Fix truncation PMF vector dimension mismatch in estimate_secondary.stan

[sbfnk]

Description

This PR closes #1181.

The trunc_rev_cmf vector in estimate_secondary.stan was declared with dimension delay_type_max[trunc_id] but the get_delay_rev_pmf() function call requests delay_type_max[trunc_id] + 1 elements, causing a dimension mismatch.

This fix aligns estimate_secondary.stan with the four other Stan files that correctly include + 1 in both the declaration and function call:

• estimate_infections.stan
• simulate_infections.stan
• simulate_secondary.stan
• estimate_truncation.stan

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.

🤖 Generated with Claude Code

Summary by CodeRabbit

Release Notes

• Bug Fixes
  • Fixed incorrect dimension declaration in truncation delay calculations that was causing a mismatch when retrieving delay distributions. The delay probability mass function vector now correctly extends to accommodate all required bins in the truncation pathway.

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[coderabbitai]

Walkthrough

A dimension mismatch bug in the truncation pathway of estimate_secondary.stan is fixed by updating the trunc_rev_cmf vector declaration to include + 1, aligning with the get_delay_rev_pmf() function call and matching the pattern used in other Stan files.

Changes

Cohort / File(s)	Summary
Dimension mismatch fix in truncation kernel NEWS.md, inst/stan/estimate_secondary.stan	Updated trunc_rev_cmf vector declaration from delay_type_max[delay_id_truncation] to delay_type_max[delay_id_truncation] + 1 to match the len argument passed to get_delay_rev_pmf(), resolving a dimension mismatch. Added corresponding bug fix entry to NEWS.md.

Suggested reviewers

• seabbs

Pre-merge checks and finishing touches

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately summarises the main change: fixing a dimension mismatch in the truncation PMF vector in estimate_secondary.stan file.
Linked Issues check	✅ Passed	The PR fulfils all coding requirements from issue #1181: the trunc_rev_cmf vector declaration now includes +1 to match the get_delay_rev_pmf function call, aligning with other Stan files.
Out of Scope Changes check	✅ Passed	All changes are within scope: the PR updates estimate_secondary.stan to fix the dimension mismatch and adds a NEWS.md entry documenting the bug fix.
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.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/1181-trunc-rev-cmf-dimension

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[github-actions]

Thank you for your contribution sbfnk 🚀! Your synthetic_recovery markdown is ready for download 👉 here 👈!
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[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if f2aa04a is merged into main:
Further explanation regarding interpretation and methodology can be found in the documentation.