colleyRstats 0.1.0
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.
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
MINOR CHANGES
- exposed new parameters for
generateMoboPlot2().
colleyRstats 0.0.3
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
MINOR CHANGES
- Updated all links, added GitHub reference.