simFastBOIN 1.3.2

New Features

Customizable Safety and Toxicity Thresholds

• Added p_saf and p_tox parameters to core functions

  • sim_boin(), sim_boin_multi(), and get_pts_and_tox() now accept custom safety and toxicity thresholds
  • p_saf: Highest toxicity probability deemed acceptable for safety (default: 0.6 * target)
  • p_tox: Lowest toxicity probability deemed unacceptable for toxicity (default: 1.4 * target)
  • These parameters are passed to get_boin_boundary() for boundary calculation
  • Stored in summary objects for reference and reproducibility

• Usage examples

  # Using default thresholds (0.6 * target and 1.4 * target)
  result_default <- sim_boin(
    n_trials = 10000,
    target = 0.30,
    p_true = c(0.10, 0.25, 0.40, 0.55, 0.70),
    n_cohort = 10,
    cohort_size = 3,
    seed = 123
  )
  
  # Using custom thresholds
  result_custom <- sim_boin(
    n_trials = 10000,
    target = 0.30,
    p_true = c(0.10, 0.25, 0.40, 0.55, 0.70),
    n_cohort = 10,
    cohort_size = 3,
    p_saf = 0.15,  # Custom safety threshold
    p_tox = 0.45,  # Custom toxicity threshold
    seed = 123
  )

Documentation Improvements

• Enhanced parameter documentation
  • Added comprehensive roxygen2 documentation for p_saf and p_tox parameters
  • All @param entries now use consistent multi-line format for better readability
  • Updated examples to demonstrate custom threshold usage
• Expanded test coverage
  • Added tests for p_saf and p_tox parameter handling in sim_boin()
  • Added tests for p_saf and p_tox parameter handling in sim_boin_multi()
  • Added tests for p_saf and p_tox parameter handling in get_pts_and_tox()
  • Verified that custom values are correctly stored in summary objects
  • Verified that default values are correctly calculated when not specified

Breaking Changes

None. All existing code continues to work as before. The new p_saf and p_tox parameters have sensible defaults (0.6 * target and 1.4 * target respectively) that match the standard BOIN methodology, ensuring full backward compatibility.

Internal Changes

• Updated function signatures to include p_saf and p_tox parameters with NULL defaults
• Modified internal logic to calculate default values when parameters are not specified
• Updated summary objects to store p_saf and p_tox values for reproducibility

simFastBOIN 1.3.1

Bug Fixes

• Fixed DESCRIPTION Date field
  • Corrected Date from 2024-12-06 to 2025-12-06
  • This was a typo in the year field that was caught during CRAN submission process

No functional changes. All code and features remain identical to version 1.3.0.

simFastBOIN 1.3.0

New Features

Progress Message Control

• Added verbose parameter to sim_boin() and sim_boin_multi()

  • Control whether progress messages are printed to console
  • verbose = FALSE (default): Run silently without progress messages
  • verbose = TRUE: Display progress messages as in previous versions
  • Particularly useful for R Markdown documents and vignettes where clean output is desired
  • Results are identical regardless of verbose setting

• Usage examples

  # Silent mode (default) - ideal for vignettes and reports
  result <- sim_boin(
    n_trials = 10000,
    target = 0.30,
    p_true = c(0.10, 0.25, 0.40, 0.55, 0.70),
    n_cohort = 10,
    cohort_size = 3,
    seed = 123
  )
  
  # With progress messages
  result <- sim_boin(
    n_trials = 10000,
    target = 0.30,
    p_true = c(0.10, 0.25, 0.40, 0.55, 0.70),
    n_cohort = 10,
    cohort_size = 3,
    verbose = TRUE,
    seed = 123
  )

Documentation Improvements

• Standardized roxygen2 documentation format
  • All parameter descriptions now use consistent multi-line format
  • Improved readability and maintenance
  • Enhanced consistency across all functions
• Updated vignettes
  • Clean output without progress messages
  • Better integration with R Markdown workflows
  • Improved presentation quality

Breaking Changes

None. All existing code continues to work as before. The new verbose parameter defaults to FALSE, which changes the default behavior to silent mode, but all functionality remains identical.

Migration Guide

For users who prefer the previous behavior with progress messages:

# Add verbose = TRUE to see progress messages
result <- sim_boin(
  n_trials = 10000,
  target = 0.30,
  p_true = p_true,
  n_cohort = 48,
  cohort_size = 3,
  verbose = TRUE,  # Add this line
  seed = 123
)

simFastBOIN 1.2.1

New Features: Multi-Scenario Simulation and HTML Output

New Multi-Scenario Simulation Function

• Added sim_boin_multi() function

  • Run BOIN simulations across multiple dose-toxicity scenarios simultaneously
  • Automatically orchestrates simulations for each scenario using sim_boin()
  • Aggregates results into a unified comparison table
  • Ideal for protocol development evaluating multiple dose-toxicity relationships
  • Returns results organized by scenario for easy comparison
  • Progress messages track simulation status for each scenario

• Usage example

  scenarios <- list(
    list(name = "Scenario 1: MTD at DL4",
         p_true = c(0.05, 0.10, 0.20, 0.30, 0.45)),
    list(name = "Scenario 2: MTD at DL3",
         p_true = c(0.10, 0.15, 0.30, 0.45, 0.60))
  )
  
  result <- sim_boin_multi(
    scenarios = scenarios,
    target = 0.30,
    n_trials = 10000,
    n_cohort = 48,
    cohort_size = 3,
    seed = 123
  )

Enhanced Print Methods: HTML Table Output

• Added html format option to print.boin_summary() and print.boin_multi_summary()

  • kable_format = "html": Generate HTML tables with enhanced styling
  • Includes striped rows, hover effects, and responsive formatting via kableExtra
  • Automatically applies visual formatting including bold headers and borders
  • Useful for web-based reports and interactive documents
  • Full support for embedded HTML display in R Markdown documents

• Updated kable_format parameter documentation

  • "pipe" (default): Markdown pipe table format
  • "simple": Minimal text table format
  • "latex": LaTeX table format
  • "html": HTML table format with enhanced styling (NEW)

• Enhanced print output examples

  # HTML table for web display
  print(result$summary, kable = TRUE, kable_format = "html")
  
  # Multi-scenario results as HTML
  print(multi_result, kable = TRUE, kable_format = "html")

Documentation and Output Formatting Enhancements

Comprehensive roxygen2 Documentation

• Added detailed roxygen2-formatted documentation to all functions
  • get_boin_boundary(): Escalation and de-escalation boundary calculation
  • get_boin_decision(): Decision table generation with decision rules
  • get_boin_stopping_boundaries(): Safety stopping rule table generation
  • get_pts_and_tox(): Patient enrollment and toxicity simulation
  • isotonic_regression(): Isotonic regression with PAVA algorithm
  • select_mtd(): MTD selection with optional boundMTD constraint
  • sim_boin(): Main simulation workflow
  • sim_boin_multi(): Multi-scenario simulation orchestration
  • print.boin_summary(): Summary table printing and formatting
  • print.boin_multi_summary(): Multi-scenario summary printing and formatting
• Enhanced function comments
  • Added section headers for major processing blocks
  • Detailed explanations of algorithm steps and decision logic
  • Clear descriptions of parameter usage and constraints
  • Clarified relationships between input parameters and outputs

Print Method Enhancements: print.boin_summary()

• Added percent parameter
  • percent = FALSE (default): Display Avg Pts and Avg DLTs as absolute numbers
  • percent = TRUE: Display as percentages of total

All changes are backward compatible. New parameters have sensible defaults.

simFastBOIN 1.2.0

Bug Fixes and Compatibility

BOIN Package Compatibility

• Restored exact compatibility with BOIN package
  • Changed DLT generation from runif() back to rbinom()
  • rbinom() ensures identical random number sequence as BOIN with same seed
  • Verified: MTD selection results now match BOIN within <0.5% across all scenarios

Default Parameter Corrections

• Updated default values to match BOIN standard
  • min_mtd_sample: Changed from 6 to 1
    • Doses with ≥1 patient can now be considered for MTD selection
    • Matches BOIN package default behavior
  • n_earlystop_rule: Changed default from “simple” to “with_stay”
    • Trial now stops when n ≥ n_earlystop AND next decision = “Stay”
    • Ensures algorithm convergence before stopping
    • Follows BOIN standard implementation

Performance Optimizations

Vectorized Implementation

• Batch processing for improved performance
  • Uses vectorized operations for fast simulation
  • Pre-allocated vectors and vectorized computations
  • Early exit for trials with no valid doses

DLT Generation Optimization

• Optimized random number generation in sim_boin()
  • Uses rbinom() for accurate DLT generation matching BOIN package
  • Vectorized operations for efficient computation
  • Performance optimization particularly notable for large-scale simulations

MTD Selection Enhancement

• Optimized select_mtd() function
  • Returns NA immediately when no valid MTD candidates exist
  • Avoids unnecessary computations for trials without viable doses
  • Improves overall simulation efficiency

Internal Improvements

• Enhanced code documentation with detailed optimization rationale
• Improved memory efficiency through pre-allocation
• Maintained backward compatibility with existing APIs

Documentation Updates

• Updated roxygen2 documentation in sim_boin.R
• Updated parameter descriptions
• Updated README.md with corrected default values

Breaking Changes

None. The changes restore compatibility and fix defaults to match standard BOIN behavior. Users running with explicit parameters should see no change.

Migration Guide

For users upgrading from simFastBOIN 1.1.0:

If you were using defaults:

# Old code (simFastBOIN 1.0.0)
result <- sim_boin(n_trials = 10000, target = 0.30, p_true = p_true, ...)

# New code (simFastBOIN 1.2.0) - No change needed!
# Default behavior now matches BOIN package
result <- sim_boin(n_trials = 10000, target = 0.30, p_true = p_true, ...)

If you were using custom parameters:

# Explicitly setting these will ensure consistent behavior across versions
result <- sim_boin(
  n_trials = 10000,
  target = 0.30,
  p_true = p_true,
  min_mtd_sample = 1,        # Now the default
  n_earlystop_rule = "with_stay",  # Now the default
  ...
)

simFastBOIN 1.0.0

Initial Release

Core Features

• High-Performance BOIN Simulation
  • Vectorized implementation for 2-5x speedup over traditional approaches
  • Batch processing of all trials simultaneously at each cohort
  • Efficient matrix operations for state management
• Automatic Decision Table Generation
  • sim_boin() automatically generates BOIN boundaries and decision tables
  • No need for manual pre-computation
  • User-friendly API with minimal required parameters
• Safety Features
  • Optional extrasafe parameter for safety stopping at lowest dose
  • Dose elimination rules based on posterior probability
  • Configurable safety thresholds
• Professional Output
  • Publication-ready summary tables
  • Optional knitr::kable format for RMarkdown
  • Detailed trial-level results available

Main Functions

• sim_boin(): Run BOIN trial simulations
• get_boin_boundary(): Calculate BOIN interval boundaries
• get_boin_decision(): Generate decision table
• get_boin_stopping_boundaries(): Generate safety stopping boundaries
• isotonic_regression(): Apply isotonic regression for dose-toxicity estimation
• summarize_simulation_boin(): Aggregate simulation results

Performance

• 10,000 trials with 9 doses and 48 cohorts: ~1-2 seconds
• Memory efficient: <100MB for typical simulations
• Scales with number of cohorts, not number of trials

Documentation

• Comprehensive function documentation with examples
• Detailed README with quick start guide
• Performance benchmarks and comparisons