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PSRICalc — Plant Stress Response Index Calculator

Direct PSRI Calculation from Germination Data

Author: Richard A. Feiss
Version: 1.0.0
License: MIT
Institution: Minnesota Center for Prion Research and Outreach (MNPRO), University of Minnesota

Overview

PSRICalc provides clean, direct calculation of Plant Stress Response Index (PSRI) values from time-series germination data with optional radicle vigor integration. Built on the methodological foundation of the Osmotic Stress Response Index (OSRI) framework developed by Walne et al. (2020), PSRICalc offers a simplified, transparent approach suitable for agricultural research and statistical analysis.

Unlike complex optimization-based approaches, PSRICalc focuses on direct calculation using established germination parameters: Maximum Stress-adjusted Germination (MSG), Maximum Rate of Germination (MRG), and Mean Time to Germination (MTG).

Why PSRICalc Exists

The need emerged for a standalone, reproducible method to calculate PSRI values without the complexity of full optimization workflows. Researchers needed:

• Transparent methodology: Clear, auditable calculations
• Statistical compatibility: Individual replicate values for proper ANOVA
• Publication readiness: Defendable, straightforward approach
• Accessibility: No complex optimization dependencies

PSRICalc addresses these needs by extracting the core PSRI calculation logic into a focused, user-friendly R package.

Key Features

• Direct calculation: No iterative optimization required
• Radicle integration: Optional vigor assessment from radicle measurements
  
• Quality control: Built-in mass balance validation
• Statistical ready: Produces individual replicate values for analysis
• Well documented: Complete function documentation with examples
• CRAN compliant: Professional R package standards

Scientific Attribution

PSRICalc builds directly on the Osmotic Stress Response Index (OSRI) methodology established by:

Walne, C.H., Gaudin, A., Henry, W.B., and Reddy, K.R. (2020). In vitro seed germination response of corn hybrids to osmotic stress conditions. Agrosystems, Geosciences & Environment, 3(1), e20087. https://doi.org/10.1002/agg2.20087

Installation

# From CRAN (when available)
install.packages("PSRICalc")

# From source
devtools::install_github("username/PSRICalc")

Basic Usage

library(PSRICalc)

# Calculate PSRI from germination data
result <- calculate_psri(
  germination_counts = c(5, 8, 10),
  time_points = c(3, 5, 7),
  total_seeds = 15,
  species = "corn"
)

print(result$PSRI)

Human–AI Development Transparency

Development followed a collaborative human-machine process with full human oversight. All scientific methodology, mathematical formulations, and validation were designed and conceived by the author.

AI systems (Anthropic Claude) provided substantial assistance with: - R package structure and CRAN compliance - Function implementation and code debugging - Documentation formatting and roxygen2 syntax - Code organization and best practices - Professional presentation standards

AI systems did not contribute to: - Scientific methodology design - Mathematical formulations - Biological interpretation - Research conclusions

Citation

If you use PSRICalc in your research, please cite:

Feiss, R.A. (2025). PSRICalc: Plant Stress Response Index Calculator. 
R package version 1.0.0.

License

MIT License - see LICENSE file for details.

Related Work

PSRICalc is part of a broader research ecosystem including the GALAHAD and SQUIRE optimization frameworks, but operates independently with no external dependencies beyond base R.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.