PSRICalcSM: Plant Stress Response Index Calculator - Softmax Method

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.

Version:	1.0.0
Depends:	R (≥ 4.0.0)
Suggests:	testthat (≥ 3.0.0)
Published:	2026-02-20
DOI:	10.32614/CRAN.package.PSRICalcSM
Author:	Richard Feiss [aut, cre], University of Minnesota [cph]
Maintainer:	Richard Feiss <feiss026 at umn.edu>
BugReports:	https://github.com/RFeissIV/PSRICalcSM/issues
License:	MIT + file LICENSE
URL:	https://github.com/RFeissIV/PSRICalcSM
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	PSRICalcSM results

Documentation:

Reference manual:

PSRICalcSM.html , PSRICalcSM.pdf

Downloads:

Package source:	PSRICalcSM_1.0.0.tar.gz
Windows binaries:	r-devel: PSRICalcSM_1.0.0.zip, r-release: PSRICalcSM_1.0.0.zip, r-oldrel: PSRICalcSM_1.0.0.zip
macOS binaries:	r-release (arm64): PSRICalcSM_1.0.0.tgz, r-oldrel (arm64): PSRICalcSM_1.0.0.tgz, r-release (x86_64): PSRICalcSM_1.0.0.tgz, r-oldrel (x86_64): PSRICalcSM_1.0.0.tgz

Linking:

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