# -*- mode: org -*-
#+TITLE:     Rstudio
#+DATE: June, 2018
#+STARTUP: overview indent
#+OPTIONS: num:nil toc:t

* Table of Contents                                                     :TOC:
- [[#installing-rstudio][Installing RStudio]]
  - [[#linux-debian-ubuntu][Linux (debian, ubuntu)]]
  - [[#mac-osx-and-windows][Mac OSX and Windows]]
- [[#rstudio-documentation][RStudio documentation]]
- [[#using-git-from-rstudio][Using Git from RStudio]]
  - [[#cloning-a-repository][Cloning a repository]]
  - [[#modifying-a-file][Modifying a file]]

* 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:
- Debian (stretch) ships with [[https://packages.debian.org/stretch/r-base][R 3.3.3-1]], [[https://packages.debian.org/stretch/r-cran-knitr][knitr 1.15.1]], and  [[https://packages.debian.org/stretch/r-cran-ggplot2][ggplot 2.2.1]]
- Ubuntu (bionic 18.04) ships with [[https://packages.ubuntu.com/bionic/r-base][R 3.4.4]], and [[https://packages.ubuntu.com/bionic/r-cran-knitr][knitr 1.17]], and [[https://packages.ubuntu.com/bionic/r-cran-ggplot2][ggplot 2.2.1]]
- Ubuntu (artful 17.04) ships with [[https://packages.ubuntu.com/artful/r-base][R 3.4.2]], and [[https://packages.ubuntu.com/artful/r-cran-knitr][knitr 1.15]], and [[https://packages.ubuntu.com/artful/r-cran-ggplot2][ggplot 2.2.1]]
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):
#+BEGIN_SRC shell
apt-get update ; sudo apt-get install r-base r-cran-knitr r-cran-ggplot2 
#+END_SRC

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):
#+BEGIN_SRC R
install.packages("knitr")
install.packages("ggplot2")
#+END_SRC

If you plan to export pdf documents with LaTeX, you probably also want
to run (as root):
#+begin_src sh :results output :exports both
apt-get update ; apt-get install texlive-base
#+end_src

*** Installing RStudio
RStudio is unfortunately not packaged within Debian so the easiest is
to download the corresponding Debian package on the [[https://www.rstudio.com/products/rstudio/download/#download][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:

#+BEGIN_SRC shell
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
#+END_SRC
** Mac OSX and Windows
- Install R and Python following the instructions given in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/19c2b1de7766484bae73f3ab133463c6][separate resource]].
- Download and install RStudio from the [[https://www.rstudio.com/products/rstudio/download/#download][RStudio webpage]] by choosing the right operating system.
- Download and install MiKTeX from the [[https://miktex.org/download][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=:
#+BEGIN_SRC R
install.packages("knitr", dep=TRUE)
install.packages("ggplot2", dep=TRUE)
#+END_SRC
* RStudio documentation
The RStudio team has created a lot of very good material and
tutorials. You should definitively look at the [[https://www.rstudio.com/resources/cheatsheets/][Cheat sheets
webpage]]. In particular you may want to have look at the following
ones:
- [[https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf][The RStudio IDE]],
- [[https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf][R Markdown]] (here is also a [[https://rmarkdown.rstudio.com/][nice step-by-step presentation of Rmarkdown]]),
- The [[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf][R Markdown Reference guide]],
- [[https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf][Data visualization with ggplot2]],
- [[https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf][Data transformation with dplyr]]
In case it helps, here are some (sometimes outdated) French versions
of these documents: 
- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf][L'IDE RStudio]]
- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf][Visualisation de données avec ggplot2]]
- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf][Transformation de données avec dplyr]]
- [[https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf][Un court document sur R Markdown]]

* Using Git from RStudio
If you have never used git with RStudio, *we strongly advise that you
follow [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/d132a854b0464ad29085cedaded23136][our tutorial on using git from RStudio]]* (/"RStudio et Gitlab"/
). Before proceeding, make sure you also have followed the
*[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85]["git/GitLab configuration" tutorial]]*.

Alternatively, you may want to watch [[https://www.youtube.com/embed/uHYcDQDbMY8][this video]] (in English). If you
do not like videos, you should have a look at the [[https://swcarpentry.github.io/git-novice/14-supplemental-rstudio/index.html][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=
  #+BEGIN_CENTER
  [[file:rstudio_images/new_project.png]]

  [[file:rstudio_images/git.png]]
  #+END_CENTER
- Get the URL from your GitLab repository:
  #+BEGIN_CENTER
  [[file:rstudio_images/adresse_depot.png]]
  #+END_CENTER
- 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/). 
  #+BEGIN_CENTER
  [[file:rstudio_images/clone.png]]
  #+END_CENTER
- If you're behind a proxy, git should be configured
  accordingly. Check the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85]["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:
  #+BEGIN_CENTER
  [[file:rstudio_images/rstudio.png]]
  #+END_CENTER
- 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
  #+BEGIN_CENTER
  [[file:rstudio_images/commit.png]]

  [[file:rstudio_images/commit2.png]]
  #+END_CENTER
- Select the lines to commit and then click on =commit=
  #+BEGIN_CENTER
  [[file:rstudio_images/commit5.png]]
  #+END_CENTER
  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
  #+BEGIN_CENTER
  [[file:rstudio_images/push.png]]

  [[file:rstudio_images/push2.png]]

  [[file:rstudio_images/push3.png]]
  #+END_CENTER
  *NB*: You won't be able to propagate your modifications on GitLab if
  some modifications have been done on GitLab in the meantime. 
  [[file:rstudio_images/push4.png]]
- You should first merge these remote modifications locally. Click on
  =pull= to get these modifications on your machine.