PLOS ONE 2025 - Crop Ideotype Optimization

Crop Growth Modelling: AI-Driven Ideotype Optimization

Code and data to replicate results from:

Correa, E.S. (2025). Decoding Living Systems: Reassessing Crop Model Frontiers via Biological Dynamics and Optimized Phenotype. PLOS ONE.
Preprint May 16, 2025 https://doi.org/10.1101/2025.05.15.652350

What's included

📁 PLOS2025_Crop_Growth_Modelling/

• 1_Sensitivity_Analysis/ - Morris method (20 replications, 95% CI)
• 2_Genetic_Algorithm/ - Optimization across 4 environments
• 3_Similarity_Analysis/ - Ideotype-cultivar mapping

Key Results

Metric	Value
Virtual cultivars evaluated	5,364
Environments analyzed	4
Best breeding candidate	WAB56-50 (70.7% similarity)
Genetic gap to optima	22-30%

Quick Start

% Step 1: Sensitivity Analysis (~10 seconds)
cd PLOS2025_Crop_Growth_Modelling/1_Sensitivity_Analysis/replicate_results
main_replicate_results

% Step 2: Genetic Algorithm (~30 seconds)
cd ../../2_Genetic_Algorithm/replicate_results
main_replicate_results

% Step 3: Similarity Analysis (~20 seconds)
cd ../../3_Similarity_Analysis
main_similarity_analysis

Requirements

• MATLAB R2024b
• DSSAT v4.8 (for run_from_scratch only)
• R v4.4.2 (for run_from_scratch only)

License

CC BY 4.0