Reuse generation-time support grid across Rt Newton updates

[ajh-oai]

Description

This PR closes #1273.

This is a focused Stan performance change in the reproduction-number to growth-rate conversion path. R_to_r() now constructs the generation-time support grid once per call and reuses it both for the mean generation-time calculation and for each Newton update, instead of rebuilding linspaced_vector(...) inside every iteration.

The existing 3-argument R_to_r_newton_step() entry point is retained as a thin wrapper so current test-facing usage remains unchanged. This stays separate from #1274, which is working on other Stan hot paths.

Benchmarks

I benchmarked the change locally with paired CmdStan runs on the package's infection-estimation workflow (example_confirmed[1:60], fixed generation time, standard incubation/reporting delays, 2 chains, 250 warmup + 250 sampling draws, seeds 101/202/303/404, order balanced across baseline and branch runs).

Metric	Baseline mean	Branch mean	Mean paired change
infections Stan profile block	2.6146 s	2.5102 s	-3.97%
CmdStan total runtime	8.9775 s	8.9130 s	-0.70%

All four paired runs improved in the profiled infections block (-3.63% to -4.61%) and in total CmdStan runtime (-0.25% to -1.13%). The repository's Stan benchmark workflow should also post its standard benchmark comparison comment for this PR.

Validation

• git diff --check
• Local paired CmdStan benchmark described above; both baseline and branch models compiled and sampled successfully.

AI assistance disclosure

Codex helped identify the optimization seam, benchmark the candidate changes, and prepare this PR. I reviewed the final patch and benchmark results before submission.

Initial submission checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have tested my changes locally (using devtools::test() and devtools::check()).
• I have added or updated unit tests where necessary.
• I have updated the documentation if required and rebuilt docs if yes (using devtools::document()).
• I have followed the established coding standards (and checked using lintr::lint_package()).
• I have added a news item linked to this PR.

After the initial Pull Request

• I have reviewed Checks for this PR and addressed any issues as far as I am able.

Summary by CodeRabbit

Release Notes

• Refactor
  • Optimised internal computation logic to reduce redundant calculations and improve processing efficiency.

[coderabbitai]

Walkthrough

The PR refactors R_to_r_newton_step to support precomputed zero_series through a new 4-argument overload, whilst the existing 3-argument version becomes a wrapper. The calling function R_to_r is updated to compute zero_series once and reuse it across multiple operations, eliminating redundant vector construction during iterative Newton updates.

Changes

Newton-step precomputation optimisation

Layer / File(s)	Summary
Precomputed zero_series in Newton iterations inst/stan/functions/rt.stan	New 4-argument R_to_r_newton_step overload accepts precomputed zero_series; existing 3-argument version refactored to wrapper that constructs zero_series and delegates to the new overload. R_to_r updated to compute zero_series once per call and reuse it for mean_gt computation and Newton iteration loop instead of recomputing inside each iteration.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: reusing the generation-time support grid across Newton updates instead of rebuilding it each iteration.
Linked Issues check	✅ Passed	The pull request implements the objective from #1273 by identifying and implementing a micro-optimization that reduces vector construction overhead in iterative Stan code, improving runtime performance.
Out of Scope Changes check	✅ Passed	All changes are directly scoped to the R_to_r() and R_to_r_newton_step() functions in the Stan implementation, addressing the stated performance optimisation objective without introducing unrelated modifications.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

🧹 Nitpick comments (1)

inst/stan/functions/rt.stan (1)

84-100: ⚡ Quick win

Document the zero_series parameter.

The docstring should document all parameters of the function it precedes. Add an @param entry for zero_series to describe its purpose (the precomputed index sequence [0, 1, ..., len-1]).

📝 Suggested documentation addition

 * `@param` R Reproduction number
 * `@param` r Current estimate of the growth rate
 * `@param` pmf Generation time probability mass function (first index: 0)
+ * `@param` zero_series Precomputed index sequence (0, 1, ..., len-1) for weighted calculations
 * `@return` The Newton step for updating r

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@inst/stan/functions/rt.stan` around lines 84 - 100, Add a missing `@param` doc
for the zero_series argument in the rt_from_R Newton-step function's docstring:
describe zero_series as the precomputed index sequence (0, 1, ..., len-1) used
to align pmf and lagging terms in the calculation, and note its expected
type/length relative to pmf; update the function comment block that contains the
other `@param` entries (R, r, pmf) to include this new `@param` for zero_series so
all parameters are documented.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Nitpick comments:
In `@inst/stan/functions/rt.stan`:
- Around line 84-100: Add a missing `@param` doc for the zero_series argument in
the rt_from_R Newton-step function's docstring: describe zero_series as the
precomputed index sequence (0, 1, ..., len-1) used to align pmf and lagging
terms in the calculation, and note its expected type/length relative to pmf;
update the function comment block that contains the other `@param` entries (R, r,
pmf) to include this new `@param` for zero_series so all parameters are
documented.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 4c34eb22-cd8a-484b-9998-0c140924f8c9

📥 Commits

Reviewing files that changed from the base of the PR and between 4e30598 and 9eac792.

📒 Files selected for processing (1)

• inst/stan/functions/rt.stan

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 187de36 is merged into main:

• ✔️default: 23s -> 24s [-4.43%, +12.94%]
• ✔️no_delays: 25.8s -> 25.6s [-8.69%, +7.03%]
• ✔️random_walk: 22s -> 17.9s [-169.5%, +132.35%]
• ✔️stationary: 12.3s -> 13.8s [-1.31%, +26.07%]
• ✔️uncertain: 1.16m -> 1.15m [-9.18%, +8.08%]
  Further explanation regarding interpretation and methodology can be found in the documentation.

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 9ae081f is merged into main:

• ✔️default: 23.5s -> 33.1s [-54.31%, +135.6%]
• ✔️no_delays: 24.2s -> 23.6s [-9.68%, +5.05%]
• ✔️random_walk: 22.6s -> 9.52s [-131.52%, +15.59%]
• ✔️stationary: 11.9s -> 12.4s [-9.98%, +17.63%]
• ✔️uncertain: 1.09m -> 1.12m [-13.19%, +17.96%]
  Further explanation regarding interpretation and methodology can be found in the documentation.