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Implement MC-SIMEX method and enhance comparison notebooks - #33
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Sep 16, 2026
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- Added MC-SIMEX method
- Notebook now compares to both Yi and MC-SIMEX.
- p value is calculated correctly - by permuting the patients to compare to null, rather than assuming a chi^2 with 1 DOF
- Optimizations to speed up likelihood scans without hurting the results - we only need to know whether there is a solution above or below 1 or 3.84, not necessarily what the optimal solution is.
A group-to-group flip was billed twice, and exclusion used the other group's cost instead of the tail NLL. Co-authored-by: Cursor <cursoragent@cursor.com>
Chi-squared with 1 df ignores assignment search, so p fell as measurement error grew. Cox-only still uses chi-squared. Co-authored-by: Cursor <cursoragent@cursor.com>
… discrete-e ladder to 0.20/0.25/0.40 after the flip-cost fix. Co-authored-by: Cursor <cursoragent@cursor.com>
…lve budgets. Use shared n=50 HR=6 methods_comparison_* datacards with e=0.05/0.10/0.25, and set N_PERMUTATIONS=19, N_HR_SCAN=25, SIMEX_B=20 plus a 3600s nbconvert timeout so CI can finish. Co-authored-by: Cursor <cursoragent@cursor.com>
…nts in place. Outcome permutations keep the death-time grid size fixed, so rebuild r/d incidence on the existing Gurobi model instead of constructing a new calculator and model for every shuffle. Co-authored-by: Cursor <cursoragent@cursor.com>
…ison. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Keep CI on small hr_example cards; gate n=50 methods_comparison behind KOMBINE_FULL_COMPARISON, restore pip Gurobi, and dedupe brentq hazard-ratio CI into utilities. Co-authored-by: Cursor <cursoragent@cursor.com>
Makes full local comparison (KOMBINE_FULL_COMPARISON) tractable while keeping significant p-values; include the rebin script used to regenerate the cards. Co-authored-by: Cursor <cursoragent@cursor.com>
Restore fine-grained source cards, write K=4 copies under a gitignored rebinned/ directory from ensure_rebinned(), and call that from notebook 07 full-comparison mode. Co-authored-by: Cursor <cursoragent@cursor.com>
Import ensure_rebinned via docs.kombine so pylint and nbconvert work without installing test/ or path-hacking the datacards directory. Co-authored-by: Cursor <cursoragent@cursor.com>
Add missing docstrings and silence too-many-arguments on rewrite_card so docs lint stays at 10/10. Co-authored-by: Cursor <cursoragent@cursor.com>
Drop KOMBINE_SKIP_SLOW_ANALYSES and invert the mode switch so local runs use rebinned methods_comparison cards unless the quick n=20 hr_example path is requested. Co-authored-by: Cursor <cursoragent@cursor.com>
Use excess_at_most sign tests to bracket profile-likelihood band edges without full OPTIMAL solves at every trial p, with brentq polish and full-min fallback on unknown. Default crossing_mode stays full; notebook 07 enables feasibility for KM bands. Co-authored-by: Cursor <cursoragent@cursor.com>
Accumulate Work across excess_at_most and run_MINLP fallback chains so benchmarks can compare effort without wall-clock sleep contamination. Co-authored-by: Cursor <cursoragent@cursor.com>
Record outer-oracle status during level crossing search so endpoint clipping skips redundant full minimizes when outside is already proven. Add OracleCostTracker for Work-based probe biasing. Co-authored-by: Cursor <cursoragent@cursor.com>
Report oracle/minimize/total Work, speedup vs full baseline, and add skip-full plus optional time-limit flags for long Poisson runs. Co-authored-by: Cursor <cursoragent@cursor.com>
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