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Add Dunnett-type 4-dose GSD vignette and bump version to 0.3.0#52

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keaven wants to merge 19 commits intomainfrom
46-s7-change-generate_corr-to-s7
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Add Dunnett-type 4-dose GSD vignette and bump version to 0.3.0#52
keaven wants to merge 19 commits intomainfrom
46-s7-change-generate_corr-to-s7

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@keaven keaven commented Apr 29, 2026

Summary

This PR adds a new vignette demonstrating the WPGSD methodology for a Dunnett-type dose-finding trial and bumps the package version to 0.3.0.

New Vignette: Dunnett-type dose-finding with group sequential design

Demonstrates the WPGSD approach for a trial with 4 experimental dose groups vs. a common control with:

  • Endpoint: Overall Survival (OS)
  • Multiplicity: Equal weights (1/4), equal transitions (1/3) among dose arms
  • Group sequential design: Interim analysis at ~40% information fraction
  • Futility: Common non-binding futility bound via gsDesign (HSD beta-spending)
  • Efficacy: WPGSD Type 3 (separate alpha spending) with Lan-DeMets O'Brien-Fleming, compared to Bonferroni
  • Closed testing: Full closed testing procedure with hypothetical observed p-values

Key results

  • Correlation matrix (8x8) verified against manual computation for all 5 cases
  • Correlations of ~0.50 between dose-vs-control comparisons at same analysis (shared control arm)
  • WPGSD bounds are meaningfully less conservative than Bonferroni bounds
  • generate_corr() handles 4+ hypotheses correctly with no code changes needed

Other changes

  • Version bump: 0.2.0 -> 0.3.0
  • Bibliography: Added Dunnett (1955) reference to wpgsd.bib

keaven and others added 13 commits August 29, 2025 17:19
@keaven
Initial S7 class EventTable added using Sonnet 4
f39a49d
@keaven
Style code (GHA)
16386a0
@keaven
Release v0.2.0: Complete S7 class system implementation
ea0f4ce 
- Add EventTable and CorrelationMatrix S7 classes with type safety and validation
- Implement generate_corr_s7() with EventTable input and proper column ordering
- Update vignettes with S7 examples and improved math typesetting
- Reorganize pkgdown reference documentation for better discoverability
- Maintain full backward compatibility with existing functions
- Add comprehensive test suite (105+ tests) covering all S7 functionality
- Update NEWS.md with detailed release notes for v0.2.0
@keaven
Release v0.2.0: Add S7 class system with EventTable and CorrelationMa…
d01f9a9 
…trix

- Add S7 class system for enhanced type safety and validation
- Implement EventTable S7 class with comprehensive data validation
- Implement CorrelationMatrix S7 class with mathematical constraints
- Add generate_corr_s7() function with EventTable input and proper column ordering
- Add S7 constructors, converters, and utility functions
- Update vignettes with S7 examples and improved math formatting
- Reorganize pkgdown reference documentation with logical groupings
- Maintain full backward compatibility with existing functions
- Add comprehensive test suite (105+ tests)
- Update NEWS.md with detailed release notes
@keaven
Fix package build issues and documentation
0b8842d 
- Fixed correlation matrix symmetry validation tolerance (1e-12 with check.attributes=FALSE)
- Removed non-ASCII character from print method (× to x)
- Renamed non-portable filename: s7 prompts.md -> s7_prompts.md
- Added missing @export for generate_event_table_cc function
- Added EventTable to package exports
- Simplified roxygen documentation to avoid parsing issues
- All 132 unit tests passing
- Package builds and installs successfully
- pkgdown documentation site updated
@keaven
Release v0.2.0: Major S7 integration and vignette improvements
baf9fe5 
- Implement complete S7 class system with EventTable and CorrelationMatrix classes
- Add robust validation for correlation matrices and event data
- Fix correlation matrix validation tolerance issues (1e-12 precision)
- Resolve non-ASCII character issues in documentation
- Add missing @export tags for proper function exports
- Significantly improve adj-seq-p vignette with 80% code reduction
- Add systematic helper functions for better maintainability
- Enhanced mathematical notation and multiplicity strategy visualization
- Add comprehensive citations and improved explanations
- Update NEWS.md with detailed changelog for v0.2.0
- All 132 tests passing with enhanced test coverage
- Complete documentation and pkgdown site generation
@keaven
Minor vignette formatting improvement
a072543 
Add blank line before bullet points for better readability in adj-seq-p vignette
@keaven
feat: Complete S7 wrapper function elimination and validation refacto…
282ea49 
…ring

- Remove redundant wrapper functions new_event_table() and new_correlation_matrix()
- Enhance S7 class documentation with comprehensive parameter descriptions
- Consolidate validation logic into validate_event_data_core() eliminating ~80% duplication
- Update all examples, tests, and documentation to use direct S7 constructors
- Relax Event validation to allow non-integer values while maintaining H1/H2/Analysis as integers
- Regenerate package documentation and fix NAMESPACE exports
- Update pkgdown configuration to reflect API changes
- Add comprehensive NEWS.md documentation for v0.2.0 changes

Improves code maintainability and follows S7 best practices for class documentation.
@keaven
fix: Remove empty adj-seq-p-simplified.Rmd vignette causing UNKNOWN T…
8c7e25e 
…ITLE in navigation

- Deleted empty vignettes/adj-seq-p-simplified.Rmd file (0 bytes)
- Removed corresponding docs/articles/adj-seq-p-simplified.html
- Rebuilt pkgdown site to fix navigation dropdown
- Resolves UNKNOWN TITLE issue in Articles menu
@keaven
feat: Organize help files in logical sections for better usability
e59abbf 
- Added structured reference sections to _pkgdown.yml:
  * S7 Classes and Constructors
  * Event Table Generation
  * Correlation Matrix Computation
  * Statistical Testing and Analysis
  * Data Manipulation and Subsetting
  * Data Validation
  * Utility Functions
  * Package Information
- Improves user experience by grouping related functions together
- Reference documentation now displays functions in logical categories
@keaven
Style code (GHA)
e2244f4
@keaven
Add Dunnett-type 4-dose GSD vignette with correlation verification
2b77d64
@keaven
Bump version to 0.3.0
a449358
@keaven keaven linked an issue Apr 29, 2026 that may be closed by this pull request
s7: change generate_corr to s7 #46
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keaven and others added 2 commits April 29, 2026 20:44
@keaven
Fix S7 EventTable validation and update NEWS.md for v0.3.0
4d951fd 
- Fix validator to allow single-analysis/hypothesis EventTables
- Guard floor() calls with is.numeric checks
- Fix paste/paste0 inconsistency in error messages
- Correct test expectations to match actual error messages
- Add NEWS.md entry for v0.3.0
@keaven
Style code (GHA)
dc64376
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nanxstats commented Apr 30, 2026

Here is a prompt you can use to clean things up:

1. Remove these committed files/directories and commit:

- ..Rcheck/
- wpgsd.Rcheck/
- wpgsd_0.1.0.tar.gz
- wpgsd_0.2.0.tar.gz
- vignettes/adj-seq-p.html

2. Then, add appropriate rules to .gitignore to prevent them from being accidentally committed in the future, for example:

```
# Output files from R CMD check
/*.Rcheck/

# Output files from R CMD build
/*.tar.gz

# produced vignettes
vignettes/*.html
vignettes/*.pdf
```

3. Find canonical format and locations (tests, vignettes, etc.) within R packages to place the content of these files and remove them from the current location:

- examples/*.R
- EventTable_README.md

4. Use hyphens `-` as separator in vignette file names consistently (tidyverse package convention) so the rendered HTML pages have canonical clean URLs.

keaven and others added 3 commits April 30, 2026 06:56
@keaven
Fix R CMD check documentation errors and warnings
4c4ffb2 
- Fix duplicate/merged roxygen blocks in s7_classes.R and compute_correlations.R
- Add @name tags for S7 class definitions (EventTable, CorrelationMatrix)
- Separate @importFrom block from EventTable roxygen with NULL
- Remove orphaned validate_event_data_core roxygen block from s7_classes.R
- Fix stray backtick in @param event in generate_event_table_.R and generate_event_ol.R
- Fix EventTable example data to be valid (complete event table)
- Regenerate all affected Rd files
@keaven
Style code (GHA)
f935da5
@keaven
Add EventTable to pkgdown reference index
234aacd
@keaven keaven requested a review from Copilot April 30, 2026 14:41
Copilot AI reviewed Apr 30, 2026
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Copilot wasn't able to review this pull request because it exceeds the maximum number of lines (20,000). Try reducing the number of changed lines and requesting a review from Copilot again.

@keaven keaven requested review from LittleBeannie and Copilot April 30, 2026 14:41
Copilot AI reviewed Apr 30, 2026
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Copilot wasn't able to review this pull request because it exceeds the maximum number of lines (20,000). Try reducing the number of changed lines and requesting a review from Copilot again.

@keaven
Fix generate_corr() for K>2 analyses and rewrite Dunnett vignette
1620b6f 
- Fix within-hypothesis and between-hypotheses correlation loops in
  generate_corr() to correctly enumerate all analysis pairs when K>2
- Add test for generate_corr() with 2 hypotheses and 3 analyses
- Rewrite Dunnett vignette: 2 doses / 3 analyses (2 interims + final)
  instead of 4 doses / 2 analyses, exercising full K>2 generality
- Update NEWS.md with bug fix and vignette changes
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s7: change generate_corr to s7

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@keaven @nanxstats