Package: PSRICalcSM
Type: Package
Title: Plant Stress Response Index Calculator - Softmax Method
Version: 1.0.0
Authors@R: c(
    person("Richard", "Feiss", 
           email = "feiss026@umn.edu", 
           role = c("aut", "cre"),
           comment = c(ORCID = "0009-0008-0409-6042")),
    person("University of Minnesota", 
           role = "cph")
    )
Description: Implements the softmax aggregation method for calculating Plant 
    Stress Response Index (PSRI) from time-series germination data under 
    environmental stressors including prions, xenobiotics, osmotic stress, 
    heavy metals, and chemical contaminants. Provides zero-robust PSRI 
    computation through adaptive softmax weighting of germination components 
    (Maximum Stress-adjusted Germination, Maximum Rate of Germination, 
    complementary Mean Time to Germination, and Radicle Vigor Score), 
    eliminating the zero-collapse failure mode of the geometric mean approach 
    implemented in 'PSRICalc'. Includes perplexity-based temperature 
    parameter calibration and modular component functions for transparent 
    germination analysis. Built on the methodological foundation of the 
    Osmotic Stress Response Index (OSRI) framework developed by Walne et al. 
    (2020) <doi:10.1002/agg2.20087>. Note: 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.
License: MIT + file LICENSE
Depends: R (>= 4.0.0)
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
URL: https://github.com/RFeissIV/PSRICalcSM
BugReports: https://github.com/RFeissIV/PSRICalcSM/issues
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-02-18 15:58:06 UTC; feiss026
Author: Richard Feiss [aut, cre] (ORCID:
    <https://orcid.org/0009-0008-0409-6042>),
  University of Minnesota [cph]
Maintainer: Richard Feiss <feiss026@umn.edu>
Repository: CRAN
Date/Publication: 2026-02-20 11:30:07 UTC
Built: R 4.6.0; ; 2026-04-25 21:23:10 UTC; unix
