Merge pull request #52 from Merck/46-s7-change-generate_corr-to-s7

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

Author: keaven

..Rcheck/00check.log

@@ -0,0 +1,14 @@
+* using log directory ‘/Users/Anderkea/Documents/GitHub/wpgsd/..Rcheck’
+* using R version 4.5.0 (2025-04-11)
+* using platform: aarch64-apple-darwin20
+* R was compiled by
+    Apple clang version 14.0.0 (clang-1400.0.29.202)
+    GNU Fortran (GCC) 14.2.0
+* running under: macOS Sequoia 15.6.1
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘./DESCRIPTION’ ... ERROR
+Required fields missing or empty:
+  ‘Author’ ‘Maintainer’
+* DONE
+Status: 1 ERROR

.Rbuildignore

@@ -8,3 +8,5 @@
 ^\.github$
 ^codecov\.yml$
 ^CITATION\.cff$
+^doc$
+^Meta$

.gitignore

@@ -4,3 +4,5 @@
 .Ruserdata
 .DS_Store
 docs
+/doc/
+/Meta/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wpgsd
 Title: Weighted Parametric Group Sequential Design
-Version: 0.1.0
+Version: 0.3.0
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = "aut"),
     person("Zifang", "Guo", email = "zifang.guo@merck.com", role = "aut"),
@@ -31,6 +31,7 @@ Imports:
     gsDesign,
     mvtnorm,
     rlang (>= 0.4.11),
+    S7,
     stats,
     tibble,
     tidyselect
@@ -48,4 +49,4 @@ VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3

EventTable_README.md

@@ -0,0 +1,128 @@
+# EventTable S7 Class Implementation
+
+## Overview
+
+The `EventTable` S7 class provides a type-safe, validated data structure for representing event count data used in the wpgsd package. This is the first step in converting the wpgsd package to use S7 classes throughout.
+
+## Features
+
+### Core Properties
+- **data**: A tibble containing the event count data with required columns `H1`, `H2`, `Analysis`, `Event`
+- **n_hypotheses**: Automatically calculated number of hypotheses
+- **n_analyses**: Automatically calculated number of analyses
+
+### Validation
+- Validates presence of required columns (`H1`, `H2`, `Analysis`, `Event`)
+- Ensures proper data types (all numeric)
+- Validates logical constraints:
+  - Hypothesis indices must be positive integers
+  - Analysis numbers must be positive integers  
+  - Event counts must be non-negative
+- Enforces mathematical consistency requirements:
+  - For a fixed H1, H2 pair, Event counts must be non-decreasing as Analysis increases
+  - For off-diagonal entries (H1 ≠ H2), diagonal entries must exist with Event ≥ off-diagonal Event for the same Analysis
+  - These constraints ensure proper mathematical properties for correlation matrix calculations
+
+### Methods
+- **print()**: Clean formatted output showing key information
+- **summary()**: Detailed summary including event count statistics
+- **subset_event_table()**: Subset by analysis or hypotheses
+- **as_event_table()**: Convert tibble to EventTable
+- **validate_event_table_data()**: Validate data format before processing
+
+## Usage Examples
+
+### Basic Usage
+```r
+library(wpgsd)
+
+# Create event data
+event_data <- tibble::tribble(
+  ~H1, ~H2, ~Analysis, ~Event,
+  1, 1, 1, 155,
+  2, 2, 1, 160,
+  1, 2, 1, 85,
+  1, 1, 2, 305,
+  2, 2, 2, 320,
+  1, 2, 2, 170
+)
+
+# Create EventTable object
+event_table <- EventTable(data = event_data)
+print(event_table)
+```
+
+### Data Validation
+```r
+# The constructor automatically validates data
+tryCatch({
+  invalid_data <- tibble::tibble(
+    H1 = c(1, -2),  # Invalid: negative hypothesis index
+    H2 = c(1, 2),
+    Analysis = c(1, 1),
+    Event = c(100, 200)
+  )
+  EventTable(data = invalid_data)
+}, error = function(e) {
+  cat("Validation error:", e$message)
+})
+```
+
+### Subsetting
+```r
+# Subset by analysis
+analysis_1 <- subset_event_table(event_table, analysis = 1)
+
+# Subset by hypotheses
+h1_h2 <- subset_event_table(event_table, hypotheses = c(1, 2))
+```
+
+### Integration with Existing Functions
+```r
+# Use with existing wpgsd functions
+correlation_matrix <- generate_corr(event_table@data)
+```
+
+## Files Created
+
+- `R/s7_classes.R`: Main S7 class definition
+- `tests/testthat/test-s7-event-table.R`: Comprehensive unit tests
+- `examples/test_event_table.R`: Basic usage examples
+- `examples/event_table_integration.R`: Integration with existing functions
+
+## Dependencies
+
+- Added `S7` to package imports in `DESCRIPTION`
+- Uses existing dependencies: `tibble`, `dplyr`
+
+## Benefits
+
+1. **Type Safety**: Prevents invalid data from being passed to wpgsd functions
+2. **Validation**: Automatic validation of data format and constraints
+3. **Documentation**: Self-documenting data structures
+4. **Method Dispatch**: Extensible with specialized methods
+5. **User Experience**: Clear error messages and helpful summaries
+
+## Next Steps
+
+This EventTable implementation provides the foundation for converting the wpgsd package to S7 classes. Future steps include:
+
+1. Create `CorrelationMatrix` S7 class for `generate_corr()` output
+2. Create `Bounds` S7 class for `generate_bounds()` output  
+3. Update existing functions to accept/return S7 objects
+4. Maintain backward compatibility with existing tibble/data.frame inputs
+
+## Testing
+
+Run the comprehensive test suite:
+```r
+testthat::test_file("tests/testthat/test-s7-event-table.R")
+```
+
+The tests cover:
+- Object creation with valid data
+- Validation of required columns
+- Data type and value validation
+- Print and summary methods
+- Subsetting functionality
+- Data conversion utilities

NAMESPACE

@@ -2,17 +2,40 @@
 
 export(":=")
 export(.data)
+export(CorrelationMatrix)
+export(EventTable)
+export(as_correlation_matrix)
+export(as_event_table)
 export(as_label)
 export(as_name)
 export(calc_seq_p)
+export(check_event_data)
 export(closed_test)
+export(compute_correlations)
 export(enquo)
 export(enquos)
 export(find_astar)
 export(find_xi)
+export(gen_corr)
 export(generate_bounds)
 export(generate_corr)
+export(generate_corr_s7)
 export(generate_event_table)
+export(generate_event_table_)
+export(generate_event_table_cc)
+export(generate_event_table_ol)
+export(subset_correlation_matrix)
+export(subset_event_table)
+export(validate_event_table_data)
+importFrom(S7,S7_inherits)
+importFrom(S7,S7_object)
+importFrom(S7,class_character)
+importFrom(S7,class_data.frame)
+importFrom(S7,class_integer)
+importFrom(S7,method)
+importFrom(S7,new_S3_class)
+importFrom(S7,new_class)
+importFrom(S7,new_object)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)

NEWS.md

@@ -1,3 +1,75 @@
+# wpgsd 0.3.0
+
+## New Features
+
+- **Dunnett-type dose-finding vignette**: Added new vignette demonstrating Dunnett-type group sequential design with 2 experimental arms vs. common control and 3 analyses (2 interims + final), exercising correlation computation for K > 2.
+
+## Improvements
+
+- Completed S7 wrapper function elimination and validation refactoring.
+- Organized help files into logical sections for better usability.
+- Removed empty `adj-seq-p-simplified.Rmd` vignette that caused UNKNOWN TITLE in pkgdown navigation.
+
+## Bug Fixes
+
+- Fixed `generate_corr()` correlation computation for K > 2 analyses: within-hypothesis and between-hypotheses loops now correctly enumerate all analysis pairs.
+- Fixed S7 `EventTable` validator to allow single-analysis and single-hypothesis event tables (e.g., after subsetting).
+- Fixed `validate_event_data_core()` crash when non-numeric data is passed to `floor()` checks.
+- Fixed inconsistent error message formatting in diagonal entry validation (`paste` → `paste0`).
+- Corrected test expectations to match actual validation error messages.
+
+# wpgsd 0.2.0
+
+## Major Features
+
+- **S7 Class System Integration**: Complete implementation of S7 classes for enhanced type safety and validation
+  - `EventTable` class with robust validation for event data structures
+  - `CorrelationMatrix` class with symmetry and positive definiteness validation
+  - Improved `generate_corr()` function with S7 class support
+
+## Code Quality Improvements
+
+### Validation System Refactoring
+- **Eliminated ~80% code duplication** between `check_event_data()`, `validate_event_table_data()`, and `EventTable` validator method through centralized `validate_event_data_core()` function
+- **Improved validation consistency** with three validation levels: "basic", "strict", and "s7" to support different use cases
+- **Enhanced error handling** with clearer, more specific error messages for validation failures
+- **Relaxed Event value requirements** to allow non-integer values (e.g., 100.5 events) while maintaining H1, H2, and Analysis as positive integers
+
+### S7 Class Implementation Improvements  
+- **Removed redundant wrapper functions** `new_event_table()` and `new_correlation_matrix()` following S7 best practices
+- **Enhanced S7 class documentation** with comprehensive parameter descriptions, validation details, and usage examples
+- **Improved API consistency** by using direct S7 class constructors (`EventTable()`, `CorrelationMatrix()`) throughout codebase
+- **Updated all examples and tests** to use proper S7 constructor patterns instead of wrapper functions
+
+### Testing and Documentation Updates
+- **Updated test suite** to reflect validation changes and S7 constructor usage
+- **Regenerated package documentation** with roxygen2 to remove deprecated wrapper function documentation
+- **Enhanced code maintainability** through consolidated validation logic and cleaner S7 implementation
+
+## Bug Fixes and Improvements
+
+- Fixed correlation matrix validation tolerance issues (improved numerical precision handling with 1e-12 tolerance)
+- Resolved non-ASCII character issues in documentation for better portability
+- Added missing `@export` tags for proper function exports
+- Enhanced roxygen2 documentation with clearer parameter descriptions
+
+## Documentation and Vignettes
+
+- **Significantly improved `adj-seq-p` vignette**:
+  - Reduced code repetition by ~80% through systematic helper functions
+  - Enhanced readability while maintaining technical accuracy
+  - Added comprehensive multiplicity strategy visualization
+  - Improved mathematical notation and explanations
+  - Added proper citations (@zhao2025adjusted)
+- Updated correlation calculation vignette with S7 class examples
+
+## Package Infrastructure
+
+- Enhanced unit tests with 132+ passing test cases
+- Improved package build process with better error handling
+- Updated NAMESPACE with proper exports
+- Enhanced pkgdown documentation site generation
+
 # wpgsd 0.1.0
 
 - Initial release.

R/calc_seq_p.R

@@ -80,37 +80,38 @@
 #' )
 #' }
 calc_seq_p <- function(
-    test_analysis = 2,
-    test_hypothesis = "H1, H2, H3",
-    p_obs = tibble::tibble(
-      analysis = 1:2,
-      H1 = c(0.02, 0.0015),
-      H2 = c(0.01, 0.01),
-      H3 = c(0.01, 0.004)
+  test_analysis = 2,
+  test_hypothesis = "H1, H2, H3",
+  p_obs = tibble::tibble(
+    analysis = 1:2,
+    H1 = c(0.02, 0.0015),
+    H2 = c(0.01, 0.01),
+    H3 = c(0.01, 0.004)
+  ),
+  alpha_spending_type = 2,
+  n_analysis = 2,
+  initial_weight = c(0.3, 0.3, 0.4),
+  transition_mat = matrix(c(
+    0.0000000, 0.4285714, 0.5714286,
+    0.4285714, 0.0000000, 0.5714286,
+    0.5000000, 0.5000000, 0.0000000
+  ), nrow = 3, byrow = TRUE),
+  z_corr = matrix(
+    c(
+      1.0000000, 0.7627701, 0.6666667, 0.7071068, 0.5393599, 0.4714045,
+      0.7627701, 1.0000000, 0.6992059, 0.5393599, 0.7071068, 0.4944132,
+      0.6666667, 0.6992059, 1.0000000, 0.4714045, 0.4944132, 0.7071068,
+      0.7071068, 0.5393599, 0.4714045, 1.0000000, 0.7627701, 0.6666667,
+      0.5393599, 0.7071068, 0.4944132, 0.7627701, 1.0000000, 0.6992059,
+      0.4714045, 0.4944132, 0.7071068, 0.6666667, 0.6992059, 1.0000000
     ),
-    alpha_spending_type = 2,
-    n_analysis = 2,
-    initial_weight = c(0.3, 0.3, 0.4),
-    transition_mat = matrix(c(
-      0.0000000, 0.4285714, 0.5714286,
-      0.4285714, 0.0000000, 0.5714286,
-      0.5000000, 0.5000000, 0.0000000
-    ), nrow = 3, byrow = TRUE),
-    z_corr = matrix(
-      c(
-        1.0000000, 0.7627701, 0.6666667, 0.7071068, 0.5393599, 0.4714045,
-        0.7627701, 1.0000000, 0.6992059, 0.5393599, 0.7071068, 0.4944132,
-        0.6666667, 0.6992059, 1.0000000, 0.4714045, 0.4944132, 0.7071068,
-        0.7071068, 0.5393599, 0.4714045, 1.0000000, 0.7627701, 0.6666667,
-        0.5393599, 0.7071068, 0.4944132, 0.7627701, 1.0000000, 0.6992059,
-        0.4714045, 0.4944132, 0.7071068, 0.6666667, 0.6992059, 1.0000000
-      ),
-      nrow = 6, byrow = TRUE
-    ),
-    spending_fun = gsDesign::sfHSD,
-    spending_fun_par = -4,
-    info_frac = c(0.5, 1),
-    interval = c(1e-4, 0.2)) {
+    nrow = 6, byrow = TRUE
+  ),
+  spending_fun = gsDesign::sfHSD,
+  spending_fun_par = -4,
+  info_frac = c(0.5, 1),
+  interval = c(1e-4, 0.2)
+) {
   foo <- function(x) {
     all_hypothesis <- strsplit(test_hypothesis, split = ", ") %>% unlist()
     all_hypothesis_idx <- as.numeric(gsub(".*?([0-9]+).*", "\\1", all_hypothesis))