Statistical correctness audit: post-hoc FWER, Firth CI, ANCOVA EMM, Box-Cox guard + UI - #5

Merged

philippkrumm merged 91 commits into

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feature/advanced-stats-automation

Jun 13, 2026

Commits on Mar 17, 2026

Feat: integrate advanced stats automation and auto-pilot GUI
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4674989

Commits on Mar 18, 2026

Refine plot mastering workflow and clean workspace
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ac09d25

Commits on Mar 19, 2026

Harden advanced nonparametric ANOVA fallback and reporting
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9675788

Commits on Mar 20, 2026

new non parametric anovas and new plot aesthetics window. changes are not confirmed and tested. non paramteric anovas sollten auf mathematische richtigkeit überprüft werden.
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a9be076
Refactor: 4-Punkt-Roadmap — Audit, Validation, Smoke-Test, Import-Cleanup

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fcbeed3
Chore: Add project tooling and update .gitignore

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7cb3dcc
Remove redundant Advanced Tests menu entry

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bdba332
UI Overhaul: Refactoring UI principles applied

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3dcc651

Commits on Mar 21, 2026

Feat: Clinical Models — ANCOVA, LMM, Logistic Regression

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a7026bf
Validation: Numerical benchmark suite — 12/12 checks externally verified

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0f4eaa0
Feat: Effect size coverage — fix Wilcoxon r, add Welch Cohen's f, full exporter support

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2a20720
Chore: Update path references Source_Code/ → src/ and bump version to 2.0

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0165ca6

Commits on Mar 26, 2026

Feat: UI overhaul, validation suite, nonparametric ANOVAs, effect sizes, docs

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398c187
Merge: integrate remote src/ refactor with local UI + validation changes

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9f198a5
Chore: Add PyInstaller build config, icon converter, Windows version info

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502c9db
Chore: spec — universal2 target for macOS, add signing/notarization guide

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0f38a0d

Commits on Mar 31, 2026

new readme etc. new clinical tests and info points
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e198b89

Commits on Apr 1, 2026

new excel file layout and sheets
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1f27521
new html export
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e3455c2
Plan: HTML export frontend design improvements

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5813e18
Fix decision tree in HTML export + peer-review features

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a69c44e

Commits on Apr 2, 2026

new html and UX design file
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f1c84e0
Improve Help Hub UX, dialog styling, and macOS Qt startup handling; ignore venv backups
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5de0671
feat: enhance HTML reporting, plot designer, and headless test stability
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b721a38
refactor: extract advanced statistical testing pipeline and engines
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9554443
refactor: split stats_functions into posthoc outlier and analysis cores
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b7687cc
refactor: modularize analyzer/tester and polish report plot designer
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0a60883

Commits on Apr 7, 2026

chore: git cleanup — remove temp files, generated output, expand .gitignore

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d100530

Commits on Apr 10, 2026

feat: add interaction and profile plots for factorial ANOVA designs

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9331f66

Commits on Apr 11, 2026

test: extend R validation suite — effect sizes, new test types, mixed ANOVA fix

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4c558ad

Commits on Apr 14, 2026

feat: add transform & retest support to CorrelationModel (log10/sqrt/boxcox)

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4418488
feat: pass x_transform/y_transform from analysis_context to CorrelationModel
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3f4ca86
feat: add correlation transform dropdowns to autopilot UI

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a378f57
fix: guard corr_transform_widget visibility against early-return and headless paths

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4c39201
feat: show transform & recheck nodes in correlation decision tree
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test: integration tests for correlation transform & retest pipeline
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feat: report Box-Cox lambda and shift c for full transformation reproducibility

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dd1ac88
feat: factorial ANOVA effects table, file-save dialogs, and UI polish

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46fe2bb

Commits on Apr 16, 2026

Commits on Apr 17, 2026

Alte analyse Wege gelöscht, plot designer umgebaut,
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e287a85

Commits on May 7, 2026

new way of bringin in data. not finished!!
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2b9199a

Commits on May 8, 2026

feat: raw data range selector dialog + QSS polish

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c1b26ef

Commits on May 11, 2026

refactor: extract domain modules, fix data integrity bugs, add test suite

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601ce72

Commits on May 12, 2026

Commits on May 13, 2026

besserer decision tree
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e77e12d

Commits on May 25, 2026

allgemeine verbesserungen, neue decsion trees, gro
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26b58ee
chore: post-audit stable checkpoint before src restructure
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5c3af39
refactor: restructure src into logical sub-packages (core, analysis, autopilot, export, visualization, ui)
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21f0a2e
chore: remove dead scripts and empty start.bat
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3405668
deleted excel export, new audit, summary of the repo,
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b110bc0
fix: remove all pre-existing pyflakes warnings across 7 source files\n\nDrop unused imports, dead local variable assignments, and redundant\nmodule-level re-imports. Key changes:\n- statisticaltest…
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3d17c5e
Fix Pyrefly type errors in assumption checks, fix A1 Welch logic, resolve namespace shadowing
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4263227
Fix path resolutions, decision logic notes, and font typos
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311a24e

Commits on May 26, 2026

docs: overhaul guides, fix GitHub rendering, remove personal configs
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2e67a98

Commits on May 30, 2026

refactor: simplify decision tree & flowchart labels to plain English (3rd-sem med student level)
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ca2fe9e
refactor: stats engine, UI, docs & help content overhaul
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f3f275e

Commits on May 31, 2026

fix: align decision-tree test, drop dead tree code, add CI

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1abaa7f

Commits on Jun 1, 2026

refactor(html_exporter): extract _FormattingMixin

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92f90db
refactor(html_exporter): extract _AssetsMixin

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40a0dcc
refactor(html_exporter): extract _StatRowsMixin

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b226be0
refactor(html_exporter): extract _AssociationMixin

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0af272e
refactor(html_exporter): extract _ChartsMixin

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f345aa1
refactor(html_exporter): extract _SummariesMixin

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365b36f
fix(statisticaltester): forward df to advanced-ANOVA test functions

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d83da8f
refactor(html_exporter): drop duplicated inline report template

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4cc3aed
fix(analysis_core): read the correct "injected_df" context key

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fa3e3fd

Commits on Jun 2, 2026

feat(plot-designer): Add grouped mode, estimation, forest, and beeswarm plots
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9d01c13
refactor(visualizer): Integrate Welch's tests into standard parametric branch
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68d9bf2

Commits on Jun 3, 2026

fix(plot-designer): repair Phase-3 syntax crash + pairwise effect/CI data flow

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0fe588e
feat(plot-designer): conditional show/hide controls by plot type
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ee09daa
fix(nonparametric-anova): correct Freedman-Lane main-effect df + partial eta^2

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184d985

Commits on Jun 4, 2026

feat(nonparametric-anova): add comparison-selection dialog to Freedman-Lane post-hoc

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e777ec5
feat(nonparametric-anova): add BL dialog post-hoc + fix Wilcoxon scipy compat

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35ce951
test(nonparametric-anova): persist FL/BL regression + dialog tests to validation/

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2093849
test(nonparametric-anova): add NaN/missing-data coverage to FL + BL tests

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91393e7
test(nonparametric-anova): add error guards + catastrophic-NaN tests to FL/BL

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411f46c

Commits on Jun 10, 2026

fix: NaN-safe BoxCox transformation + robustness fixes
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d64b16f

Commits on Jun 13, 2026

fix(stats/posthoc): exact simultaneous CIs for Dunnett and Games-Howell

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23eec3f
refactor(core): decouple Welch-ANOVA post-hoc selection, enable dialog routing

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2755a34
feat(stats/firth): penalized profile-likelihood CI for Firth logistic

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d4fdc98
fix(stats/ancova): true estimated marginal means via balanced reference grid

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f324493
fix(stats/transform): guard against Box-Cox lambda divergence, fall back to log

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078ce87
fix(stats/nonpar): Bonett-Wright SE for Spearman CI, drop invalid MWU power

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403afee
style(ui/export): WCAG contrast, chart automargins, tree spacing, diagnostics

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58e9fe4
fix(core): use stdlib logging instead of IPython re-export

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17cf55d
ci: run tests on pull_request and main only, not every feature push

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b418cc4
docs(howto): update post-hoc, Box-Cox and Firth sections to match behaviour

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b89cd5f
test(welch-posthoc): clean up report companions written during the test

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fe2bd66