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PSRICalcSM  

Plant Stress Response Index Calculator - Softmax Method
View on CRAN: Click here


Download and install PSRICalcSM package within the R console
Install from CRAN:
install.packages("PSRICalcSM")

Install from Github:
library("remotes")
install_github("cran/PSRICalcSM")

Install by package version:
library("remotes")
install_version("PSRICalcSM", "1.0.0")



Attach the package and use:
library("PSRICalcSM")
Maintained by
Richard Feiss
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-02-20
Latest Update: 2026-02-20
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.
How to cite:
Richard Feiss (2026). PSRICalcSM: Plant Stress Response Index Calculator - Softmax Method. R package version 1.0.0, https://cran.r-project.org/web/packages/PSRICalcSM. Accessed 28 Jul. 2026.
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Functions, R codes and Examples using the PSRICalcSM R package
Full PSRICalcSM package functions and examples
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