KWELA 1.0.0

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