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Revision of the RStudio resources

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#+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/jump_to_id/d132a854b0464ad29085cedaded23136][our tutorial on using git from Rstudio]]* (/"Rstudio et Gitlab"/ in French). Before
proceeding, make sure you also have followed the *[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85]["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In case it helps, here are some (sometimes outdated) French versions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
* Installing RStudio
** Linux (debian, ubuntu)
We provide here only instructions for debian-based distributions. Feel
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).
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:
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]]
......@@ -48,7 +20,7 @@ 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
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
......@@ -57,7 +29,7 @@ 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):
RStudio):
#+BEGIN_SRC R
install.packages("knitr")
install.packages("ggplot2")
......@@ -69,11 +41,10 @@ to run (as root):
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:
*** 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/
......@@ -87,14 +58,41 @@ sudo apt-get update ; sudo apt-get -f install # to fix possibly missing dependen
should be tested and improved.
#+END_QUOTE
- Download and install R from the [[https://cran.r-project.org/][CRAN webpage]] by choosing the right operating system.
- 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 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=:
- 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
* Using Git from Rstudio
* 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+session01bis/jump_to_id/d132a854b0464ad29085cedaded23136][our tutorial on using git from RStudio]]* (/"RStudio et Gitlab"/
in French). Before proceeding, make sure you also have followed the
*[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85]["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.
** Cloning a repository
Open RStudio and do the following steps:
- Create a new version controled project: =File / New Project / Version Control=
......@@ -103,7 +101,7 @@ Open RStudio and do the following steps:
[[file:rstudio_images/git.png]]
#+END_CENTER
- Get the url from your gitlab repository:
- Get the URL from your GitLab repository:
#+BEGIN_CENTER
[[file:rstudio_images/adresse_depot.png]]
#+END_CENTER
......
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