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Add BestDose dose optimization feature ported from Pmetrics_rust bestdose branch: - R/PM_bestdose.R: PM_bestdose and PM_bestdose_problem R6 classes for Bayesian dose optimization with support for concentration and AUC targets - src/rust/src/bestdose_executor.rs: Rust backend for BestDose optimization using pmcore's BestDoseProblem with ODE model support - Updated lib.rs with bestdose, bestdose_prepare, bestdose_optimize exports - Updated extendr-wrappers.R with R-side wrapper functions - Updated NAMESPACE with PM_bestdose, PM_bestdose_problem, bestdose exports - Bumped pmcore dependency from 0.21.1 to 0.22.1 (required for bestdose) - Added libloading dependency for dynamic model loading - Added bestdose example data (past, prior, target CSVs) and test script - Fixed executor.rs mutability issue for pmcore 0.22.1 compatibility
Reworked bd and bd_post R6 classes: bd_post$optimize() now returns a bd object, and bd$new() supports one-shot usage. Removed dead Rust code (bestdose(), bestdose_ode(), bestdose_analytical()). Fixed bias_weight being NULL and print() breaking with variable dose counts. Updated PMcore dep to use relative time_offset gap semantics.
- Combine clean one-shot/two-stage API with inline future=list(...) support - Add top-5 weighted plot curves, triangle dose indicators, plot() method - Fix .sim_future() dose recycling when past doses are present
…sed most of the logs for bestdose, needs more work
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Thanks for the feedback on #309. I've created this new PR, which merges into #309, to address your comment. I will work on the changes and keep this PR's description up to date as I make progress.
Original PR: #309
Triggering comment (#309 (comment)):
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