Reproducibility_in_Plant_Pathology

Reproducibility in Plant Pathology

This repository contains the data and code for our article:

Sparks, A.H., Del Ponte, E.M., Alves, K. S., Foster, Z., Grünwald, N. J. (2023). Openness and computational reproducibility in plant pathology: where do we stand and a way forward, Phytopathology https://doi.org/10.1094/PHYTO-10-21-0430-PER.

Our pre-print is online on the agriRxiv preprint server:

Sparks, A.H., Del Ponte, E.M., Alves, K. S., Foster, Z., Grünwald, N. J. (2023). Openness and computational reproducibility in plant pathology: where do we stand and a way forward. agriRxiv, Accessed 07 Aug 2024. Online at https://doi.org/10.31220/agriRxiv.2021.00082

The paper is a systematic and quantitative review of articles published in 21 plant pathology journals that spans five years of publications. It provides a basis for identifying what has been done so far in the discipline of plant pathology’s published research to ensure computational reproducibility. The results show that as a discipline, plant pathologists are not widely sharing data or code openly, making the works largely unreproducible. Based on these results and our own experiences, we offer suggestions as to how we can further improve reproducibility in the discipline of plant pathology, but which are not unique to the discipline, that would allow reviewers to make better suggestions, readers to learn more from the work and earns author more citations for their work.

How to cite

Please cite this compendium as:

Sparks, A.H., Del Ponte, E.M., Alves, K. S., Foster, Z., Grünwald, N. J. (2024). Compendium of R code and data for ‘Status and Best Practices for Reproducible Research In Plant Pathology’. Accessed 07 Aug 2024. Online at https://doi.org/10.5281/zenodo.1250664

How to download or install

The R package

This repository is organized as an R package. There is one R function, import_notes() that is used in the paper’s figure and table making when the file, analysis/paper/paper.Rmd is knit. Additionally, a bibliography file, “references.bib”, of the articles that were examined and the notes from the evaluation, “Reproducibility_in_plant_pathology_notes.ods” of the articles are both located in inst/extdata directory. We have used the R package structure to help manage dependencies, to take advantage of continuous integration for automated code testing and for file organisation.

You can download the compendium as a zip from from this URL: https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology/archive/main.zip

Or you can install this compendium as an R package, Reproducibility.in.Plant.Pathology, from GitHub with:

if (!require("remotes"))
  install.packages("remotes")
remotes::install_github("openplantpathology/Reproducibility_in_Plant_Pathology"
)

Once the download is complete, open the Reproducibility_in_Plant_Pathology.Rproj in RStudio to begin working with the package and compendium files.

The Docker Instance

Get the latest instance from Dockerhub, launch it and go to localhost:8787 in your browser. Login with rstudio, password is rstudio.

docker pull adamhsparks/reproducibility_in_plant_pathology
docker run -d -p 8787:8787 adamhsparks/reproducibility_in_plant_pathology

The Paper

The file structure follows a normal R package with one exception. The top-level “/analysis” directory contains the directories and files necessary to re-knit the MS Word document of the paper from an Rmd file, “/analysis/paper/paper.Rmd”.

A script, knit_paper.R, is located in analysis/paper/knit_paper.R that will knit the manuscript and the supplementary materials in a Docker session.

Meta

Licensing

Code: MIT year: 2024, copyright holder: Adam H. Sparks

Data: CC-0 attribution requested in reuse

Adam H. Sparks Senior Research Scientist Farming Systems Innovation Primary Industries Development Department of Primary Industries and Regional Development Level 6.34, 1 Nash St., Perth WA 6000

https://adamhsparks.netlify.app

Code of Conduct

Please note that the Reproducibility.in.Plant.Pathology project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.