diff --git a/module2/ressources/rstudio.org b/module2/ressources/rstudio.org index 3715bb3bf214627ffa843fb90079881eacd450a4..352e6959e74fc457b75d4a2da63a2966ee3955e3 100644 --- a/module2/ressources/rstudio.org +++ b/module2/ressources/rstudio.org @@ -5,42 +5,14 @@ #+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transformation with dplyr]] -In case it helps, here are some (sometimes outdated) French versions -of these documents: -- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf][L'IDE Rstudio]] --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