Fix date-dimension mismatch in forecast_infections

[sbfnk-bot]

Description

This PR closes #1318.

Fixed a bug in forecast_infections() where calling summary() after modifying estimates$args caused a date-dimension mismatch when extending the R trajectory beyond the original observation period. The fix moves the summary() call to before the args modification block.

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

• Bug Fixes
  • Fixed a date-dimension mismatch that occurred when extending forecasts beyond the original observation period. The correction ensures date calculations use the original fit dimensions rather than modified parameters, eliminating alignment issues in extended forecast trajectories and improving forecast reliability.

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Walkthrough

This PR addresses a date-dimension mismatch bug in forecast_infections() where dates were calculated using modified arguments instead of original fit dimensions. The fix involves moving the summary parameter computation to an earlier stage in simulate_infections.R, prior to time-related argument adjustments, ensuring dates align correctly with extracted parameters.

Changes

Cohort / File(s)	Summary
Documentation Update NEWS.md	Adds bug fixes section documenting the resolution of a date-dimension mismatch in forecast_infections() where the summary call used modified arguments instead of original fit dimensions.
Parameter Summary Ordering R/simulate_infections.R	Relocates the computation of summary(estimates, type = "parameters") to execute before time-related arguments are redefined, ensuring dates extraction occurs with the correct parameter dimensions and preventing length mismatches.

Possibly related PRs

• Fix plot issue: summary(type='parameters') now returns all dates #1169: Addresses the same root issue of when summary(type = "parameters") extracts and coerces dates, repositioning date extraction to occur before summary adjustments.
• Fix forecast_infections test failures from reduced fixture size #1207: Fixes the forecast_infections date/R-length mismatch by aligning R summaries and dates with the original fit before extending the R trajectory.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Fix date-dimension mismatch in forecast_infections' directly and accurately summarises the main change: fixing a specific bug in the forecast_infections function.
Linked Issues check	✅ Passed	The pull request addresses the date-dimension mismatch issue by moving summary() computation before args modification in R/simulate_infections.R, ensuring dates are calculated from original fit dimensions as required by issue #1318.
Out of Scope Changes check	✅ Passed	All changes are directly scoped to fixing the date-dimension mismatch: NEWS.md documents the bug fix and R/simulate_infections.R implements the fix by repositioning the summary() call.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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🧹 Nitpick comments (1)

NEWS.md (1)

5-5: Start the entry with the action verb "Fixed" per repository conventions.

The coding guidelines require NEWS.md entries to start with action verbs ('Added', 'Fixed', 'Updated', 'Changed'). Consider rephrasing for consistency with other entries in the file.

📝 Suggested rewording

-- A bug was fixed in `forecast_infections()` where the summary call to extract dates was using modified args instead of the original fit dimensions, causing a date-dimension mismatch when extending the R trajectory beyond the original observation period.
+- Fixed a bug in `forecast_infections()` where the summary call to extract dates was using modified args instead of the original fit dimensions, causing a date-dimension mismatch when extending the R trajectory beyond the original observation period.

As per coding guidelines: "Start with action verbs: 'Added', 'Fixed', 'Updated', 'Changed'"

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@NEWS.md` at line 5, Update the NEWS.md entry to begin with the action verb
"Fixed" to match repository conventions: rephrase the line so it starts "Fixed"
and then describes the bug in forecast_infections(), e.g. "Fixed a bug in
forecast_infections() where the summary call to extract dates used modified args
instead of the original fit dimensions, causing a date-dimension mismatch when
extending the R trajectory beyond the original observation period." Ensure the
entry references forecast_infections() and retains the same technical detail.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@NEWS.md`:
- Line 5: Update the NEWS.md entry to begin with the action verb "Fixed" to
match repository conventions: rephrase the line so it starts "Fixed" and then
describes the bug in forecast_infections(), e.g. "Fixed a bug in
forecast_infections() where the summary call to extract dates used modified args
instead of the original fit dimensions, causing a date-dimension mismatch when
extending the R trajectory beyond the original observation period." Ensure the
entry references forecast_infections() and retains the same technical detail.

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📥 Commits

Reviewing files that changed from the base of the PR and between 8454b07 and 26128fb.

📒 Files selected for processing (2)

• NEWS.md
• R/simulate_infections.R

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[seabbs]

There needs to be evidence that this works. I suggest adding a unit test that would fail on main and now passes that replicates the usage in the synthetic example case. It would be nice to run the synthetic generator here as well (or show evidence if this was done)

[sbfnk-bot]

Thanks for the review! I've addressed the feedback:

1. Fixed NEWS.md to start with "Fixed" per coding guidelines
2. Added a unit test (test-forecast-infections.R) that replicates the failing scenario - extending R trajectory beyond the original observation period

Running the synthetic validation locally now to provide evidence.

[sbfnk-bot]

Synthetic validation evidence:

Ran the core rt.R scenario locally with the fix:

Initial fit complete
forecast_infections with extended R: SUCCESS
get_samples: SUCCESS
Extracted sim_cases, nrow: 140 

Synthetic validation core steps completed successfully!

This confirms the fix works for the exact scenario that was failing (140-element R trajectory on a 100-day fit).

[sbfnk-bot]

Triggered the synthetic validation workflow on this branch: https://github.com/epiforecasts/EpiNow2/actions/runs/22853331016

This should pass now (previous runs were failing with the date-dimension mismatch bug this PR fixes).