Research compendium website

This repository contains the development version of RMarkdown code and data example files to customize and generate a responsive website for a research compendium - a compilation of data and computer code to reproduce the results of a publication.

Website example: https://emdelponte.github.io/research-compendium-website/

Authors of this repository

Emerson Del Ponte ([email protected])

Overview of contents

The root of the repository contains files that set the website structure (menus, etc.) and style (.yml, .css), as well as the citation/reference style. There are four .Rmd files to generate each website page, which are separated according to the convention of a research compendium.

• index.Rmd: Describe the research, objectives, authorship, etc.
• data.Rmd: Contains the raw or raw-derived data.
• code.Rmd: Produces the main analysis report with a template that follows the Wickham and Grolemund's model for a data science project: import -> tidy -> transform-visualize-model -> communicate
• manuscript.Rmd: An example html manuscript template. It is intended to work as a pre-print version of the paper.

There are three basic folders:

• data/ - raw and further processed data.
• docs/ - html files of the research compendia with all text and figures.
• supp/ - supplementary files that are not data or R codes.

Copying this compendium template

Use GitHub import, don't fork, to make a copy of this repo in your own GitHub account. (Note: This is like a GitHub Fork, but not connected to the upstream changes so you won't see forked from emdelponte/research-compendium-website in your own repository or other information like This branch is 117 commits ahead of emdelponte:master also won't appear in your repository, which makes things nicer since this is just a template for your own compendium. They don't need to be linked.

Licenses

Manuscript: CC-BY-4.0

Code: MIT year: 2017, copyright holder: Emerson Del Ponte

Data: [CC-0[(https://creativecommons.org/publicdomain/zero/1.0/)] attribution requested in reuse

Credits

This compendium was developed based on the ideas and examples in other resources which suggest a research compendium structured as an R package. However, this is not an R package as I focused mainly on four main Rmd files that are used to generate the html output of the compendium, but there there is clear separation of the data and the output files.

Marwick et al. 2017

jhollist manuscriptpackage

cboettig template

benmarwick researchcompendium

Reproducibility_in_Plant_Pathology

R for Data Science

Contact

Emerson Del Ponte, Associate Professor, Departmento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG Brazil (+55) 31 38991103 [email protected] Twitter: @emdelponte