ART, Dunn, nparLD, ggstatsplot, effectsize).
• Consistent snake_case aliases with discoverable prefixes for the whole API (e.g., report_art(), report_dunn_test(), plot_between_stats(), check_assumptions_anova()). The original names remain fully supported.
• New option options(colleyRstats.leading_zero = FALSE) for APA-style p-values and effect sizes without the leading zero (e.g., p=.033).
• Significance brackets in the asterisk plot helpers are now stacked relative to the data range, so the layout works for any dependent-variable scale (1-7 Likert and 0-100 TLX alike).

BUG FIXES

• reportggstatsplot() now recognizes the unpaired non-parametric test ("Wilcoxon rank sum test", reported with its W statistic); previously such results fell through to a generic fallback format. The signed-rank (paired) variant keeps the V statistic. The p-value is also compared before rounding, so e.g. p = 0.0009 is reported as "p < 0.001" again.
• reportNPAV(), reportART(), and reportNparLD() with write_to_clipboard = TRUE now write all significant effects to the clipboard at once; previously each effect overwrote the previous one and only the last sentence survived. These functions now also invisibly return the reported sentences.
• The asterisk plot helpers (ggbetweenstatsWithPriorNormalityCheckAsterisk(), ggwithinstatsWithPriorNormalityCheckAsterisk()) no longer drop significant comparisons whose adjusted p-value is exactly 0.01 or 0.001.
• replace_values() no longer round-trips untouched numeric columns through as.character(), which silently truncated values to 15 significant digits.
• reportggstatsplotPostHoc() handles missing values in the dependent variable (na.rm = TRUE) and falls back to the raw level name when a label_mappings entry is missing instead of producing malformed text.
• reportNparLD() output now correctly says "nparLD analysis" instead of "NPAV", and the required \df LaTeX command is documented.
• reportDunnTestTable() and reportArtConTable(): orderByP = TRUE now takes precedence over the default alphabetical ordering instead of being silently undone by it.
• Partial eta squared in reportART()/reportNPAV() is now computed from the unrounded F statistic.
• rFromWilcoxAdjusted() caps the adjusted p-value at 1, avoiding NaN results.
• generateMoboPlot2() stops with a clear error when the phase column lacks "sampling"/"optimization" rows instead of producing -Inf positions.
• normalize() rejects a zero-width input range instead of returning Inf/NaN.
• remove_outliers_REI() now actually uses its range argument (validation plus an out-of-range warning) and ignores NA responses when tallying instead of poisoning row counts.
• reshape_data() reports a clear error when marker-delimited sections have unequal column counts.
• checkAssumptionsForAnova() distinguishes "normality could not be assessed" from "normality violated" and uses a consistent p < 0.05 boundary.
• Effect-size failures in the Dunn/ART post-hoc reporters now emit a warning instead of being silently swallowed.
• The four gg*WithPriorNormalityCheck*() wrappers now pass the palette in the "pals::glasbey" format required by current ggstatsplot; the deprecated package=/palette= pair was being ignored with a warning, so plots silently used the default palette instead of glasbey.

PERFORMANCE

• add_pareto_emoa_column() uses emoa::is_dominated() directly instead of matching rows against the Pareto front with floating-point equality (was O(front size x rows)).
• The mobo plots draw their annotation segments once via annotate() instead of once per data row.
• ggwithinstatsWithPriorNormalityCheckAsterisk() no longer runs an unused Levene test.

DEPENDENCIES

• Reduced hard dependencies: ARTool, car, clipr, conflicted, FSA, ggtext, readxl, report, rstatix, writexl, and xtable moved from Imports to Suggests (functions that need them check at runtime and degrade gracefully or stop with an informative message). car is no longer used by the package code at all.
• ggplot2 moved from Imports to Depends: the ggproto stats of ggpmisc 0.7.0/ggpp 0.6.0 resolve their parent classes via the search path, so generateMoboPlot()/generateMoboPlot2() fail with "object 'Stat' not found" whenever ggplot2 is not attached. Attaching colleyRstats now attaches ggplot2 as well.

MISC

• Removed the duplicate inst/WORDLIST.txt and the redundant tests.yml CI workflow (R-CMD-check already runs the tests).

colleyRstats 0.0.5

MINOR CHANGES

• new function add_pareto_moocore_column(). Should be less buggy than the one from emoa

colleyRstats 0.0.4 (2026-05-03)

MINOR CHANGES

• exposed new parameters for generateMoboPlot2().

colleyRstats 0.0.3 (2026-04-24)

MINOR CHANGES

• Fixed documentation defaults for colleyRstats_setup() and generateMoboPlot2().
• Made generateMoboPlot2() default to fillColourGroup = "ConditionID" so the documented default works out of the box.
• Simplified the GitHub Actions test workflow to install dependencies from package metadata.
• Expanded tests for plotting and reporting behavior.
• Added a getting-started vignette and linked it from the README.

colleyRstats 0.0.2 (2026-01-08)

MINOR CHANGES

• Updated all links, added GitHub reference.