Changes in version 1.0.0 (2026-02-28)                  

Initial CRAN Release

6-Layer Hierarchical Architecture

  - Layer 1: Hard Gate - Biological constraint filter with stochastic
    rescue (research mode only)
  - Layer 2: Per-Well Scoring - Profile-dependent adaptive transforms
  - Layer 3: Adaptive Combination - Separation-aware score combiner
  - Layer 4: Adaptive Cutoff - Youden-optimized threshold per
    plate/group
  - Layer 5: Replicate Consensus - Treatment-level classification
  - Layer 6: Instability Detection - Matrix interference override

Dual-Mode Operation

  - mode = "diagnostic" (default): Deterministic classification from
    TTT/MP/RAF evidence only. No stochastic rescue, no stochastic score
    blending.
  - mode = "research": Full adaptive architecture with stochastic rescue
    and distributional scoring.

Instability Detection

  - compute_instability_flags(): 6 deterministic metrics per treatment
    (Fano deviation, crossing variability, Wasserstein/Energy distance
    from both controls, TTT dispersion, RAF-MP inconsistency)
  - Configurable strictness: "moderate" (2+ flags), "strict" (1+),
    "lenient" (3+)
  - Override: INCONCLUSIVE_MATRIX_EFFECT when minimum flags exceeded

Auto-Profile Selection

  - profile = "auto" selects based on Cohen's d separation quality

Group-Aware Mixed-Assay Support

  - Per-group PC/NC distributions, stats, thresholds, and RAF parameters
  - Enables mixed RT-QuIC + Nano-QuIC under single kwela_analyze() call

RAF Integration

  - Artifact detection via RAF/MP ratio analysis
  - RAF concordance scoring for quality assessment

Replicate Consensus Rules

  - "strict", "majority" (default), "flexible", "threshold"

Stochastic Metrics Library

  - Energy distance, Wasserstein distance, Jensen-Shannon divergence
  - CRPS, Dawid-Sebastiani, interval score
  - SSMD, Fano factor, coefficient of variation
  - Cohen's d separation assessment