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Changelog

Source: NEWS.md

colleyRstats 0.1.5 (development)

BUG FIXES

  • colleyRstats_setup() made it impossible to attach a meta-package afterwards. library(colleyRstats), colleyRstats_setup(), library(easystats) died on the third line with .onAttach failed in attachNamespace() for 'easystats': object 'quietly' not found, which broke every downstream analysis script that opens that way. The cause was the set_conflicts = TRUE default: conflicted::conflict_prefer() does not merely record a preference, it activates conflicted, which attaches a .conflicts environment carrying its own library() and require() shims. Every later attach in the session then went through those shims, which forward quietly and verbose into base::library() as unevaluated symbols; a package whose .onAttach inspects the calling library() frame – meta-packages do this to decide whether to print their banner – evaluated those symbols in a frame that does not bind them, and the attach failed outright. set_conflicts now defaults to FALSE, so nothing takes over library() unless it is asked to. The preference list is unchanged and still takes effect when you opt in.

  • Preferences that fail to register are no longer discarded silently. The try() around the loop existed so that one unsettable preference could not abort the rest, but it also swallowed the fact that it had failed; with verbose = TRUE the failures are now named.

  • Figures saved at the column presets came out unreadable. colleyRstats_setup() set text sizes in absolute points (axis text 17 pt, axis titles 20 pt, plot titles 28 pt, strip text 22 pt) while save_paper_figure(columns = 1) writes a 3.33 x 2.22 in PDF. Points do not shrink with the canvas, so on a single-column figure the type came out about three times what fits: axis titles ran off the page entirely, and three-level factor labels such as demonstration/language/reward overprinted into an unreadable smear. Type size is now derived from the width the figure is actually written at.

  • generateEffectPlot() fixed its legend title at 14 pt, and the four ggstatsplot wrappers fixed text at 16 pt and plot.subtitle at 17 pt. These absolute values overrode whatever theme the caller had chosen, so they survived any attempt to scale a figure down. They are now relative to the theme.

  • Significance-bracket labels were fixed at 4 mm (about 11 pt). ggsignif measures text in millimetres while themes measure it in points, so the label kept its physical size no matter how small the figure was drawn and ended up larger than the axis text beside it. Bracket text now follows the active theme; at the historical 17 pt base it is still 4 mm, so existing figures do not shift.

NEW FEATURES

  • New colley_theme(base_size, base_family), the package theme as a function. Every text element is a multiple of base_size rather than an absolute point size, so one theme serves a journal column, a full-width figure and a slide – only the number changes. The multipliers are axis titles 1.15, axis text 1.0, plot title 1.65, subtitle 1.0, caption 0.8, legend text 0.9, strip text 1.3.
  • New figure_base_size(width), the rule that turns a figure width into a type size: 3.33 in gives 7 pt and 7 in gives 9 pt, interpolated between and clamped outside. Exported so the choice is inspectable rather than buried.
  • save_paper_figure() gains base_size. The default NULL derives it from the width, which is the fix above; pass a number to choose it, or NA to leave the plot’s own text sizes untouched. The confirmation message now names the size used.
  • colleyRstats_setup() gains base_size (default 17), passed through to colley_theme().
  • A pkgdown site (_pkgdown.yml plus a deploy workflow) puts the 56 help topics into a grouped reference index – session setup, pipelines, test selection, assumptions, plots, reporting, effect sizes, LaTeX output, data preparation – instead of one alphabetical wall.

DOCUMENTATION

  • The README and vignette("getting-started") now show the session-setup pattern, including where colleyRstats_setup() belongs relative to your library() calls and what happens if it goes first. Neither had covered this, which is how the conflicted defect above reached three downstream analysis repositories.
  • The snake_case spellings (report_art(), plot_effect(), check_assumptions_anova(), …) are now stated to be the canonical ones, and the documentation uses them throughout: README, vignettes, and the pkgdown reference index. Every affected help page gained a Naming section saying which spelling to prefer and that the other is not going away. Previously the aliases file described snake_case as the discoverable API while the README taught camelCase exclusively, and nothing told a reader which to use.

BACKWARD COMPATIBILITY

  • The camelCase function names (reportART(), generateEffectPlot(), and the rest) are now marked superseded. Nothing changes at runtime: they are the same function objects, they emit no warnings, and they are not scheduled for removal. Only the documentation’s recommendation has changed.
  • colleyRstats_setup(set_options = TRUE) now emits a deprecation warning instead of an easily missed message, and the warning is no longer suppressed by verbose = FALSE. The argument has had no effect since global options() handling was removed for CRAN compliance; set_options = FALSE is unaffected.
  • colleyRstats_setup() no longer sets conflicted preferences by default. Pass set_conflicts = TRUE for them, and place that call after every library() call in the script rather than before. That ordering is a requirement – once conflicted is active, attaching a meta-package fails – and it is also where the preferences do most good, since conflicted resolves only those names that are ambiguous among the packages attached at the time.
  • colleyRstats_setup() with no arguments produces the same text sizes as before: the default base_size = 17 reproduces the previous absolute values exactly (17 / 19.55 / 28.05 / 15.3 / 22.1 pt), and there is a regression test pinning them.
  • Figures written through save_paper_figure() do change, which is the point of the fix – they become legible at the size they are placed at. To keep a figure exactly as it was, pass base_size = NA.
  • Because the theme is now built as see::theme_lucid(base_size = ...) rather than theme_lucid() with sizes overridden on top, margins and spacing scale with the text instead of staying at the 11 pt defaults. This is part of why elements used to collide.

colleyRstats 0.1.4

CRAN release: 2026-07-25

BUG FIXES

  • reportART() reported no F statistic and no effect size for mixed ART models. stats::anova() names the F column F value for a between-only (lm) fit but plain F for a mixed (lmer) one, and only the former was read – so every model containing a random term (+ (1 | participant), i.e. any within-subjects design) produced \F{3}{108}{} with the statistic missing, silently dropped the partial eta-squared, and left the opening parenthesis unclosed. The F column is now resolved by whichever name it carries.
  • reportART() now always closes the statistics parenthesis. It was appended only when an effect size could be computed, so sentences without one shipped unbalanced parentheses into LaTeX.
  • reportggstatsplotPostHoc() emitted a stray ) after the p-value: ... (\m{3.8}, \sd{1.6}); \padj{0.001}). The mean/SD parenthetical closed too early, leaving the p-value outside the parentheses it belongs to and the sentence unbalanced. It now reads ... (\m{3.8}, \sd{1.6}; \padj{0.001})., matching reportArtCon().
  • Degrees of freedom are formatted for display. Greenhouse-Geisser corrected, Kenward-Roger and Welch dfs are fractional and were pasted at full double precision, e.g. \F{1.80875305770353}{66.9238631350305}{0.11} and F(2, 180.000000000002). Whole dfs stay whole; fractional ones are rounded to two decimals.
  • reportggstatsplot() chooses the indefinite article from the method name, so it reads “An ANOVA …” rather than “A ANOVA …”.

DOCUMENTATION

colleyRstats 0.1.3

CRAN release: 2026-07-16

NEW FEATURES

  • New vignette “Analyzing a typical user study” (vignette("analyzing-a-user-study")): a complete walkthrough from raw within-subjects data to manuscript-ready figures and LaTeX text.
  • Friendlier errors everywhere a column name is passed: plotting and reporting functions now validate x/y/iv/dv/factors/objectives up front and report which column is missing plus the available columns, instead of failing later with a cryptic dplyr/rlang error.
  • The plot wrappers warn when xlabels does not match the number of observed groups (previously the axis labels silently misaligned).
  • not_empty() now names the offending argument in its default error message.
  • remove_outliers_REI() accepts variables as a character vector (e.g. c("var1", "var2")) in addition to the comma-separated string.
  • add_pareto_emoa_column() / add_pareto_moocore_column() verify that the objective columns exist and are numeric.

BUG FIXES

  • ?replace_values works again: a malformed roxygen @name tag had redirected its documentation to a stray data-the-data-frame help page.
  • reportArtCon() now escapes the dependent variable and condition names for LaTeX and renders the IV via the same name-macro policy as reportDunnTest(); previously names with underscores produced uncompilable LaTeX.
  • The reshape_data() example was not runnable (requireNamespace() was called with a vector and a misspelled package name).
  • latex_preamble() no longer documents its path argument twice; rFromNPAV()’s documentation block is no longer split by a stray comment line.
  • reportNPAV() no longer refers to the non-existent reportNPAVChi() when the input lacks a Pr(>F) column.
  • README: removed the section documenting the non-existent reportNPAVChi(), refreshed the stale reportNPAV() deprecation date, fixed the double anova() call in the reportART() example, and documented the newer API (recommend_test, pipelines, Overleaf output) and all vignettes.

PERFORMANCE

colleyRstats 0.1.2

CRAN release: 2026-07-06

NEW FEATURES

  • Principled model selection: classify_outcome() determines a variable’s measurement scale (continuous, ordinal, binary, count, nominal) and recommend_test() turns scale x clustering x assumption checks into a concrete recommendation – including mixed models – with the matching reporter, a ready-to-edit fit call, a rationale, and an APA-style methods sentence.
  • Mixed-model reporters: reportGLMM() (lme4 / glmmTMB / lm / glm; odds and incidence-rate ratios are chosen automatically from the family) and reportCLMM() (ordinal::clmm / clm).
  • Overleaf-oriented output layer: use_colleyrstats_sty() ships the macro package, emit_name_macros() / define_result_macro() generate \newcommand stubs and single-source-of-truth result macros, expand_latex_macros() – with options(colleyRstats.macros = FALSE) – expands everything to plain math, and emit_overleaf() bundles a whole analysis into a compilable Overleaf project.
  • latex_escape() escapes LaTeX special characters in user-supplied names.
  • New vignettes: “Choosing the right test (and mixed models)” and “From R to Overleaf: publication-ready output”.

DEPENDENCIES

  • Lowered several minimum version requirements for broader compatibility.

colleyRstats 0.1.1

CRAN release: 2026-06-22

BUG FIXES

  • adjustment of the post-hoc test due to changes in the ggstatsplot implementation

colleyRstats 0.1.0

CRAN release: 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). PDFs use Cairo for embedded fonts on Windows/Linux; on macOS the default pdf device is used because R’s cairo there can crash the session (observed as segfaults on GitHub Actions macOS runners). A device argument allows overriding.
  • 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

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

colleyRstats 0.0.4

CRAN release: 2026-05-03

MINOR CHANGES

colleyRstats 0.0.3

CRAN release: 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

CRAN release: 2026-01-08

MINOR CHANGES

  • Updated all links, added GitHub reference.