Add Chapter 2 Documentation: Extending Hierarchical Model to Correlated Biomarkers #129
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Codecov Report✅ All modified and coverable lines are covered by tests. |
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📖 https://ucd-serg.github.io/serodynamics/preview/pr129 |
- Added entry to NEWS.md for Chapter 2 documentation on correlated biomarker model - Added 'mathrm' to WORDLIST to resolve spellcheck error
…RG/serodynamics into correlated-biomarkers-qmd
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Hi @d-morrison — as we talked about in our last meeting, could you review the notation here and share any overall feedback on this |
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| ## New features | ||
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| * Added Chapter 2 documentation on correlated biomarker model (#129) |
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| * Added Chapter 2 documentation on correlated biomarker model (#129) | |
| * Added documentation on correlated biomarker model (#129) |
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(@Kwan-Jenny I'm taking a look at this PR this afternoon and posted this edit early by accident; you can ignore it until I finish the full review)
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@Kwan-Jenny coming along! see notes in docx version on Teams
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| ## Overview | ||
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| - Incorporates feedback from Dr. Morrison and Dr. Aiemjoy\ |
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remove progress notes from document; comments like this should go into the PR description on Github instead
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| ## New features | ||
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| * Added Chapter 2 documentation on correlated biomarker model (#129) |
There was a problem hiding this comment.
(@Kwan-Jenny I'm taking a look at this PR this afternoon and posted this edit early by accident; you can ignore it until I finish the full review)
This PR adds a new Quarto (
.qmd) presentation file titled "Extending the Hierarchical Model for Antibody Kinetics" to theserodynamicsdocumentation.Key features:
Model Focus:
Incorporates feedback from Dr. Morrison and Dr. Aiemjoy to focus exclusively on the Teunis (2016) within-host antibody kinetics model.
Clarifies model dynamics, parameter definitions, and the distinction between estimated vs. derived quantities.
Updates notation for consistency across project documentation.
Covariance Structure Extension:
Reviews current block-diagonal covariance assumption (
Σ_K ⊗ I_J) that treats biomarkers as independent.Proposes extended model with full biomarker covariance matrix (
Σ_K ⊗ Σ_J) to capture correlation across antigen–isotype combinations.Includes Kronecker product examples and expanded matrix forms for clarity.
Simulation & Validation Plan:
Outlines steps to simulate individuals with correlated biomarkers.
Compares independence model (
I_J) vs. correlated model (Σ_J) via DIC/WAIC and posterior predictive checks.Forms the basis for Chapter 2’s methodological framework and simulation study.
Next Steps:
Implement full
Σ_Jprior in JAGS.Run simulation experiments to test model recovery of known correlation.
Apply extended model to Shigella longitudinal dataset once validated.
This
.qmdfile will serve as both a reproducible Beamer slide deck and internal reference for model development in Chapter 2.