Effect of Nitrogen Regime on Rice Grain Nutritional Traits and Multi-Trait Selection of Superior Genotypes

## OverviewDataset, R scripts, and reproducibility materials accompanying the JCS manuscript:“Effect of Nitrogen Regime on Rice Grain Nutritional Traits and Multi-Trait Selection of Superior Genotypes”. ## Contents- /data/ — input CSVs.- /scripts/ — four R scripts: 1) 1_MixedModel_ANOVA.R — α-lattice mixed models; Type-III ANOVA; RLRT for random terms; variance components; BLUPs/EMMeans; entry-mean H²; descriptive stats. 2) 2_BLUP_ByENV_AdjustedMeans.R — per-environment GEN BLUPs + adjusted means with SE. 3) 3_PCA_Clustering_Correlation.R — PCA; k-means diagnostics (elbow, silhouette, gap); cluster biplots; Pearson correlation heatmaps; composites. 4) 4_MultiTrait_Selection_Pipeline.R — MTSI, MGIDI, Smith–Hazel; AMMI/GGE confirmations; stability & consensus visuals.- /Reproducibility/ — session snapshots (sessionInfo*.txt), package_info.csv, and SHA-256/MD5 checksums.- /outputs/ — derived figures/tables (can be regenerated). ## How to reproduce- R ≥ 4.5.1 (Windows 11 tested), RStudio ≥ 2025.5.1.513 recommended.- Open the project root in RStudio and run scripts 1→4 (or use `Rscript` from terminal).- Scripts quietly install missing packages; no internet is needed at runtime once installed. ## Licensing- Data, figures, and documentation: CC BY 4.0 (LICENSES/LICENSE-data-CCBY4.txt).- Code (all R scripts): MIT (LICENSES/LICENSE-code-MIT.txt).Note: The deposit’s UI license is CC-BY-4.0; code remains MIT by file headers and license file. ## CitationPlease cite the Zenodo record (10.5281/zenodo.17148175) and the JCS article when available.