clarify jags code

[d-morrison]

Refactors y1 calculation in JAGS code by introducing change_y intermediate variable.

Shouldn't affect numerical results, as shown by the run_mod() snapshot tests.

[Copilot]

Pull request overview

This PR improves the readability and maintainability of the JAGS model code by refactoring the calculation of y1 to use an intermediate variable and moving inline comments to separate lines for better clarity.

• Extracted the change_y intermediate variable from the inline y1 calculation
• Moved the explanatory comment about par[,,2] to a separate line
• Improved code alignment for better readability

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
inst/extdata/model.jags	Refactored y1 calculation by introducing change_y intermediate variable and improved comment placement
DESCRIPTION	Version bump from 0.0.0.9044 to 0.0.0.9045 to reflect the code clarification

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

[claude]

Claude finished @d-morrison's task in 1m 28s —— View job

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Code Review — clarify-jags

• Gather context and read changed files
• Review CLAUDE.md for repo guidelines (none found)
• Analyze the diff and provide feedback
• Post final review

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This is a clean, focused refactoring of inst/extdata/model.jags. Here's my assessment:

What's Good

Introduction of change_y — Naming the intermediate value exp(par[subj,cur_antigen_iso,2]) as change_y is a clear improvement. It makes the y1 assignment self-documenting:

# Before:
y1[subj,cur_antigen_iso] <- y0[subj,cur_antigen_iso] + exp(par[subj,cur_antigen_iso,2])

# After:
change_y[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,2])
y1[subj,cur_antigen_iso]       <- y0[subj,cur_antigen_iso] + change_y[subj,cur_antigen_iso]

The name change_y is semantically accurate (it is the change in antibody level from y₀ to y₁), and the formula for y1 now reads as plain math: y1 = y0 + change_y.

Alignment improvement — Aligning all five <- operators at the same column makes the block easier to scan visually.

JAGS semantics — Introducing deterministic nodes doesn't affect the sampling algorithm, so numerical equivalence with the snapshot tests is expected and appropriate.

Minor Observation: Comment Wording

The inline comment changed from:

# par[,,2] must be log(y1-y0)

to:

# par[,,2] is log(y1-y0):

The original "must be" subtly conveyed a parameterization constraint — that this is not an arbitrary choice but a deliberate reparameterization to ensure positivity of change_y. The new "is" is more neutral. This is a very minor point; both readings are mathematically correct. If you want to preserve that nuance, consider:

# par[,,2] is log(y1-y0), ensuring change_y > 0:

Copilot also suggested a more verbose form ("represents log(change in y from baseline (y0) to peak (y1))") but I think the current short form is fine given that change_y is now named directly below the comment.

Summary

The refactoring achieves its goal: the y1 line is now more readable without any change in model semantics. The PR is well-scoped and the snapshot test coverage backs up the claim of numerical equivalence. Ready to merge.