Revise Chapter 2 documentation: fix notation conflicts and clarify model structure

[Copilot]

Addressed technical review feedback on antibody kinetics model documentation. Primary issues: notation collision between statistical parameters and kinetic rates, unclear model relationships, and ambiguous distributional assumptions.

Notation standardization

• Growth/decay rates: μ_y → γ_y, μ_b → γ_b (antibody production, pathogen replication)
• Clearance rate: γ → κ (eliminates conflict with gamma notation)
• Applied consistently across all equations, tables, and ODE systems

Model structure clarification

Before: Comparison table suggesting Teunis (2016) vs serodynamics were different models with statements about "simplifications"

After: Explicit statement that models are structurally identical; provided notation mapping table only

Component	Teunis (2016)	serodynamics
Antibody production rate	μ	γ_y
Pathogen replication	μ₀	γ_b
Clearance rate	c	κ

Distributional assumptions

Separated parameter sets to clarify where Gaussian priors apply:

• Serokinetic parameters (7D, untransformed): y_0, b_0, γ_b, γ_y, κ, α, ρ — no Gaussian assumption
• Serodynamic parameters (5D, log-transformed): log(y_0), log(y_1-y_0), log(t_1), log(α), log(ρ-1) — Gaussian(μ_j, Σ_{P,j})

Added explicit note distinguishing where transformation enables Gaussian modeling of inherently positive/bounded kinetic parameters.

Minor

• Removed in-document progress notes (moved to PR description)
• Updated NEWS.md entry per style guide

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[Kwan-Jenny]

@copilot,

Based on the changes and revisions you’ve made in this PR, I’d like to see a preview build, similar to
https://ucdavis.github.io/serodynamics/preview/pr187/.

[Copilot]

@copilot,

Based on the changes and revisions you’ve made in this PR, I’d like to see a preview build, similar to
...

The automatic preview build doesn't trigger for this PR because it's a stacked PR with base branch correlated-biomarkers-qmd, and the pkgdown workflow only runs for PRs to main.

Options to get a preview:

1. Wait for the parent PR: Once PR Add Chapter 2 Documentation: Extending Hierarchical Model to Correlated Biomarkers #129 (the parent correlated-biomarkers-qmd branch) is merged to main, you can create a new PR from this branch to main, which will automatically generate a preview.

2. Local preview: Build the pkgdown site locally:

   pkgdown::build_site()

   Then open docs/index.html in your browser.

3. Manual workflow trigger: A maintainer with write access can manually trigger the pkgdown workflow via GitHub Actions UI, though this requires additional setup for PR preview mode.

The changes to vignettes/articles/chapter2_correlated_biomarkers.qmd will render correctly once deployed - the document successfully renders with Quarto as verified in the previous work.