Thermal-time NDVI reveals stay-green dynamics and yield determinants under contrasting nitrogen regimes in rice

10.5281/zenodo.17096240 What this deposit contains--------------------------This package reproduces the analyses and figures reported in the manuscript. It includes R and Pythonscripts, curated input data, and a complete environment snapshot. Folder layout-------------- Script_Software/ - Script_Rstudio/: NDVI_Anova_Descriptive_RLRT.R (α-lattice MET), NDVI_PCA_Corr_cluster.R, NDVI_regression.R, NDVI_blup.R - Script_python/: NDVI_publication.ipynb, ndvi_pipeline_publication.py, requirements.txt, environment.yml, README.md- Dataset_Input_Output/ - dataset_Rstudio/: NDVI_anova_input_publication.csv, BLUP_ByENV_AdjustedMeans_SE.csv, BLUP_NDVI.csv - dataset_python/: NDVI_ADD_phenology.xlsx, NDVI_Dates_DM.xlsx, NDVI_results_Tb10_*.xlsx- Reproducibility/: sessionInfo_R_complete.txt, project_packages_versions.csv, installed_packages.csv- LICENSE (MIT for code), LICENSE_DATA.txt (CC BY 4.0 for data/figures/tables)- checksums.txt, compute_checksums.R How to rebuild (R)------------------1) Restore package versions:options(repos=c(CRAN="https://cran.rstudio.com"))if(!requireNamespace("remotes", quietly=TRUE)) install.packages("remotes")man <- read.csv("Reproducibility/project_packages_versions.csv", stringsAsFactors=FALSE)for(i in seq_len(nrow(man))){ remotes::install_version(man$Package[i], version=as.character(man$Version[i]), repos="https://cran.rstudio.com", upgrade="never")}2) From the Zenodo root, run:source("Script_Software/Script_Rstudio/NDVI_Anova_Descriptive_RLRT.R")source("Script_Software/Script_Rstudio/NDVI_PCA_Corr_cluster.R")source("Script_Software/Script_Rstudio/NDVI_regression.R")# Optional:source("Script_Software/Script_Rstudio/NDVI_blup.R") How to rebuild (Python)-----------------------pip install -r Script_Software/Script_python/requirements.txt# orconda env create -f Script_Software/Script_python/environment.yml Provenance & environment------------------------- R: see Reproducibility/sessionInfo_R_complete.txt (R 4.5.1, Windows 11, tz Asia/Calcutta, seed 123).- Traits/labels: SR (NDVI per °C·day), Stg (NDVI), AUC (NDVI·°C·day), Chl (µmol m⁻²; also referred to as CCI), Yield (t ha⁻¹), DTH/DTA/DTM (days). Integrity (checksums)---------------------R: source("compute_checksums.R") # regenerate checksums.txt verify_checksums("checksums.txt") # verifyPowerShell: .\compute_checksums.ps1 .\compute_checksums.ps1 -Verify ContactLukram Shantikumar [e-mail] of Basic Sciences and Humanities,College of Horticulture and Forestry, CAU (Imphal),Pasighat, Arunachal Pradesh, 791102, India