Create a Research Compendium

Launch Rstudio

Let’s begin by launching Rstudio

Install packages

Next, let’s install the packages we’ll need, starting with rrtools (if you haven’t got devtools installed, you’ll need to before you can install rrtools from GitHub).

# install.packages("devtools")
devtools::install_github("benmarwick/rrtools")

Installing rrtools imports many of the packages we’ll need today (eg, have a look at the imports section of the DESCRIPTION file).

Imports: devtools, git2r, whisker, rstudioapi, rmarkdown, knitr,
    bookdown, curl, RCurl, jsonlite, methods, httr, usethis, clisymbols,
    crayon, glue, readr (>= 1.1.1)

Now, install some additional packages we’ll need for the workshop.

install.packages(c(
    # source paper analysis
    "dplyr", "ggplot2", "ggthemes", "here",
    # bibliographic / publishing
    "citr", "rticles",
    # documentation
    "roxygen2",
    # graphics
    "Cairo"))

Get workshop materials

Today we’ll be working with a subset of materials from the published compendium of code, data, and author’s manuscript:

usethis::use_course(url = "bit.ly/rrtools_wks", destdir = "~/Desktop")

├── README.md <- .......................repo README
├── analysis.R <- ......................analysis underlying paper
├── gillespie.csv <- ...................data
├── paper.pdf <- .......................LaTex pdf of the paper
├── paper.txt <- .......................text body of the paper
├── refs.bib <- ........................bibtex bibliographic file
└── rrtools-wkshp-materials.Rproj <- ...rstudio project file

load library

First we need to load rrtools

library(rrtools) 

This performs a quick check to confirm you have Git installed and configured

If you do, you should see the following output in the console.

✔ Git is installed on this computer, your username is annakrystalli

usethis::use_git_config(user.name = "Jane", user.email = "jane@example.org")

usethis::use_git_config()

$user.name
[1] "Jane"

$user.email
[1] "jane@example.org"

create compendium

Now we’re ready to create our compendium. We use function rrtools::use_compendium and supply it with a path at which our compendium will be created. The final part of our path becomes the compendium name. Because the function effectively creates a package, only a single string of lowercase alpha characters is accepted as a name. so let’s go for rrcompendium as the final part of our path.

To create rrcompendium in a directory called Documents/workflows/ I use:

rrtools::use_compendium("~/Documents/workflows/rrcompendium")

Go ahead and create a compendium at a location of your choice. Stick with compendium name rrcompendium for ease of following the materials. If the call was successfull you should see the following console output:

✔ Setting active project to '/Users/Anna/Documents/workflows/rrcompendium'
✔ Creating 'R/'
✔ Creating 'man/'
✔ Writing 'DESCRIPTION'
✔ Writing 'NAMESPACE'
✔ Writing 'rrcompendium.Rproj'
✔ Adding '.Rproj.user' to '.gitignore'
✔ Adding '^rrcompendium\\.Rproj$', '^\\.Rproj\\.user$' to '.Rbuildignore'
✔ Opening new project 'rrcompendium' in RStudio
✔ The package rrcompendium has been created
✔ Opening the new compendium in a new RStudio session...

Next, you need to:  ↓ ↓ ↓ 
● Edit the DESCRIPTION file
● Use other 'rrtools' functions to add components to the compendium

and a new Rstudio session launched for the compendium:

Initiate git

We can initialise our compendium with .git using:

usethis::use_git()

N.B. Beware, you may have ended up with two Rstudio sessions of rrcompendium. Make sure to only have one session of a single project at one time to avoid problems.

Inspect templates

.
├── DESCRIPTION <- .............................package metadata
|                                               dependency management
├── NAMESPACE <- ...............................AUTO-GENERATED on build
├── R <- .......................................folder for functions
├── man <- .....................................AUTO-GENERATED on build
└── rrcompendium.Rproj <- ......................rstudio project file

rrtools::use_compendium() creates the bare backbone of infrastructure required for a research compendium. At this point it provides facilities to store general metadata about our compendium (eg bibliographic details to create a citation) and manage dependencies in the DESCRIPTION file and store and document functions in the R/ folder. Together these allow us to manage, install and share functionality associated with our project.

update description file

Let’s update some basic details in the DESCRIPTION file:

Package: rrcompendium
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9000
Authors@R: 
    person(given = "First",
           family = "Last",
           role = c("aut", "cre"),
           email = "first.last@example.com")
Description: What the package does (one paragraph)
License: What license it uses
ByteCompile: true
Encoding: UTF-8
LazyData: true

Title

Let’s start with giving our compendium a descriptive title:

Title: Partial Reproduction of Boettiger Ecology Letters 2018;21:1255–1267 
    with rrtools

Version

We don’t need to change the version now but using semantic versioning for our compendium can be a really useful way to track versions. In general, versions below 0.0.1 are in development, hence the DESCRIPTION file defaults to 0.0.0.9000.

Authors

Next let’s specify the author of the compendium. Edit with your own details.

Authors@R: 
    person(given = "Anna",
           family = "Krystalli",
           role = c("aut", "cre"),
           email = "annakrystalli@googlemail.com")

For more details on specifying authors, check documentation for ?person

Description

Let’s add a bit more detail about the contents of the compendium in the Description.

Description: This repository contains the research compendium of the 
    partial reproduction of Boettiger Ecology Letters 2018;21:1255–1267. 
    The compendium contains all data, code, and text associated with this       sub-section of the analysis

License

Finally, let’s add a license for the material we create. We’ll use an MIT license. Note however that his only covers the code. We can do this with:

 usethis::use_mit_license()

✔ Setting License field in DESCRIPTION to 'MIT + file LICENSE'
✔ Writing 'LICENSE.md'
✔ Adding '^LICENSE\\.md$' to '.Rbuildignore'

This creates files LICENSE and LICENSE.md and updates the DESCRIPTION file with details of the license.

License: MIT + file LICENSE

Recap

We’ve finished updating our DESCRIPTION file! 🎉

It should look a bit like this:

Package: rrcompendium
Title: Partial Reproduction of Boettiger Ecology Letters 2018;21:1255–1267 
    with rrtools
Version: 0.0.0.9000
Authors@R: 
    person(given = "Anna",
           family = "Krystalli",
           role = c("aut", "cre"),
           email = "annakrystalli@googlemail.com")
Description: This repository contains the research compendium of the partial 
    reproduction of Boettiger Ecology Letters 2018;21:1255–1267. The compendium 
    contains all data, code, and text associated with this sub-section of the 
    analysis.
License: MIT + file LICENSE
ByteCompile: true
Encoding: UTF-8
LazyData: true

and your project folder should contain:

.
├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R
├── man
└── rrcompendium.Rproj

Let’s commit our work and move on to preparing our compendium for sharing on GitHub.

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 can open your .Renviron file for editing with:

usethis::edit_r_environ()

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

Create GitHub repository

Next, we’ll create a GitHub repository to share our compendium. We can do this with function:

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
  

The function will prompt you to confirm the name and description for your GitHub repo which it parses from our DESCRIPTION file. If everything looks good select the affirmative option.

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

If creation of the repo was successfull you should see the following console output:

✔ 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

This

Create README

Every GitHub repository needs a README landing page.

We can create an rrtools README template using:

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

---
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 31 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 31 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.

The call also adds two other markdown files:

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

update README

There’s five main edits we need to make to the template:

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 31 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 31 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.

render README.md, commit and push to GitHub

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

Create analysis

We now need an analysis folder to contain our analysis and paper. We can do this using function rrtools::use_analysis()

The function has three location = options:

• top_level to create a top-level analysis/ directory

• inst to create an inst/ directory (so that all the sub-directories are available after the package is installed)

• vignettes to create a vignettes/ directory (and automatically update the DESCRIPTION).

The default is a top-level analysis/.

rrtools::use_analysis()

✔ Adding bookdown to Imports
✔ Creating 'analysis' directory and contents
✔ Creating 'analysis'
✔ Creating 'analysis/paper'
✔ Creating 'analysis/figures'
✔ Creating 'analysis/templates'
✔ Creating 'analysis/data'
✔ Creating 'analysis/data/raw_data'
✔ Creating 'analysis/data/derived_data'
✔ Creating 'references.bib' from template.
✔ Creating 'paper.Rmd' from template.

Next, you need to:  ↓ ↓ ↓ ↓ 
● Write your article/report/thesis, start at the paper.Rmd file
● Add the citation style library file (csl) to replace the default provided here, see https://github.com/citation-style-language/
● Add bibliographic details of cited items to the 'references.bib' file
● For adding captions & cross-referencing in an Rmd, see https://bookdown.org/yihui/bookdown/
● For adding citations & reference lists in an Rmd, see http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html

Note that:
⚠ Your data files are tracked by Git and will be pushed to GitHub

Regardless for location option, the contents of the created sub-directories are the same:

    analysis/
    |
    ├── paper/
    │   ├── paper.Rmd       # this is the main document to edit
    │   └── references.bib  # this contains the reference list information
    
    ├── figures/            # location of the figures produced by the Rmd
    |
    ├── data/
    │   ├── DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND
    │   ├── raw_data/       # data obtained from elsewhere
    │   └── derived_data/   # data generated during the analysis
    |
    └── templates
        ├── journal-of-archaeological-science.csl
        |                   # this sets the style of citations & reference list
        ├── template.docx   # used to style the output of the paper.Rmd
        └── template.Rmd

Let’s inspect