Biology and epidemiology of Diaporthe amygdali: understanding how environmental factors influence fungal growth, sporulation, infection and lesion development on almond. Data and source code.

1 🌱 Reproducible analysis of “Biology and epidemiology of Diaporthe amygdali: understanding how environmental factors influence fungal growth, sporulation, infection and lesion development on almond” This repository contains the full reproducible code supporting all statistical analyses performed in the article: Francia C, Lázaro E, Novellón M, Ramón-Albalat A, Beluzán F, Vicent A, Berbegal M, and Armengol J. Biology and epidemiology of Diaporthe amygdali: understanding how environmental factors influence fungal growth, sporulation, infection and lesion development on almond. Frontiers in Plant Science, 16:1717223 (2025). doi: 10.3389/fpls.2025.1717223 All analyses are organized in self-contained RStudio projects. 1.1 📁 Repository structure Code Each subproject is provided as an independent RStudio Project, with the following internal structure: Code README Elena Lázaro and Maite Novellón AUTHOR diaporthe-amygdali-environmental-effects/ ├── 1_growth-pycnidia-conidia-temp/ ├── 2_development-mature-pycnidia-almond-twigs-temp-time/ ├── 3_conidia-germination-temp-incub/ ├── 4_almond-infection-temp-wet/ ├── 5_lesion-development-almond-twigs-temp/ ├── README.qmd # This file (Quarto source) ├── README.html # Rendered HTML overview experiment-name/ ├── experiment-name.Rproj # RStudio project file ├── README.qmd # Project overview and instructions ├── script/ # Quarto (.qmd) files with individual analyses and generated HTML ├── data/ # Clean input datasets │ └── dataset.csv   1.2 🛠 How to use 1. Download and unzip the project from Zenodo. 2. Open the desired subproject (.Rproj) in RStudio. 3. Use the README.qmd in each folder to understand the analysis flow. 4. Knit the .qmd scripts in script/ to generate .html reports. 5. Outputs are saved under outputs/. 1.3 📄 Citation If you use or refer to this project, please cite the accompanying article: Francia C, Lázaro E, Novellón M, Ramón-Albalat A, Beluzán F, Vicent A, Berbegal M, and Armengol J. Biology and epidemiology of Diaporthe amygdali: understanding how environmental factors influence fungal growth, sporulation, infection and lesion development on almond. Frontiers in Plant Science, 16:1717223 (2025). doi: 10.3389/fpls.2025.1717223 1.4 🌍 License This project is shared under an open-access license (CC-BY 4.0), allowing reuse with appropriate credit. ├── outputs/ # Generated results │ ├── figures/ # Figures from analyses │ ├── models/ # Model objects │ └── tables/ # Model summaries and prediction tables