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().\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 …”.check_assumptions_anova() guidance
message).vignette("analyzing-a-user-study")): a complete
walkthrough from raw within-subjects data to manuscript-ready figures
and LaTeX text.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.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.?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.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.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.ggwithinstatsWithPriorNormalityCheck() no longer runs
an unused Levene test (the asterisk variant was already fixed in
0.1.0).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.reportGLMM() (lme4 / glmmTMB /
lm / glm; odds and incidence-rate ratios are chosen automatically from
the family) and reportCLMM() (ordinal::clmm / clm).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.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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