serocalculator 1.4.1

Bug fixes

• load_noise_params() and load_sr_params() now fail gracefully with informative messages when internet resources are unavailable, complying with CRAN policy (#505)
• Added Version Crosswalk article to pkgdown website to help users migrate code from v1.3.0 to v1.4.0
  • Provides clear tables comparing old and new function names
  • Includes code examples showing how to update existing code
  • Accessible as a prominent tab in the website navigation

New features

• Added cluster_var and stratum_var parameters to est_seroincidence() and
  est_seroincidence_by() to support cluster-robust standard error estimation.
  When cluster_var is specified, summary.seroincidence() automatically computes
  cluster-robust (sandwich) variance estimates to account for within-cluster
  correlation in clustered sampling designs such as household or school-based surveys.
• cluster_var parameter now accepts multiple variables (e.g., c("school", "classroom"))
  for multi-level clustered sampling designs. Cluster-robust standard errors will account
  for all specified clustering levels.

Bug fixes

• Fixed column naming issue in summary.seroincidence() where cluster-robust standard
  errors caused [] notation in column names (SE[,1] instead of SE).
• Added se_type column to summary.seroincidence() output to clearly indicate whether
  "standard" or "cluster-robust" standard errors are being used.
• Fixed est_seroincidence_by() to properly pass cluster and stratum variables through
  to stratified analyses. Previously, these variables were dropped during data stratification,
  causing errors when trying to use clustering with est_seroincidence_by().
• Fixed errors coming from parallel processing in examples flagged by CRAN checks using \donttest

Code organization

• Refactored clustering-related code following package organization policies:
  • Moved .compute_cluster_robust_var() to R/compute_cluster_robust_var.R
  • Each function now in its own file for better maintainability and git history
• Updated copilot-instructions.md with code organization policies

Dependencies

• Replaced ggpubr with patchwork for arranging multi-panel plots,
  removing the indirect ggrepel transitive dependency.