Open Science

• Git & GitHub workflow
  • Create a repository on GitHub & link it to RStudio
  • Write a README.md file
  • Choose and apply a license for your repository/R code
    • Licensing a GitHub repository
  • commit & push
• TO DO: Unlock Pull & Push from RStudio!

5. Missing Values

• NA (not available/missing), NAN (not a number),
• Any operation involving NA generally yields NA as the result
• is.na() function (logical result)
• TRUE represented in R as 1, FALSE represented in R as 0 (good to know when counting)

6. Subsetting Vectors

• [] place an 'index vector' in square brackets to subset a vector
• 'index vector': logical, positive/negative integers, character
  • logical: x[is.na(x)], x[!is.na(x)]
  • logical: x[!is.na(x) & x>0] (AND operator)
  • pos. integer: x[1:10] (first 10 values of x), x[c(3,5,7)] (3rd, 5th and 7th values of x)
  • neg. integer: x[-c(2, 10)] (all values except the 2nd and 10th)
  • char: vect["bar"]
• names() function
• identical() function

Complete swirl modules '7: Matrices and Data Frames' and '8: Logic' and submit your successful completion via email (domenico.giusti@uni-tuebingen.de)

swirl modules won't count towards your final grade but are highly recommended to follow. Those topics will be covered on the final exam.

Start a project in a brand new working directory

1. Click the “File” menu button, then “New Project”
2. Click “New Directory”
3. Click “New Project”
4. Type in the name of the directory to store your project, e.g. “test_rr”
5. Check "Create a git repository"
6. Hit the “Create Project” button!
7. Create a new repository on GitHub
8. git remote add origin git@github.com:dncgst/test10.git
9. git branch -M master (NOTE: RStudio names the principal branch master; GitHub recently renamed it main)
10. git push -u origin master
11. Restart RStudio after you run git push -u origin master from the command line

Associate a project with an existing working directory

1. Click the “File” menu button, then “New Project”
2. Click "Existing Directory"
3. Browse your project working directory
4. Hit the “Create Project” button!
5. Click the "Tools" menu button, then "Project Options..."
6. Select "Git/SVN" from the menu on the left
7. Version control system: Select "Git" from the dropdown menu
8. Create a new repository on GitHub
9. git remote add origin git@github.com:dncgst/test10.git
10. git branch -M master (NOTE: RStudio names the principal branch master; GitHub recently renamed it main)
11. git push -u origin master
12. Restart RStudio after you run git push -u origin master from the command line

Checkout a project from a version control repository

1. Click the “File” menu button, then “New Project”
2. Click "Version Control"
3. Click "Git (Clone a project from a Git repository)"
4. Type the repository URL: (e.g. git@github.com:dncgst/test12.git)
5. Type the Project directory name: (e.g., test12)
6. Hit the “Create Project” button!
7. Branch named main also in RStudio
8. Origin added during the cloning process

Configure Git wo/ Shell

install.packages('usethis')
library('usethis')
usethis::use_git_config(user.name = "dncgst", user.email = "dncgst@autistici.org")
usethis::edit_git_config()

Create a Personal Access Token (PAT) on GitHub

The best way to connect RStudio and GitHub is using your username and a Personal Access Token (PAT). To generate a personal access token, use the create_github_token() function from usethis. This will take you to the appropriate page on the GitHub website, where you’ll give your token a name and copy it (don’t lose it because it will never appear again!). How to Use Git/GitHub with R

library('usethis')
usethis::create_github_token() # accept default settings and generate the token
# copy the generated token
install.packages('gitcreds')
library('gitcreds')
gitcreds_set()
# enter your copied token

Start a project in a brand new working directory

1. Click the “File” menu button, then “New Project”
2. Click “New Directory”
3. Click “New Project”
4. Type in the name of the directory to store your project, e.g. “test_rr”
5. Check "Create a git repository"
6. Hit the “Create Project” button!
7. Do you first commit
8. library(usethis)
9. use the use_github() function, which will create a GitHub repo and connect it to your current RStudio project

Three principles should be kept in mind when constructing a research compendium.

• Files should be organized in a conventional folder structure;
• Data, methods, and output should be clearly separated;
• The computational environment should be specified.

Marwick et al. 2018

• Research Compendium contains links to further resources and publications on research compendia
  • GitHub · https://github.com/topics/research-compendium/
  • Zenodo · https://zenodo.org/communities/research-compendium/
  • OSF · https://osf.io/search/?q=tags:research-compendium

compendium/
├── data
|   ├── raw_data.csv
│   ├── my_data.csv
├── figures
│   └── fig1.jpg
├── src/analysis
│   ├── my_script.R
|   ├── fig1.R
├── text/doc
│   └── manuscript.Rmd
├── DESCRIPTION
├── LICENSE
└── README.md

It contains code, data, text, figures + the computing environment is described in the Dockerfile, the dependencies of files and how to automatically generate the results are described in the Makefile (e.g., benmarwick/1989-excavation-report-Madjedbebe).

compendium/
├── data
│   ├── my_data.csv
├── Dockerfile
├── figures
│   └── fig1.jpg
├── Makefile
├── src/analysis
|   ├── fig1.R
├── text/doc
│   └── manuscript.Rmd
├── DESCRIPTION
├── LICENSE
└── README.md

A version control repository can be a research compendium; A Makefile makes it executable; A reproducible environment makes it reproducible.

A Docker container can be seen as a computer inside your computer. The cool thing about this virtual computer is that you can send it to your friends; And when they start this computer and run your code they will get exactly the same results as you did.

• Get Docker https://docs.docker.com/get-docker/
  • "Docker is an open platform for developing, shipping, and running applications. Docker enables you to separate your applications from your infrastructure so you can deliver software quickly."
• Follow this tutorial: https://jsta.github.io/r-docker-tutorial/ -

• Log in w/ GitHub
• Settings / GitHub
  1. Flip the switch
  2. Create a release
  3. Get the badge (DOI)
• Edit upload and add some METADATA
• Publish

A research compendium can be used in several ways, including (but not limited to):

• Peer review: If peers can check what you have done, they can review it much more thoroughly.
• Understanding research: If you really want to understand what someone has done in their research project, the research compendium is what you need to look at.
• Teaching: Research compendia can be great examples to be used in teaching.
• Reproducibility studies / repro hacks: A research compendium allows other researchers to attempt (and hopefully succeed) to redo your computations.