What's so Open About Plant Pathology? • What's so Open About Plant Pathology?

This repository retrieves the data and code for our presentation at the 12th International Epidemiology Workshop:

Adam H. Sparks and Emerson Del Ponte. (2019). What’s so Open About Plant Pathology? version 0.0.10. Australian National University Open Science Day. 2019-02-25, https://openplantpathology.github.io/OPP.at.ANU/

The slides of the presentation were prepared in Google Slides and can be found on Speaker Deck.

The code used to generate graphs that were presented at ANU can be found in the articles.

The data are from https://openplantpathology.github.io/Reproducibility_in_Plant_Pathology/.

Sparks, A.H., Del Ponte, E.M., Everhart, S., Foster, Z.S.L., and Grünwald, N. (2018). Compendium of R code and data for ‘Status and Best Practices for Reproducible Research In Plant Pathology’. Accessed 02 Jun 2018. Online at https://doi.org/10.5281/zenodo.1250665

How to use

Install supporting package, hrbrthemes

Install hrbrthemes, which provides the theme for the ggplot2 graphs and loads the fonts.

Install the package and load it. Upon loading it follow the directions for installing and loading Roboto Condensed fonts.

install.packages("hrbrthemes", dep = TRUE)
library(hrbrthemes)

Take note of these instructions and execute them and then install the font, Roboto Condensed on your computer as directed.

Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed

Instructions for installing Roboto Condensed on your system

macOS instructions

See https://support.apple.com/en-us/HT201749

Windows instructions

See https://support.microsoft.com/en-us/help/314960/how-to-install-or-remove-a-font-in-windows

Install OPP.at.ANU

Now install the package using devtools and then use browseVignettes to see the HTML version, the raw Rmd file and only the R code of the vignette locally.

if (!require(devtools)) {
  install.packages("devtools")
  library(devtools)
}

devtools::install_github("openplantpathology/OPP.at.ANU",
                         build_vignettes = TRUE,
                         dependencies = TRUE)

browseVignettes("OPP.at.ANU")

How to cite

Please cite this compendium as:

Sparks, A.H. and Del Ponte, E. M. (2019). What’s so Open About Plant Pathology?. Australian National University Open Science Day. 2019-02-25. Accessed 28 Mar 2019. Online at https://doi.org/10.5281/zenodo.2575300

How to download or install

You can download the compendium as a zip from from this URL: https://github.com/openplantpathology/OPP.at.ANU/archive/master.zip

Or you can install this compendium as an R package, OPP.at.ANU, from GitHub with:

devtools::install_github("openplantpathology/OPP.at.ANU")

Licenses

Text and figures : CC-BY-4.0

Code : See the DESCRIPTION file

Data : CC-0 attribution requested in reuse

Contributions

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.