Getting started

Author

Filippo Gambarota

Setup

There are few tools that we need to install and configure for the course.

  • R/Rstudio (or another IDE)
  • Quarto
  • Git/Github

Quarto

Quarto is an an open-source scientific and technical publishing system. It is very easy to install and you can find instructions here https://quarto.org/docs/get-started/.

To check if Quarto is installed, you can open a terminal (e.g., Powershell or CMD in Windows) and type:

quarto --version

This should return the version of Quarto without errors or strange messages.

Git/Github

Git is a version-control system that you can easily install from here https://git-scm.com/. You can use Git from the command line depending on your operating system or you can use the Github Desktop software https://desktop.github.com/download/ to work with a GUI.

Github is the online version of Git and works as an online repository to share and store the code. In order to work with Git and Github you need to:

  • create an account https://github.com/
  • configure your local machine with an SSH key (with this you do not need to write the password every time). Configuring an SSH key is not so easy thus I suggest you to use the Github CLI tool https://cli.github.com/ where you can configure your account using SSH very easily. The instructions can be found here https://cli.github.com/manual/gh_auth_login and we need to use the gh auth login command.

Also here you can check the Git installation typing this command in the terminal:

git --version

Cloning the repository

Now that we have all the tools we can clone the repository of the course. You can navigate into the folder that you want in your machine and type:

git clone git@github.com:stat-teaching/psychometrics4neuroscience.git

Or manually (but there will not be the Git-Github link) downloading the zip folder from https://github.com/stat-teaching/psychometrics4neuroscience.

If you cloned the repository you can navigate into the folder and type:

git status

This should return some info or messages not errors or messages related to non being in a Git repository.

Now you have the repository of the course. I will update this repository during the course with new slides and materials.

Do not modify the files and everytime you start working or using this repository run:

git pull

And your local repository will be updated.

Creating your repository

For the course exercises, notes and everything else, I suggest you to create a local folder to track with Git and Github. Follow these steps:

  • create an R Project
  • create an R/ folder
  • init the git repository with the command git init
  • add all files with git add .
  • commit the changes with git commit -m "message"

Then you need to create and link the online repository. Go to Github and create a new empty repository. Copy the SSH address and run git remote add origin <ssh link>. Then run git push. In this way your local and online Git repositories will be linked.

Check these other resources to learn Git:

renv

renv is the equivalent of venv in Python. Basically allows to create a by-project library of R packages with a specific version. Sometimes packages change defaults, functions, etc. thus fixing them improve the reproducibility and remove unexpected results.

For a detailed guide about renv you can read the official documentation https://rstudio.github.io/renv/articles/renv.html.

When opening the R project of the repository, renv should prompt you to install renv itself (if missing) and then to install the packages included into the renv.lock file.

To create new project with renv you can type:

renv::init()

and following the instructions. renv will create all the required files and folders and switch to the local library.