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

* 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.n 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
* Installing Git
** 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.n redhat, fedora).

Run (as root):
#+begin_src sh :results output :exports both
apt-get update ; apt-get install git
#+end_src
** Mac OSX and Windows
- Download and install Git from the [[https://git-scm.com/downloads][Git website]].
- Optional Git clients (should not be needed if you work within
  Rstudio):
  - [[https://www.sourcetreeapp.com/][SourceTree]]
  - [[https://desktop.github.com/][GitHub Desktop]] 
    #+BEGIN_QUOTE
    [[https://github.com/desktop/desktop/issues/852][Apparently]], this works with gitlab and https.
    #+END_QUOTE
* Rstudio and git/github/gitlab
#+BEGIN_QUOTE
We may want to redo a screencast in French for this
#+END_QUOTE
- [[https://www.rstudio.com/resources/webinars/rstudio-essentials-webinar-series-managing-part-2/][This video on using git/githugb/gitlab from Rstudio]] (starting at time 9:09)

Alternatively, we can point to:
http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/
- Part 1/item 2: Setup Git in RStudio
- Part 2 (to adapt to gitlab)
- Part 3
* Cheat Sheets
The Rstudio team has created a lot of good material and tutorials. You
should definitively look at the [[https://www.rstudio.com/resources/cheatsheets/][Cheat sheets webpage]]. In particular
you want to have look at the ones on:
- [[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]],
- 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]]