diff --git a/html_src_files.lst b/html_src_files.lst index 007b5664326973a76ab140a61b794d68d0251e35..d8430d81d4aba76b83fe52ad3b4ece8d0ff463fe 100644 --- a/html_src_files.lst +++ b/html_src_files.lst @@ -21,6 +21,10 @@ ./module2/ressources/jupyter_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/8dcce91be83c4ece834abfa98b8bbfb1 ./module2/ressources/rstudio.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/09d339f009cd4b45a468583ab7730221 ./module2/ressources/rstudio_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/09d339f009cd4b45a468583ab7730221 +./module2/ressources/rstudio-install-doc.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/09d339f009cd4b45a468583ab7730221 +./module2/ressources/rstudio-install-doc_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/09d339f009cd4b45a468583ab7730221 +./module2/ressources/rstudio-git.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/09d339f009cd4b45a468583ab7730221 +./module2/ressources/rstudio-git_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/09d339f009cd4b45a468583ab7730221 ./module2/ressources/gitlab.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/448cd6f9018545d1a67405551add6fda ./module2/ressources/gitlab_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/448cd6f9018545d1a67405551add6fda ./module2/ressources/emacs_orgmode.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/954f94ce4f9a4d858d47b41793cc96c8 diff --git a/module2/ressources/rstudio-git.org b/module2/ressources/rstudio-git.org new file mode 100644 index 0000000000000000000000000000000000000000..35bace6d1ff909b0cb369ecb1077c38dde86a607 --- /dev/null +++ b/module2/ressources/rstudio-git.org @@ -0,0 +1,79 @@ +# -*- mode: org -*- +#+TITLE: Using Git from RStudio +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t + +* Table of Contents :TOC: +- [[#to-begin][To begin]] +- [[#cloning-a-repository][Cloning a repository]] +- [[#modifying-a-file][Modifying a file]] + +* To begin +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. diff --git a/module2/ressources/rstudio-git_fr.org b/module2/ressources/rstudio-git_fr.org new file mode 100644 index 0000000000000000000000000000000000000000..acb2a7ce29d92bb5d2cd61e3f1d8ad1a004b21a6 --- /dev/null +++ b/module2/ressources/rstudio-git_fr.org @@ -0,0 +1,82 @@ +# -*- mode: org -*- +#+TITLE: Utiliser Git avec RStudio +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t + +* Table des matières :TOC: +- [[#pour-commencer][Pour commencer]] +- [[#Cloner-un-dépôt][Cloner un dépôt]] +- [[#modifier-un-fichier][Modifier un fichier]] + +* Avant de commencer +La première chose à faire est de configurer Git sur votre +ordinateur. Pour ce faire, vous pouvez suivre la vidéo +[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][configurer Git pour Gitlab]] et le document +[[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/gitlab_fr.org][Git et Gitlab]] correspondant. + +Vous pourrez alors utiliser Git avec RStudio. Pour ce faire, vous +pouvez suivre la vidéo [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/d132a854b0464ad29085cedaded23136][RStudio - Gitlab]] dont les étapes +sont reprises ci-dessous. + +/(Nous vous signalons aussi cette/ [[https://www.youtube.com/embed/uHYcDQDbMY8][vidéo]] /(en anglais) ainsi que le/ [[https://swcarpentry.github.io/git-novice/14-supplemental-rstudio/index.html][tuto +pas à pas]] /(en anglais) de Software Carpentry.)/ + +* Cloner un dépôt +Ouvrir RStudio et procéder comme suit : +- Créer un nouveau projet sous contrôle de version : =File / New Project / Version Control= + #+BEGIN_CENTER + [[file:rstudio_images/new_project.png]] + + [[file:rstudio_images/git.png]] + #+END_CENTER +- Récupérer l'URL du dépôt Gitlab + #+BEGIN_CENTER + [[file:rstudio_images/adresse_depot.png]] + #+END_CENTER +- Indiquez cette URL dans le champ "Repository URL" /(vous voudrez/ + /peut-être préfixer cette URL avec =xxx@= où =xxx= est votre identifiant/ + /Gitlab pour éviter d'avoir à le ressaisir ultérieurement)/. + + #+BEGIN_CENTER + [[file:rstudio_images/clone.png]] + #+END_CENTER +- Si vous êtes derrière un proxy, il faut le définir dans Git (voir le + paragraphe "Gérer les proxy" de la page sur [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][Git et Gitlab]]). +- Git se connecte à Gitlab et récupère une copie complète du dépôt. +- RStudio redémarre dans un mode lié à Git : + #+BEGIN_CENTER + [[file:rstudio_images/rstudio.png]] + #+END_CENTER +- Le gestionnaire de fichiers à droite vous permet de parcourir le + dépôt sous contrôle de version. +* Modifier un fichier +- Ouvrir le fichier =Module2/exo1/toy_document.Rmd= et le modifier. +- Enregistrer. +- Aller dans le menu Git pour effectuer le commit. + #+BEGIN_CENTER + [[file:rstudio_images/commit.png]] + + [[file:rstudio_images/commit2.png]] + #+END_CENTER +- Sélectionner les lignes à commiter puis cliquer sur =commit=. + #+BEGIN_CENTER + [[file:rstudio_images/commit5.png]] + #+END_CENTER + Les modifications ont été commitées uniquement sur la machine. Elles + n'ont pas été propagées sur Gitlab. +- Cliquer sur =push= pour les propager sur Gitlab. + #+BEGIN_CENTER + [[file:rstudio_images/push.png]] + + [[file:rstudio_images/push2.png]] + + [[file:rstudio_images/push3.png]] + #+END_CENTER + N.B. : Vous ne pouvez pas propager vos modifications sur GitLab si + des modifications ont été faites sur GitLab entre-temps. + #+BEGIN_CENTER + [[file:rstudio_images/push4.png]] + #+END_CENTER +- Il faut d’abord récupérer ces modifications distantes sur votre + machine locale. Pour ce faire cliquer sur =pull=. diff --git a/module2/ressources/rstudio-install-doc.org b/module2/ressources/rstudio-install-doc.org new file mode 100644 index 0000000000000000000000000000000000000000..0ae60de9a3479fc872c5eedd76f3c174235f8dea --- /dev/null +++ b/module2/ressources/rstudio-install-doc.org @@ -0,0 +1,85 @@ +# -*- mode: org -*- +#+TITLE: Rstudio: installating and documentation +#+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]] + +* 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]] + diff --git a/module2/ressources/rstudio-install-doc_fr.org b/module2/ressources/rstudio-install-doc_fr.org new file mode 100644 index 0000000000000000000000000000000000000000..f5aa664ff037cb6db72170081ce0bec093c6c61e --- /dev/null +++ b/module2/ressources/rstudio-install-doc_fr.org @@ -0,0 +1,88 @@ +# -*- mode: org -*- +#+TITLE: Rstudio : installation et documentation +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t + +* Table des matières :TOC: +- [[#installer-rstudio][Installer RStudio]] + - [[#linux-debian-ubuntu][Linux (debian, ubuntu)]] + - [[#mac-osx-and-windows][Mac OSX and Windows]] +- [[#documentation-rstudio][Documentation RStudio]] + +* Installer RStudio +** Linux (debian, ubuntu) +Nous ne fournissons ici que des instructions pour les distributions + basées sur Debian. N’hésitez pas à contribuer à ce document en + fournissant des informations à jour sur les autres distributions + (RedHat, Fedora, par exemple). + +Aujourd'hui, les versions stables des distributions les plus courantes +fournissent des versions assez récentes de R : +- Debian (stretch) est livré avec [[https://packages.debian.org/stretch/r-base][R 3.3.3-1]], [[https://packages.debian.org/stretch/r-cran-knitr][knitr 1.15.1]], et [[https://packages.debian.org/stretch/r-cran-ggplot2][ggplot 2.2.1]] +- Ubuntu (bionic 18.04) est livré avec [[https://packages.ubuntu.com/bionic/r-base][R 3.4.4]], [[https://packages.ubuntu.com/bionic/r-cran-knitr][knitr 1.17]], et [[https://packages.ubuntu.com/bionic/r-cran-ggplot2][ggplot 2.2.1]] +- Ubuntu (artful 17.04) est livré avec [[https://packages.ubuntu.com/artful/r-base][R 3.4.2]], [[https://packages.ubuntu.com/artful/r-cran-knitr][knitr 1.15]], et [[https://packages.ubuntu.com/artful/r-cran-ggplot2][ggplot 2.2.1]] +Si votre distribution est plus ancienne, c'est peut-être l'occasion de +la mettre à jour... + +*** Installer R +Pour commencer, vous devez installer le langage R et quelques packages +en exécutant (à la racine) : +#+BEGIN_SRC shell +apt-get update ; sudo apt-get install r-base r-cran-knitr r-cran-ggplot2 +#+END_SRC + +Si l'installation de =r-cran-knitr= ou =r-cran-gplot2= échoue, vous pouvez +également installer ces packages manuellement en exécutant les +commandes suivantes sous R (ou RStudio) : +#+BEGIN_SRC R +install.packages("knitr") +install.packages("ggplot2") +#+END_SRC + +Si vous envisagez d'exporter des documents pdf avec LaTeX, il faudra +probablement aussi exécuter (à la racine) : +#+begin_src shell :results output :exports both +apt-get update ; apt-get install texlive-base +#+end_src + +*** Installer RStudio +RStudio n’est malheureusement pas intégré à Debian. Le plus simple est + de télécharger le paquet Debian correspondant sur le [[https://www.rstudio.com/products/rstudio/download/#download][site RStudio]], + puis de l’installer manuellement (vous devrez peut-être adapter le + numéro de version) : + +#+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 +- Installer R et Python en suivant les instruction dans une [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/19c2b1de7766484bae73f3ab133463c6][ressource spécifique]]. +- Télécharger et installer RStudio depuis le [[https://www.rstudio.com/products/rstudio/download/#download][site RStudio]] en + choisissant le bon système d'exploitation. +- Télécharger et installer MiKTeX depuis le [[https://miktex.org/download][site MiKTeX]] en choisissant le bon + système d'exploitation. Vous serez amené à installer différents + packages lors du premier export pdf. +- Ouvrir RStudio et exécuter les commandes suivantes dans la console pour + installer =knitr= et =ggplot2= +#+BEGIN_SRC R +install.packages("knitr", dep=TRUE) +install.packages("ggplot2", dep=TRUE) +#+END_SRC +* Documentation RStudio +L’équipe de RStudio a créé différents matériels et tutoriels très bien +faits. Nous vous recommandons de consulter les [[https://www.rstudio.com/resources/cheatsheets/][fiches mémo]]. En +particulier, vous pourriez être intéressés par celles-ci : +- [[https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf][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]] +Voici aussi les versions françaises de certains documents mais elles +ne sont pas toujours à jour : +- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf][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]]