Sharing through GitHub

Version control

Set up GITHUB PAT

You’ll need a Personal Authorisation Token (PAT) from GitHub to be able to interact with GitHub through R.

Use:

usethis::browse_github_pat()

to open up the GitHub panel to generate your PAT.

Copy the generated PAT to paste into your .Renviron file as system variable GITHUB_PAT.

You open and edit your .Renviron file with:

usethis::edit_r_environ()

Paste it into your .Renviron file as system variable GITHUB_PAT, save and close.

usethis::use_github()

✔ Setting active project to '/Users/Anna/Documents/workflows/rrcompendium'
● Check title and description
  Name:        rrcompendium
  Description: Partial Reproduction of Boettiger Ecology Letters 2018;21:1255–1267 with rrtools
  

Are title and description ok?
1: Not now
2: Definitely
3: Nope

✔ Creating GitHub repository
✔ Adding GitHub remote
✔ Adding GitHub links to DESCRIPTION
✔ Setting URL field in DESCRIPTION to 'https://github.com/annakrystalli/rrcompendium'
✔ Setting BugReports field in DESCRIPTION to 'https://github.com/annakrystalli/rrcompendium/issues'
✔ Pushing to GitHub and setting remote tracking branch
✔ Opening URL https://github.com/annakrystalli/rrcompendium

README

rrtools::use_readme_rmd()

✔ Creating 'README.Rmd' from template.
✔ Adding 'README.Rmd' to `.Rbuildignore`.
● Modify 'README.Rmd'
✔ Rendering README.Rmd to README.md for GitHub.
✔ Adding code of conduct.
✔ Creating 'CONDUCT.md' from template.
✔ Adding 'CONDUCT.md' to `.Rbuildignore`.
✔ Adding instructions to contributors.
✔ Creating 'CONTRIBUTING.md' from template.
✔ Adding 'CONTRIBUTING.md' to `.Rbuildignore`.

This generates README.Rmd and renders it to README.md, ready to display on GitHub. It contains:

• a template citation to show others how to cite your project.
• license information for the text, figures, code and data in your compendium

The call also adds two other markdown files:

• a code of conduct for users CONDUCT.md
• basic instructions for people who want to contribute to our compendium CONTRIBUTING.md.

---
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-"
)
``

# rrcompendium

This repository contains the data and code for our paper:

> Authors, (YYYY). _Title of paper_. Name of journal/book <https://doi.org/xxx/xxx>

Our pre-print is online here:

> Authors, (YYYY). _Title of paper_. Name of journal/book, Accessed 30 Oct 2018. Online at <https://doi.org/xxx/xxx>


### How to cite

Please cite this compendium as:

> Authors, (2018). _Compendium of R code and data for 'Title of paper'_. Accessed 30 Oct 2018. Online at <https://doi.org/xxx/xxx>

### How to download or install

You can download the compendium as a zip from from this URL: </archive/master.zip>

Or you can install this compendium as an R package, rrcompendium, from GitHub with:
### 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.

update README

This repository contains the data and code for our reproduction paper:

> Krystalli, A, (2018). _Partial Reproduction of Boettiger Ecology Letters 2018;21:1255–1267 with rrtools_.  <https://doi.org/{DOI-to-paper}>

Our reproduction pre-print is online here:

> Krystalli, A, (2018). _Partial Reproduction of Boettiger Ecology Letters 2018;21:1255–1267 with rrtools_, Accessed 30 Oct 2018. Online at <https://doi.org/{DOI-to-compendium}>

Please cite this compendium as:

> Krystalli, A, (2018). _Compendium of R code and data for 'Partial Reproduction of Boettiger Ecology Letters 2018;21:1255–1267 with rrtools'_. Accessed 30 Oct 2018. Online at <https://doi.org/{DOI-to-compendium}>

### How to download or install

You can download the compendium as a zip from from this URL: <https://github.com/annakrystalli/rrcompendium/archive/master.zip>

**Text and figures :**  [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)

**Code :** See the [DESCRIPTION](DESCRIPTION) file

**Data :** [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/), Copyright (c) 2018 Carl Boettiger.

Recap

We’ve now completed our rrtools README.Rmd! 🎉

Render it to update the README.md file which github displays

Commit and push to GitHub

and your project folder should contain:

.
├── CONDUCT.md
├── CONTRIBUTING.md
├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R
├── README.Rmd
├── README.md
├── man
└── rrcompendium.Rproj