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