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Fix #534: Add marginal model to model outline document#594

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seabbs merged 6 commits intoepinowcast:mainfrom
seabbs-bot:issue-534-marginal-model-docs
Apr 9, 2026
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Fix #534: Add marginal model to model outline document#594
seabbs merged 6 commits intoepinowcast:mainfrom
seabbs-bot:issue-534-marginal-model-docs

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@seabbs-bot seabbs-bot commented Apr 8, 2026

This is entirely from an agent so do not review until I have pinged for review as I will do a first pass

Summary

  • Adds a new "The marginal model" section to the model guide vignette (vignettes/model.Rmd)
  • Describes how the marginal model integrates out latent variables analytically using the primarycensored package
  • Signposts to primarycensored vignettes for mathematical details

Changes

  • vignettes/model.Rmd: Added marginal model section after the latent model section, covering the shift-invariant likelihood, truncation normalisation, and aggregation advantages

Test plan

  • Verify the vignette renders correctly with pkgdown::build_article("model")
  • Check cross-references to Section 1.2 (interval censoring) resolve correctly
  • Verify LaTeX equations render properly

Closes #534

This was opened by a bot. Please ping @seabbs for any questions.

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Closes epinowcast#534. Adds a section describing the marginal model approach
which integrates out latent variables analytically using the
primarycensored package, with signposts to primarycensored vignettes
for mathematical details.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
@seabbs-bot seabbs-bot force-pushed the issue-534-marginal-model-docs branch from be99518 to 9806bfe Compare April 8, 2026 16:57
seabbs-bot and others added 5 commits April 8, 2026 17:59
Use \mathbb{P} instead of \mathrm{Pr} to match the rest of the
document, and lowercase p_{L,i}, p_{R,i} in the likelihood
denominator to match the latent model convention.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
Highlight that efficiency gains come from removing latent variables,
avoiding numerical integration with analytical solutions, and
aggregating identical observations.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
Ask users to cite Park et al. when using the latent model and
primarycensored when using the marginal model. Update README
citation section to match.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
@seabbs seabbs merged commit a8280b5 into epinowcast:main Apr 9, 2026
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Add the marginal model to the model outline document

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