Refactor Run_Mod.R, improve Chapter2.qmd: extract helper, fix style, and address review comments

[Copilot]

Addresses code review feedback on the Chapter 2 Kronecker model integration.

Refactoring

• Extract build_kron_priors(): Encapsulates Kronecker prior assembly (clean base priors, add Wishart hyperparameters, inject n_blocks scalar)
• Hoist common prep_priors() call: Moves shared logic outside the correlated if-else branch

Style fixes

• Format long function calls per tidyverse guide (one argument per line)
• Fix line length violations in error messages
• Add proper @seealso cross-references with bracket notation

Cleanup

• Fix typo: 'model.If' → 'model. If' in documentation
• Remove obsolete examples-run_mod_kron.R (function was merged into run_mod())

Chapter2.qmd Documentation Improvements

• Filled in missing sections: Added comprehensive list of helper functions now in the package (Step B), expanded E.3 with clear run_mod() usage explanation
• Enhanced explanations: Rewrote Wishart hyperparameters section for better understanding, clarified distinction between independence and correlated models
• Better code examples: Added side-by-side model comparison, examples for customizing hyperparameters, code for visualizing results
• Structural improvements: Clear flow from simulation → baseline → theory → implementation → examples, clarified which functions are in package vs inline code
• Mathematical precision: Specified conditions for Wishart expectation approximation, clarified conflicting fields in clean_priors()

Result

# Before: duplicated prep_priors() + manual assembly
if (!correlated) {
  priorspec <- prep_priors(max_antigens = ..., ...)
  ...
} else {
  base_priors <- prep_priors(max_antigens = ..., ...)
  base_priors <- clean_priors(base_priors)
  kron_priors <- prep_priors_multi_b(n_blocks = ...)
  B_scalar <- list(n_blocks = ...)
  priorspec <- c(base_priors, kron_priors, B_scalar)
  ...
}

# After: single prep_priors() + helper
base_priors <- prep_priors(max_antigens = ..., ...)

if (!correlated) {
  priorspec <- base_priors
  ...
} else {
  priorspec <- build_kron_priors(base_priors, n_blocks = ...)
  ...
}

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[Kwan-Jenny]

@copilot,

Could you please review the Chapter2.qmd file once more and revise it to improve clarity and structure, ensuring that it aligns with d-morrison’s feedback?

[Copilot]

@copilot,

Could you please review the Chapter2.qmd file once more and revise it to improve clarity and structure, ensuring that it aligns with d-morrison’s feedback?

I've revised Chapter2.qmd to improve clarity and structure. Changes in commit 888e930:

Major improvements:

• Filled in empty "Step B" section with list of helper functions now in the package
• Expanded "E.3" section with clear explanation of run_mod() unified interface
• Rewrote Wishart hyperparameters section for better understanding
• Improved "Putting it together" with side-by-side independence vs correlated model examples
• Added code examples for customizing hyperparameters and comparing results
• Clarified automatic vs explicit model file creation

Structure changes:

• Made it clear which functions are now in the package (not inline)
• Added better navigation between sections
• Improved mathematical notation consistency
• Added practical usage examples throughout

The document now flows more logically from simulation → independence model → correlated model theory → unified interface → complete examples.