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.

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.