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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# OPP@ANU
[](https://travis-ci.org/openplantpathology/OPP.at.ANU)
[](https://ci.appveyor.com/project/adamhsparks/opp-at-anu/branch/master)
[](https://zenodo.org/badge/latestdoi/172012900)
[](https://www.repostatus.org/#inactive)
<img align="right" width=230 style = "margin:10px; border: 0" src="man/figures/logo.png"> 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](https://speakerdeck.com/adamhsparks/whats-so-open-about-plant-pathology).
The code used to generate graphs that were presented at ANU can be found in
the [articles](https://openplantpathology.github.io/OPP.at.ANU/articles/sparks-anu-graphs-for-open-science-presentation.html).
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.
```{r, eval=FALSE}
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.
```r
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.
```{r, eval=FALSE}
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 `r format(Sys.Date(), "%d %b %Y")`. 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:
```r
devtools::install_github("openplantpathology/OPP.at.ANU")
````
### Licenses
**Text and figures :** [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)
**Code :** See the [DESCRIPTION](DESCRIPTION) file
**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse
### Contributions
We welcome contributions from everyone. Before you get started, please see our [contributor guidelines](CONTRIBUTING.md). Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.