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971: add overdose prob to sims - #972

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danielinteractive merged 8 commits into
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971_add_overdose_prob_to_sims
Sep 18, 2026
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danielinteractive merged 8 commits into
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971_add_overdose_prob_to_sims

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closes #971

… and DASimulations.

Calculates the posterior probability that toxicity at the selected dose is strictly above max(nextBest@target).
Returns NA when no dose is selected.
Covered Design, DualDesign, DADesign, and both arms of DesignGrouped.
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@codex review

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Codex Review Summary

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Review Status Commit Review trigger
📝 Code Review ✅ Completed 2026-09-17T05:58:14.889899Z 2ef738d Manual request
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💡 Codex Review

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Reviewed commit: 2ef738ddd5

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Comment thread R/Design-methods.R
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Unit Tests Summary

    1 files     59 suites   2m 23s ⏱️
1 801 tests 1 600 ✅ 201 💤 0 ❌
5 727 runs  5 455 ✅ 272 💤 0 ❌

Results for commit d5a0d85.

♻️ This comment has been updated with latest results.

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Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
Data-methods 💔 $3.37$ $+2.56$ $0$ $0$ $0$ $0$
Design-methods 💔 $18.41$ $+14.07$ $+3$ $0$ $0$ $0$
HierarchicalDesign-methods 💔 $1.76$ $+1.41$ $0$ $0$ $0$ $0$
HierarchicalModel 💔 $5.34$ $+4.08$ $0$ $0$ $0$ $0$
Model-class 💔 $3.76$ $+3.08$ $0$ $0$ $0$ $0$
Model-methods 💔 $3.01$ $+2.78$ $0$ $0$ $0$ $0$
Model-validity 💔 $1.06$ $+1.12$ $0$ $0$ $0$ $0$
Rules-class 💔 $1.49$ $+1.44$ $0$ $0$ $0$ $0$
Rules-methods 💔 $14.72$ $+12.19$ $0$ $0$ $0$ $0$
Samples-methods 💔 $5.90$ $+4.57$ $0$ $0$ $0$ $0$
Simulations-methods 💔 $9.00$ $+7.29$ $+4$ $0$ $0$ $0$
helpers 💔 $1.69$ $+1.21$ $0$ $0$ $0$ $0$
helpers_rules 💔 $3.60$ $+2.09$ $0$ $0$ $0$ $0$
sas-results-part-1 💔 $3.70$ $+1.67$ $0$ $0$ $0$ $0$
sas-results-part-2 💔 $4.07$ $+2.34$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
Design-methods 👶 $+0.02$ h_overdose_threshold_uses_the_toxicity_threshold_of_each_rule
Design-methods 💔 $1.72$ $+1.19$ simulate_DualDesign_produces_consistent_results
Design-methods 💔 $2.44$ $+1.74$ simulate_DualDesign_produces_consistent_results_with_sentinel_patients
Design-methods 💔 $1.15$ $+1.01$ simulate_for_DesignGrouped_allows_to_stop_mono_when_combo_stops
Design-methods 💔 $1.78$ $+1.45$ simulate_for_the_class_design_returns_correct_objects
Design-methods 💔 $1.34$ $+1.00$ simulate_for_the_class_design_with_placebo_and_sentinel_patients_returns_correct_objects
Design-methods 💔 $1.32$ $+1.01$ simulate_for_the_class_design_with_placebo_returns_correct_objects
Design-methods 💔 $1.76$ $+1.32$ simulate_produces_consistent_results_with_sentinel_patients
Simulations-class 👶 $+0.02$ Simulations_validates_overdose_probabilities
Simulations-methods 👶 $+0.03$ summary_Simulations_conditions_overdose_probabilities_on_recommendations

Results for commit 5f05ad2

♻️ This comment has been updated with latest results.

Standard toxicity rules continue using the upper target boundary.
NextBestDualEndpoint now uses next_best@overdose[1], so biomarker targets such as c(200, 300) no longer force overdose probabilities to zero.
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danielinteractive merged commit 330e059 into main Sep 18, 2026
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danielinteractive deleted the 971_add_overdose_prob_to_sims branch September 18, 2026 04:12
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Add overdosing probability at the selected dose to simulation results

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