Chapter 1 manuscript: “Background & Significance” (QMD) — initial draft for review#7
Chapter 1 manuscript: “Background & Significance” (QMD) — initial draft for review#7Kwan-Jenny wants to merge 16 commits intomainfrom
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I did a quick skim this morning; looks great!! I just made a couple of small formatting requests.
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Coming along! Some to dos to start on while I take a closer look over the next few days:
- respond to all unresolved conversations:
- resolve the spellcheck errors
- update the docx on sharepoint
The rendered Word version (Chapter1.docx) and (Chapter1-Methods.docx) are available on SharePoint |
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Hi @d-morrison, The updated Word version (Chapter1.docx) is available on SharePoint |
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Pull request overview
This PR introduces the Chapter 1 manuscript "Modeling Antibody Kinetics Following Shigella Infection Using a Two-Phase Bayesian Hierarchical Framework" as a standalone Quarto document for advisor review and change tracking via GitHub. The manuscript provides background and significance on serodynamics modeling, covering immunological foundations, statistical frameworks, and the rationale for applying Bayesian hierarchical models to characterize Shigella antibody dynamics.
Key Changes
- Adds a comprehensive Chapter 1 manuscript with full metadata, abstract, and references
- Implements Quarto configuration for multi-format output (PDF, Word, HTML)
- Includes 85 new domain-specific terms in the spell-check wordlist
Reviewed changes
Copilot reviewed 7 out of 8 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/articles/Chapter1.qmd | Main manuscript file containing background, methods, and appendices for Shigella antibody kinetics modeling |
| vignettes/articles/references_chapter1.bib | Bibliography file with 33 references supporting the manuscript |
| vignettes/articles/styles/epidemics.csl | Citation Style Language file for Epidemics journal formatting |
| vignettes/articles/Chapter1.docx | Rendered Word document output (binary file) |
| _quarto.yml | Updated Quarto configuration with bibliography, CSL, and multi-format rendering settings |
| inst/WORDLIST | Added 85 domain-specific technical terms for spell-checking |
| NEWS.md | Updated changelog documenting the new Chapter 1 vignette |
| DESCRIPTION | Version bump to 0.0.0.9005 and RoxygenNote update |
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| where $\mu$ denotes the antibody production rate during the rise phase, $\alpha$ is the decay rate, and $\rho$ controls the shape of antibody waning. |
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The variable name uses Greek mu symbol (μ) inconsistently. In line 216, the rise rate parameter is defined as "mu_y", but in line 298, it's referred to as just "mu" (without the subscript y). This inconsistency should be corrected to ensure clarity - either use "mu_y" throughout or clarify the distinction between "mu" and "mu_y".
| where $\mu$ denotes the antibody production rate during the rise phase, $\alpha$ is the decay rate, and $\rho$ controls the shape of antibody waning. | |
| where $\mu_y$ denotes the antibody production rate during the rise phase, $\alpha$ is the decay rate, and $\rho$ controls the shape of antibody waning. |
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I think I need to clarify the difference between mu and mu_y somewhere in the manuscript.
What’s in this PR
Adds the standalone Chapter 1 manuscript as a Quarto file:
vignettes/articles/Chapter1.qmdIncludes full metadata (title, abstract, affiliations), references (
references_chapter1.bib), and Epidemics CSL.Content covers: Overview & Significance, Immunological Foundations, Modeling Frameworks & Serodynamics, and Gaps & Rationale.
Why
How to review