Changes in version 1.0.1                        

Documentation

  - ?synergyMixR now answers: a package help page gives one paragraph on
    what the package is for, the main entry points grouped by task, and
    where to go next.
  - Runnable @examples added or corrected across 158 help pages. Each
    runs offline in seconds, writes nothing outside tempdir(), and is
    executed by R CMD check; anything needing a device, a download or an
    optional backend is fenced with the reason stated.
  - The README's quick start runs as written: it attaches the package,
    builds its own inputs, and uses only hard dependencies.

Bug fixes

  - select_optimal_K_r_mfa_twostage() and
    select_optimal_K_r_mpca_twostage() failed on their own defaults --
    criterion = "ICL" with icl_temperature = 2 -- because
    apply_temperature() is referenced but defined nowhere in the
    package, with globalVariables() keeping R CMD check quiet about it.
    The call sites now check, compute ICL from untempered
    responsibilities, which is ICL at T = 1, and warn that the tempering
    did not happen rather than inventing a transform.

                        Changes in version 1.0.0                        

Initial Public Release

  - Core mixture model implementations: MPCA (Mixture of Probabilistic
    Component Analyzers) and MFA (Mixture of Factor Analyzers)
  - EM algorithm implementations in C++ via Rcpp/RcppArmadillo for
    performance
  - Soft EM with responsibility-weighted updates
  - K-means based initialization for cluster assignments
  - Comprehensive model selection tools:
      - BIC-based grid search over (K, r)
      - ICL (Integrated Complete-data Likelihood) with temperature
        parameter
      - Cross-Validation with 1-SE rule
      - Bootstrap stability selection for K
      - Two-stage selection for stability
  - r-selection framework: global, clusterwise, and hybrid modes
  - Rotation and flip utilities for synergy alignment
  - Complete EMG preprocessing pipeline (DC removal, bandpass, notch,
    rectification, envelope, normalization)
  - Visualization functions for muscle synergy analysis with unified
    ggplot2 theme
  - Simulation utilities for generating mixture data with optional AR(1)
    temporal noise
  - HPC parallel computation support via future/PBS
  - Comprehensive testing infrastructure with testthat
  - Quickstart vignette and package documentation