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message: 'To cite package "KWELA" in publications use:'
type: software
license: MIT
title: 'KWELA: Hierarchical Adaptive ''RT-QuIC'' Classification for Complex Matrices'
version: 1.0.0
doi: 10.32614/CRAN.package.KWELA
abstract: 'Extends ''RT-QuIC'' (Real-Time Quaking-Induced Conversion) statistical
  analysis to complex environmental matrices through hierarchical adaptive classification.
  ''KWELA'' is named after a deity of the Fore people of Papua New Guinea, among whom
  Kuru, a notable human prion disease, was identified. Implements a 6-layer architecture:
  hard gate biological constraints, per-well adaptive scoring, separation-aware combination,
  Youden-optimized cutoffs, replicate consensus, and matrix instability detection.
  Features dual-mode operation (diagnostic/research), auto-profile selection (Standard/Sensitive/Matrix-Robust),
  RAF integration for artifact detection, matrix-aware baseline correction, and multiple
  consensus rules. Methods include energy distance (Szekely and Rizzo (2013) <https://doi.org/10.1016/j.jspi.2013.03.018>),
  CRPS (Gneiting and Raftery (2007) <https://doi.org/10.1198/016214506000001437>),
  SSMD (Zhang (2007) <https://doi.org/10.1016/j.ygeno.2007.01.005>), and Jensen-Shannon
  divergence (Lin (1991) <https://doi.org/10.1109/18.61115>). This package implements
  methodology currently under peer review; please contact the author before publication
  using this approach. Development followed an iterative human-machine collaboration
  where all algorithmic design, statistical methodologies, and biological validation
  logic were conceptualized, tested, and iteratively refined by Richard A. Feiss through
  repeated cycles of running experimental data, evaluating analytical outputs, and
  selecting among candidate algorithms and approaches. AI systems (''Anthropic Claude''
  and ''OpenAI GPT'') served as coding assistants and analytical sounding boards under
  continuous human direction. The selection of statistical methods, evaluation of
  biological plausibility, and all final methodology decisions were made by the human
  author. AI systems did not independently originate algorithms, statistical approaches,
  or scientific methodologies.'
authors:
- family-names: Feiss IV
  given-names: Richard A.
  email: feiss026@umn.edu
  orcid: https://orcid.org/0009-0008-0409-6042
repository: https://rfeissiv.r-universe.dev
repository-code: https://github.com/RFeissIV/KWELA
commit: 3837d16b92e0c494d7bce607adf5bc3c2ec3b182
url: https://github.com/RFeissIV/KWELA
date-released: '2026-02-28'
contact:
- family-names: Feiss IV
  given-names: Richard A.
  email: feiss026@umn.edu
  orcid: https://orcid.org/0009-0008-0409-6042