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

Del Ponte, E.M. Sparks, A.H. (2018). Open ideas, data and code sharing: epidemiologists should be in front!. Proceedings of the 12th International Epidemiology Workshop

The abstract can be found in https://github.com/openplantpathology/OPP.at.IEW12/tree/master/inst/abstract.

The slides of the presentation were prepared in Google Slides and can be found here.

The code used to generate graphs that were presented at IEW12 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.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

### Install OPP.at.IEW12

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.IEW12",
build_vignettes = TRUE,
dependencies = TRUE)

browseVignettes("OPP.at.IEW12")

### How to cite

EM Del Ponte, AH Sparks, (2018). Compendium of R code and data for ‘Open ideas, data and code sharing: epidemiologists should be in front!’. Accessed 04 Jul 2018. Online at https://doi.org/10.5281/zenodo.1286101

You can download the compendium as a zip from from this URL: https://github.com/openplantpathology/OPP.at.IEW12/archive/master.zip

Or you can install this compendium as an R package, OPP.at.IEW12, from GitHub with:

devtools::install_github("openplantpathology/OPP.at.IEW12")