Changelog

Source: NEWS.md

mitey 0.3.1

New Features

• Convenience plotting function - Added plot_si_fit_result() which accepts si_estim() output directly, handling weight aggregation automatically for both normal and gamma distributions

Bug Fixes

• Fixed logical operator in weighted_var() (| changed to || for scalar comparison)
• Fixed inverted denominator formula in weighted_var() documentation
• Added defensive guards in weighted_var() for degenerate inputs (fewer than 2 values, zero weights)
• Fixed na.rm handling in weighted_var() to also filter NA weights
• Removed unreachable dead code in calculate_si_probability_matrix()
• Fixed ggplot2 deprecation warning (size changed to linewidth in plot_si_fit())
• Fixed ggplot_build() type check in tests for newer ggplot2 versions
• Added match.arg() validation for dist parameter in integrate_components_wrapper()

API Changes

• Reduced exported functions from 18 to 5. Internal helper functions (f0, flower, fupper, f_norm, f_gam, conv_tri_dist, integrate_component, integrate_components_wrapper, wt_loglik, weighted_var, calculate_si_probability_matrix, create_day_diff_matrix, calculate_truncation_correction) are now marked as internal. They remain accessible via mitey::: if needed.

Documentation

• Fixed incomplete @param r documentation in conv_tri_dist()
• Added explicit Author and Maintainer fields to DESCRIPTION for R 4.5.2 compatibility
• Updated .Rbuildignore to exclude .DS_Store, .Rhistory, ..Rcheck, and .claude directories

mitey 0.3.0

New Features

• Multiple restarts for EM algorithm - Added n_starts parameter to si_estim() to run the EM algorithm from multiple starting points and select the best result based on log-likelihood. This helps avoid local optima when initial values are far from the true parameters (fixes #7)

• Convergence diagnostics - Added tol parameter to si_estim() for early stopping when parameters stabilize. Returns converged and iterations in output

• Log-likelihood output - si_estim() now returns loglik for model comparison

• CITATION file - Added proper citation information with Zenodo DOI and methodology paper reference

Improvements

• Expanded test coverage with new tests for generate_synthetic_epidemic(), plot_si_fit(), convergence diagnostics, and multiple restarts
• Updated R version requirement to R >= 4.0.0
• Fixed dependency table in README (ggplot2 is required, brms is suggested)
• Added codecov integration for test coverage reporting

mitey 0.2.0

CRAN release: 2025-09-02

• CRAN release - mitey is now available on CRAN!
• Updated function names for consistency (rt_estim() → wallinga_lipsitch())
• Enhanced documentation and examples
  
• Improved package metadata and CRAN compliance
• All features from 0.1.0 maintained with refinements

mitey 0.1.0

• Initial release
• Implements Vink et al. (2014) method for serial interval estimation (si_estim())
• Implements Wallinga & Lipsitch (2007) method for time-varying reproduction number estimation (rt_estim(), rt_estim_w_boot())
• Includes comprehensive validation against historical datasets
• Supports both Normal and Gamma serial interval distributions
• Provides bootstrap confidence intervals and visualization functions
• Developed to support epidemiological analysis in Ainslie et al. (2025)
• Complete documentation with four vignettes demonstrating usage and validation