Rstudio

Table of Contents

Installing RStudio

Linux (debian, ubuntu)

We provide here only instructions for Debian-based distributions. Feel free to contribute to this document to provide up-to-date information for other distributions (e.g., RedHat, Fedora).

Today, the stable versions of the most common distributions provide recent enough versions of R:

If your distribution is older than this, well, it may be a good time for upgrading…

Installing R

First, you need to install the R language and convenient packages by running (as root): 

apt-get update ; sudo apt-get install r-base r-cran-knitr r-cran-ggplot2

Alternatively, if the installation of r-cran-gplot2 or r-cran-knitr fails, you may want to install them locally (through the R packaging system) and manually by running the following commands in R (or RStudio): 

install.packages("knitr")
install.packages("ggplot2")

If you plan to export pdf documents with LaTeX, you probably also want to run (as root): 

apt-get update ; apt-get install texlive-base

Installing RStudio

RStudio is unfortunately not packaged within Debian so the easiest is to download the corresponding Debian package on the RStudio webpage and then to install it manually (you may have to adjust the version number in the following example). Here is how to install it: 

cd /tmp/
wget https://download1.rstudio.org/rstudio-xenial-1.1.453-amd64.deb
sudo dpkg -i rstudio-xenial-1.1.453-amd64.deb
sudo apt-get update ; sudo apt-get -f install # to fix possibly missing dependencies

Mac OSX and Windows

Some instructions on installing R and knitr must be missing. This should be tested and improved.

  • Download and install R from the CRAN webpage by choosing the right operating system.
  • Download and install RStudio from the RStudio webpage by choosing the right operating system.
  • Download and install MiKTeX from the MiKTeX webpage by choosing the right operating system. You will be prompted to install some specific packages when exporting to pdf.
  • Open RStudio and type the following commands in the console to install knitr and ggplot2:
install.packages("knitr", dep=TRUE)
install.packages("ggplot2", dep=TRUE)

RStudio documentation

The RStudio team has created a lot of very good material and tutorials. You should definitively look at the Cheat sheets webpage. In particular you may want to have look at the following ones:

In case it helps, here are some (sometimes outdated) French versions of these documents:

Using Git from RStudio

If you have never used git with RStudio, we strongly advise that you follow our tutorial on using git from RStudio ("RStudio et Gitlab" in French). Before proceeding, make sure you also have followed the "git/GitLab configuration" tutorial (in French).

Alternatively, you may want to watch this video (in English). If you do not like videos, you should have a look at the step-by-step explanations from Software Carpentry. It comes with many screenshots and is quite progressive.

Cloning a repository

Open RStudio and do the following steps:

  • Create a new version controled project: File / New Project / Version Control

    new_project.png

    git.png

  • Get the URL from your GitLab repository:

    adresse_depot.png

  • Indicate this URL in the "Repository URL" field (you may want to prefix this URL with xxx@ where xxx is your Gitlab id to avoid repeatedly giving it later on).

    clone.png

  • If you're behind a proxy, git should be configured accordingly. Check the "Dealing with proxies" section.
  • Git will then connect to Gitlab and fetch a whole copy of the repository.

  • RStudio should restart in a mode related to Git:

    rstudio.png

  • The file manager on the right, allows you to browse the version controled repository.

Modifying a file

  • Open Module2/exo1/toy_document.Rmd and perform a simple modification.
  • Save

  • Go to the Git menu to commit

    commit.png

    commit2.png

  • Select the lines to commit and then click on commit

    commit5.png

    Your modifications have now been commited on your local machine. They haven't been propagated to GitLab yet.

  • Click on push to propagate them on GitLab

    push.png

    push2.png

    push3.png

    NB: You won't be able to propagate your modifications on GitLab if some modifications have been done on GitLab in the meantime. push4.png

  • You should first merge these remote modifications locally. Click on pull to get these modifications on your machine.