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reproducibility_in_plant_pathology

A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.

https://github.com/openplantpathology/reproducibility_in_plant_pathology

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary

Keywords

open-science plant-pathology r reproducible-research reproducible-science research-compendium rstats
Last synced: 4 months ago · JSON representation

Repository

A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.

Basic Info
Statistics
  • Stars: 23
  • Watchers: 7
  • Forks: 6
  • Open Issues: 0
  • Releases: 8
Topics
open-science plant-pathology r reproducible-research reproducible-science research-compendium rstats
Created over 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct Codemeta

README.md

Reproducibility in Plant Pathology

Publish Docker DOI Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows. <!-- badges: end -->

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, “Reproducibilityinplantpathologynotes.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:

r 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.

bash 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.

Owner

  • Name: Open Plant Pathology
  • Login: openplantpathology
  • Kind: organization
  • Email: openplantpathology@gmail.com
  • Location: Global

A community that values open data and computational tools for advancing epidemiology and pathogen population biology and ecology

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    "r",
    "rstats",
    "research-compendium"
  ]
}

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 1,473
  • Total Committers: 4
  • Avg Commits per committer: 368.25
  • Development Distribution Score (DDS): 0.024
Past Year
  • Commits: 152
  • Committers: 1
  • Avg Commits per committer: 152.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Adam Sparks a****s@g****m 1,437
Niklaus Grunwald g****n@s****u 19
Zachary Foster z****9@g****m 10
Emerson M. Del Ponte d****e@u****r 7
Committer Domains (Top 20 + Academic)
ufv.br: 1 science.oregonstate.edu: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 28
  • Total pull requests: 26
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 15 minutes
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 5.57
  • Average comments per pull request: 0.08
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adamhsparks (21)
  • emdelponte (3)
  • grunwald (2)
  • zachary-foster (2)
Pull Request Authors
  • adamhsparks (25)
  • zachary-foster (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • dplyr * imports
  • magrittr * imports
  • readODS * imports
  • bayesplot * suggests
  • bayestestR * suggests
  • bib2df * suggests
  • bibtex * suggests
  • brms * suggests
  • extrafont * suggests
  • flextable * suggests
  • ggplot2 >= 3.3.0 suggests
  • ggridges * suggests
  • git2r * suggests
  • googlesheets4 * suggests
  • here * suggests
  • irr * suggests
  • janitor * suggests
  • knitr * suggests
  • officedown * suggests
  • officer * suggests
  • pander * suggests
  • parallel * suggests
  • patchwork * suggests
  • psych * suggests
  • rcrossref * suggests
  • readr * suggests
  • rmarkdown * suggests
  • roxygen2 >= 6.0.1 suggests
  • sessioninfo * suggests
  • spelling * suggests
  • stringr * suggests
  • testthat * suggests
  • tibble * suggests
  • tidyverse * suggests
.github/workflows/publish_docker.yml actions
  • actions/checkout master composite
  • elgohr/Publish-Docker-Github-Action v4 composite
Dockerfile docker
  • rocker/verse 4.2.1 build