Changelog • appendMCP

appendMCP (development version)

Fixed misalignment of group-sequential rejection boundaries in update_p_thresholds_cpp: thresholds are now placed at each hypothesis’s analyses_analysed columns (matching the observed p-value placement) instead of starting at analysis 1. Previously, any multi-look hypothesis whose first tested analysis was not analysis 1 (e.g. OS tested at analyses 2 & 3) had its interim boundary silently discarded and its interim tested against the final-look boundary, inflating simulated unconditional power (Tables 6a/6b) above the full-alpha local power and over-spending alpha. Design boundaries and local power (Tables 1/4/5) were unaffected.

Fixed alpha bug that didn’t propagate from config before
Fixed alpha bug with reporting local power
Fixed zero-power for propagated-weight hypotheses in update_p_thresholds_cpp
Fixed bug in enroll_rate processing for complex piecewise constant enrollment rates
Fixed differential dropout: updated get_dist_tite and plot_distribution_tte_ahr to use ahr_dd
Fixed process_analyses_2 to handle cases where hypothesis_analysed is a subset (e.g., c(2,3))
Fixed vignettes and templates after timeline_figure refactor
Fixed process_config() to use system.file() for template paths (QC-012)
Fixed process_distribution to validate required columns (QC-013)
Fixed check_analyses_structure to allow power_subsets_any/power_subsets_all columns (QC-001)
Added test_method to hypotheses allowed columns; added diagonal == 0 check; relaxed graph row sum to <= 1 (QC-003/005/006/007/015)
Documented all 22 return fields in process_config @return (QC-009)
Handle NA/NULL robustly for nominal and sfpar in boundary computation

Switched to huxtable for all table outputs
Refactored create_summary_tables: fixed hypothesis sorting and endpoint lookup
Resolved all no visible binding R CMD check notes
Resolved seq_linter warnings; moved archived.R out of package R/ folder
Fixed trailing whitespace and style issues across codebase
Rounded inline numeric values in Rmd templates; increased timeline plot height
Removed deprecated get_boundaries_old and stale vignette HTML outputs
Added number_sims to config
Exported create_summary_tables()
Added support for studies with no binary endpoints; added custom graph plotting