926: Implement backfill cohorts simulations#927
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… `response` information for patients
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Pull request overview
This PR implements backfill cohort simulations for phase I dose-escalation studies, addressing issue #926. It introduces comprehensive functionality for managing backfill cohorts including new classes for opening rules, recruitment strategies, and cohort management.
Changes:
- Added new
Backfill,Opening, andRecruitmentclass hierarchies for managing backfill cohorts - Extended
Dataclass withbackfilledandresponseslots to track patient backfill status and efficacy responses - Enhanced
Designclass with backfill support and updated simulation methods - Added
CohortSizeRandomfor random cohort sizes and extendedStoppingPatientsNearDosewith backfill exclusion option
Reviewed changes
Copilot reviewed 123 out of 168 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| vignettes/vignettes.bib | Added citation for Barnett et al. 2023 backfilling paper |
| tests/testthat/test-*.R | Comprehensive test coverage for new backfill functionality |
| R/Backfill-*.R | New classes and methods for backfill cohort management |
| R/Data-*.R | Extended Data class with backfill and response tracking |
| R/Design-*.R | Integration of backfill into design and simulation workflows |
| R/Simulations-*.R | Added backfill statistics to simulation summaries |
| man/*.Rd | Documentation for all new classes and methods |
| examples/*.R | Examples demonstrating backfill usage |
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…mPack into danielinteractive/issue926
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@danielinteractive The URL only exist after merge, that's why the URL check failed. You can comment out the url for now to pass the check and make the url available in main and after merge have another commit to uncomment the url. |
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@danielinteractive I checked your changes. It might be easier to merge my new PR first: #931 Since you need anyway to get rid of URL check error first. If my PR get merged first, I think only additional trouble for you is to resolve conflict in DESCRIPTION and/or NAMESPACE |
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@pengguanya thanks yeah I will see about the order, no worries |
closes #926