swiss-fd-susceptibility

This repository contains the code and generated outputs associated with the following manuscript:

Integrated field and laboratory assessment of Swiss grapevine cultivar susceptibility to Flavescence dorée reveals a central role for plant--vector interactions

The repository contains the Quarto documents and generated outputs required to reproduce the statistical analyses presented in the manuscript.

The datasets used in the analyses are archived on Zenodo and are imported directly by the Quarto documents.

An internet connection is therefore required when rendering the analyses.

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Data availability

The datasets used in the analyses are publicly available on Zenodo:

Data DOI: https://doi.org/10.5281/zenodo.21885421

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Repository structure

Each statistical analysis is stored in an independent folder.

swiss_fd_cultivar_susceptibility/

├── README.md
├── LICENSE
├── CITATION.cff
│
├── infection_probability/
├── insect_mortality/
├── field_macro_scale/
├── field_meso_scale/
├── field_micro_scale/
├── relative_titre/
└── ...

Each analysis folder contains the corresponding Quarto document and its generated outputs, when applicable:

<analysis_name>.qmd
figures/
tables/

The figures/ directory contains figures generated by the corresponding analysis.

The tables/ directory contains tables reported in the Supplementary Material. Analyses that do not generate a manuscript or Supplementary table may not contain a tables/ directory.

Each Quarto document is self-contained and can be rendered independently.

Software requirements

The analyses were developed using:

• R 4.5.2
• Quarto 1.7 or later

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Required R packages

The required packages are loaded at the beginning of each Quarto document.

If necessary, they can be installed from the R console using:

install.packages(c(
  "glmmTMB",
  "DHARMa",
  "emmeans",
  "dplyr",
  "ggplot2",
  "scales",
  "knitr"
))

Some analyses may require additional packages, which are loaded automatically by the corresponding Quarto document.

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Running an analysis

1. Download or clone the repository.

2. Open the folder corresponding to the analysis of interest.

3. Open the corresponding Quarto document (*.qmd) in RStudio.

4. Set the working directory to the folder containing the Quarto (.qmd) document:

   Session → Set Working Directory → To Source File Location

5. Click Render.

An internet connection is required because the input datasets are retrieved directly from Zenodo.

Rendering the Quarto document automatically performs the complete analysis, generates the corresponding figures and tables when applicable, and creates an HTML report.

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Generated outputs

Depending on the analysis, rendering a Quarto document may produce:

*.html
figures/
tables/

Figures reported in the manuscript are exported to the figures/ directory.

Tables reported in the manuscript or Supplementary Material are exported to the tables/ directory when applicable.

If a CSV file generated by a previous run is open in Excel, it must be closed before rendering, otherwise R may be unable to overwrite the file.

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Reproducibility

Each Quarto document contains the complete workflow used for the corresponding statistical analysis, including, where applicable:

• data import directly from Zenodo;
• data preparation;
• descriptive statistics;
• model selection;
• model diagnostics;
• statistical inference;
• figure generation;
• Supplementary table generation.

Output file paths are relative to the corresponding analysis folder. Input datasets are retrieved directly from the archived Zenodo record using the URLs specified in each Quarto document.

No additional scripts or local copies of the datasets are required to reproduce the analyses.