ggstatsplot implementationanalyze_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.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).report_art(),
report_dunn_test(), plot_between_stats(),
check_assumptions_anova()). The original names remain fully
supported.options(colleyRstats.leading_zero = FALSE)
for APA-style p-values and effect sizes without the leading zero (e.g.,
p=.033).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.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.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.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.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)).annotate() instead of once per data row.ggwithinstatsWithPriorNormalityCheckAsterisk() no
longer runs an unused Levene test.car is no
longer used by the package code at all.generateMoboPlot()/generateMoboPlot2() fail
with “object ‘Stat’ not found” whenever ggplot2 is not attached.
Attaching colleyRstats now attaches ggplot2 as well.inst/WORDLIST.txt and the
redundant tests.yml CI workflow (R-CMD-check already runs
the tests).add_pareto_moocore_column(). Should be
less buggy than the one from emoagenerateMoboPlot2().colleyRstats_setup()
and generateMoboPlot2().generateMoboPlot2() default to
fillColourGroup = "ConditionID" so the documented default
works out of the box.
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