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

This document provides information on how to install 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+session01bis/courseware/66bc811404b8481da5f794de54681c5e/d6b5dbe8add046e4bde324ed3fc936fa/3][our tutorial on using git from Rstudio]]* (in French). Before
proceeding, make sure you also have followed the *[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/f6580ad8e997400faeffe9af4fd37063/2]["git/GitLab
configuration" tutorial]]* (in French). 

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.

Last, you should know that 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In case it helps, here are some (sometimes outdated) French versions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]]

* 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 emacs and org-mode:
- 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
Beforehand, 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 (depending on when you do this, you
can obviously change the version number). 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
#+BEGIN_QUOTE
  Some instructions on installing R and knitr must be missing. This
  should be tested and improved.
#+END_QUOTE
Download and install rstudio from the [[https://www.rstudio.com/products/rstudio/download/#download][Rstudio webpage]] by choosing the
right operating system.

Then open Rstudio and type the following commands in the console to
install knitr and ggplot2:
#+BEGIN_SRC R
install.packages("knitr")
install.packages("ggplot2")
#+END_SRC