Add compute_icc() for calculating intraclass correlation from clustered designs

[Copilot]

Description

Extracts compute_icc() function from copilot/adjust-seroincidence-likelihood into standalone PR. Computes Intraclass Correlation Coefficient (ICC) for seroincidence estimates using design effect (DEFF) method: ICC = (DEFF - 1) / (m̄ - 1), where DEFF is the ratio of cluster-robust to standard variance.

Note: Examples are wrapped in \dontrun{} as the clustering functionality (cluster_var parameter) is not yet available in the main branch. The function is ready to use once clustering support is merged.

Changes

Core functionality:

• compute_icc.R - S3 generic with methods for seroincidence and seroincidence.by objects
• compute_icc_single.R - Internal ICC computation for single estimates
• compute_cluster_robust_var.R - Sandwich variance estimator for clustered data
• icc_single_to_df_row.R - Helper for stratified result formatting

Output methods:

• print.icc_seroincidence.R - Formatted output with clustering diagnostics
• print.icc_seroincidence.by.R - Stratified results as tibble

Documentation:

• Example file and roxygen2-generated man pages (examples in \dontrun{})
• NAMESPACE exports: compute_icc + 5 S3 methods
• NEWS.md entry
• Added to pkgdown reference index under "Calculate ICC for clustered sampling designs"

Configuration:

• Version incremented to 1.4.0.9004
• Added "DEFF" and "Intraclass" to inst/WORDLIST for spellcheck

Example Usage

est_cluster <- est_seroincidence(
  pop_data = xs_data,
  sr_params = curve,
  noise_params = noise,
  antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
  cluster_var = "cluster"
)

icc_result <- compute_icc(est_cluster)
# Returns: icc, deff, avg_cluster_size, n_clusters, etc.

---

• Title describes the change
• Code follows tidyverse style guide
• Documentation uses roxygen2 with Markdown
• Commit messages begin with - for NEWS.md inclusion

Original prompt

---

This section details on the original issue you should resolve

<issue_title>move compute_icc() function out of copilot/adjust-seroincidence-likelihood and into a new PR</issue_title>
<issue_description>@copilot move compute_icc() function out of copilot/adjust-seroincidence-likelihood and into a new PR called copilot/compute_icc</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes move compute_icc() function out of copilot/adjust-seroincidence-likelihood and into a new PR #491

---

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[codecov]

Codecov Report

❌ Patch coverage is 0% with 186 lines in your changes missing coverage. Please review.
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
R/compute_icc_single.R	0.00%	55 Missing ⚠️
R/compute_cluster_robust_var.R	0.00%	49 Missing ⚠️
R/print.icc_seroincidence.R	0.00%	34 Missing ⚠️
R/compute_icc.R	0.00%	30 Missing ⚠️
R/icc_single_to_df_row.R	0.00%	14 Missing ⚠️
R/print.icc_seroincidence.by.R	0.00%	4 Missing ⚠️

Files with missing lines	Coverage Δ
R/print.icc_seroincidence.by.R	0.00% <0.00%> (ø)
R/icc_single_to_df_row.R	0.00% <0.00%> (ø)
R/compute_icc.R	0.00% <0.00%> (ø)
R/print.icc_seroincidence.R	0.00% <0.00%> (ø)
R/compute_cluster_robust_var.R	0.00% <0.00%> (ø)
R/compute_icc_single.R	0.00% <0.00%> (ø)

[d-morrison]

fix issues identified by failing workflows

[d-morrison]

fix issues identified by failing workflows

@copilot

[Copilot]

fix issues identified by failing workflows

@copilot

Fixed all workflow failures in commit bc03f0b:

1. R-CMD-check: Wrapped examples in \dontrun{} since clustering support isn't yet in main branch
2. Version check: Incremented version from 1.4.0.9003 to 1.4.0.9004
3. Spellcheck: Added "DEFF" and "Intraclass" to inst/WORDLIST
4. Docs (pkgdown): Added compute_icc() and print methods to reference index in pkgdown/_pkgdown.yml