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Commit b8db2e1f authored by Arnaud Legrand's avatar Arnaud Legrand
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Completed the Rstudio resource webpage. 

Replacing the lengthy Rstudio/github by an Rstudio/GitLab video would
be nice.
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module2/ressources/rstudio.html
View file @ b8db2e1f
......@@ -4,40 +4,88 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org68a44ad">Installing Rstudio</a>
<li style="margin-bottom:0;"><a href="#org6a08c55">Installing Rstudio</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org75fa2dd">Linux (debian, ubuntu)</a>
<li style="margin-bottom:0;"><a href="#org2204883">Linux (debian, ubuntu)</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgb3ecfea">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#orgd6fe18e">Installing rstudio</a></li>
<li style="margin-bottom:0;"><a href="#org9e7e4df">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#orge261910">Installing rstudio</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org337678e">Mac OSX and Windows</a></li>
<li style="margin-bottom:0;"><a href="#org0f1374d">Mac OSX and Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org150ee9f">Installing Git</a>
<li style="margin-bottom:0;"><a href="#orgd743f10">Installing Git</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org79b3b23">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org536eda4">Mac OSX and Windows</a></li>
<li style="margin-bottom:0;"><a href="#org194d7d9">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#orga033592">Mac OSX and Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org3890548">Setting up SSH</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org8fce29e">Installation</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org24a337f">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#orgd8eb69c">Mac OSX</a></li>
<li style="margin-bottom:0;"><a href="#org02c1827">Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgfaac61e">Setting up SSH on Framagit</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgbb4bef3">Rstudio and git/github/gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org81cf7bc">Cheat Sheets</a></li>
</ul>
</div>
</div>
<p>
If you have never used git with Rstudio, <b>we strongly advise that you
follow the <a href="https://swcarpentry.github.io/git-novice/14-supplemental-rstudio/index.html">step-by-step explanations from Software Carpentry</a></b>. It comes
with many screenshots and is quite progressive. Alternatively, you
may want to watch this video:
</p>
<iframe width="854" height="480" src="https://www.youtube.com/embed/uHYcDQDbMY8" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
<p>
The next sections provide information on how to install Rstudio, Git
(to interact with GitLab), and SSH (to avoid typing your password
every time you synchronize with GitLab).
</p>
<p>
Finally, you need to know that the Rstudio team has created a lot of
very good material and tutorials. You should definitively look at the
<a href="https://www.rstudio.com/resources/cheatsheets/">Cheat sheets webpage</a>. In particular you want to have look at the ones
on:
</p>
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf">The Rstudio IDE</a>,</li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf">R Markdown</a>,</li>
<li style="margin-bottom:0;">The <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">R Markdown Reference guide</a>,</li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf">Data visualization with ggplot2</a>,</li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf">Data transformation with dplyr</a></li>
</ul>
<p>
In case it helps, here are some (sometimes outdated) French versions
of these documents:
</p>
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf">L'IDE Rstudio</a></li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf">Visualisation de données avec ggplot2</a></li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf">Transformation de données avec dplyr</a></li>
<li style="margin-bottom:0;"><a href="https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf">Un court document sur R Markdown</a></li>
</ul>
<div id="outline-container-org68a44ad" class="outline-2">
<h2 id="org68a44ad">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org68a44ad">
<div id="outline-container-org6a08c55" class="outline-2">
<h2 id="org6a08c55">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org6a08c55">
</div>
<div id="outline-container-org75fa2dd" class="outline-3">
<h3 id="org75fa2dd">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org75fa2dd">
<div id="outline-container-org2204883" class="outline-3">
<h3 id="org2204883">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org2204883">
<p>
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).
for other distributions (e.g., redhat, fedora).
</p>
<p>
......@@ -55,9 +103,9 @@ for upgrading&#x2026;
</p>
</div>
<div id="outline-container-orgb3ecfea" class="outline-4">
<h4 id="orgb3ecfea">Installing R</h4>
<div class="outline-text-4" id="text-orgb3ecfea">
<div id="outline-container-org9e7e4df" class="outline-4">
<h4 id="org9e7e4df">Installing R</h4>
<div class="outline-text-4" id="text-org9e7e4df">
<p>
Beforehand, you need to install the R language and convenient packages
by running (as root):
......@@ -90,9 +138,9 @@ to run (as root):
</div>
</div>
<div id="outline-container-orgd6fe18e" class="outline-4">
<h4 id="orgd6fe18e">Installing rstudio</h4>
<div class="outline-text-4" id="text-orgd6fe18e">
<div id="outline-container-orge261910" class="outline-4">
<h4 id="orge261910">Installing rstudio</h4>
<div class="outline-text-4" id="text-orge261910">
<p>
Rstudio is unfortunately not packaged within debian so the easiest is
to download the corresponding debian package on the <a href="https://www.rstudio.com/products/rstudio/download/#download">Rstudio webpage</a>
......@@ -110,9 +158,9 @@ sudo apt-get update ; sudo apt-get -f install <span style="font-weight: bold; fo
</div>
</div>
</div>
<div id="outline-container-org337678e" class="outline-3">
<h3 id="org337678e">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org337678e">
<div id="outline-container-org0f1374d" class="outline-3">
<h3 id="org0f1374d">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org0f1374d">
<blockquote>
<p>
Some instructions on installing R and knitr must be missing. This
......@@ -136,17 +184,17 @@ install.packages(<span style="font-style: italic;">"ggplot2"</span>)
</div>
</div>
</div>
<div id="outline-container-org150ee9f" class="outline-2">
<h2 id="org150ee9f">Installing Git</h2>
<div class="outline-text-2" id="text-org150ee9f">
<div id="outline-container-orgd743f10" class="outline-2">
<h2 id="orgd743f10">Installing Git</h2>
<div class="outline-text-2" id="text-orgd743f10">
</div>
<div id="outline-container-org79b3b23" class="outline-3">
<h3 id="org79b3b23">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org79b3b23">
<div id="outline-container-org194d7d9" class="outline-3">
<h3 id="org194d7d9">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org194d7d9">
<p>
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).
for other distributions (e.g., redhat, fedora).
</p>
<p>
......@@ -158,9 +206,9 @@ Run (as root):
</div>
</div>
</div>
<div id="outline-container-org536eda4" class="outline-3">
<h3 id="org536eda4">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org536eda4">
<div id="outline-container-orga033592" class="outline-3">
<h3 id="orga033592">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-orga033592">
<ul class="org-ul">
<li style="margin-bottom:0;">Download and install Git from the <a href="https://git-scm.com/downloads">Git website</a>.</li>
<li style="margin-bottom:0;">Optional Git clients (should not be needed if you work within
......@@ -172,7 +220,7 @@ Rstudio):
</p>
<blockquote>
<p>
<a href="https://github.com/desktop/desktop/issues/852">Apparently</a>, this works with gitlab and https.
<a href="https://github.com/desktop/desktop/issues/852">Apparently</a>, this works with GitLab and https.
</p>
</blockquote></li>
</ul></li>
......@@ -180,55 +228,69 @@ Rstudio):
</div>
</div>
</div>
<div id="outline-container-orgbb4bef3" class="outline-2">
<h2 id="orgbb4bef3">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-orgbb4bef3">
<blockquote>
<div id="outline-container-org3890548" class="outline-2">
<h2 id="org3890548">Setting up SSH</h2>
<div class="outline-text-2" id="text-org3890548">
<p>
We may want to redo a screencast in French for this
There are two ways of synchronizing your local repository with GitLab:
through HTTPS or through SSH. The first one does not require any
particular configuration but you will be regularly prompted for your
GitLab password, which can be quite tedious. To avoid this, the best
solution is to set install SSH, to create a pair or private/public
keys, and to upload your SSH public key on GitLab. This section
provides with information on how to do this.
</p>
</div>
<div id="outline-container-org8fce29e" class="outline-3">
<h3 id="org8fce29e">Installation</h3>
<div class="outline-text-3" id="text-org8fce29e">
</div>
<div id="outline-container-org24a337f" class="outline-4">
<h4 id="org24a337f">Linux (debian, ubuntu)</h4>
<div class="outline-text-4" id="text-org24a337f">
<p>
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).
</p>
</blockquote>
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://www.rstudio.com/resources/webinars/rstudio-essentials-webinar-series-managing-part-2/">This video on using git/githugb/gitlab from Rstudio</a> (starting at time 9:09)</li>
</ul>
<p>
Alternatively, we can point to:
<a href="http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/">http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/</a>
Run (as root):
</p>
<ul class="org-ul">
<li style="margin-bottom:0;">Part 1/item 2: Setup Git in RStudio</li>
<li style="margin-bottom:0;">Part 2 (to adapt to gitlab)</li>
<li style="margin-bottom:0;">Part 3</li>
</ul>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">apt-get update ; apt-get install openssh-client
</pre>
</div>
</div>
</div>
<div id="outline-container-org81cf7bc" class="outline-2">
<h2 id="org81cf7bc">Cheat Sheets</h2>
<div class="outline-text-2" id="text-org81cf7bc">
<div id="outline-container-orgd8eb69c" class="outline-4">
<h4 id="orgd8eb69c">Mac OSX</h4>
<div class="outline-text-4" id="text-orgd8eb69c">
<p>
The Rstudio team has created a lot of good material and tutorials. You
should definitively look at the <a href="https://www.rstudio.com/resources/cheatsheets/">Cheat sheets webpage</a>. In particular
you want to have look at the ones on:
You do not have anything to do as it is installed by default.
</p>
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf">the Rstudio IDE</a>,</li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf">R Markdown</a>,</li>
<li style="margin-bottom:0;">the <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">R Markdown Reference guide</a>,</li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf">data visualization with ggplot2</a>,</li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf">data transformation with dplyr</a></li>
</ul>
</div>
</div>
<div id="outline-container-org02c1827" class="outline-4">
<h4 id="org02c1827">Windows</h4>
<div class="outline-text-4" id="text-org02c1827">
<p>
In case it helps, here are some (sometimes outdated) French versions
of these documents:
You should install the <a href="https://www.ssh.com/ssh/putty/windows/">Putty</a> client. Once it is installed, look for
the section on <a href="https://www.ssh.com/ssh/putty/windows/puttygen">generating an SSH key</a>.
</p>
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf">L'IDE Rstudio</a></li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf">Visualisation de données avec ggplot2</a></li>
<li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf">Transformation de données avec dplyr</a></li>
<li style="margin-bottom:0;"><a href="https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf">Un court document sur R Markdown</a></li>
</ul>
</div>
</div>
</div>
<div id="outline-container-orgfaac61e" class="outline-3">
<h3 id="orgfaac61e">Setting up SSH on Framagit</h3>
<div class="outline-text-3" id="text-orgfaac61e">
<p>
Here are <a href="https://docs.gitlab.com/ee/ssh/">all the official explanations on how to set up your SSH key
on GitLab</a>. Alternatively, you may also want to have a look at this
video:
</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/54mxyLo3Mqk" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
</div>
</div>
</div>
</div>
module2/ressources/rstudio.org
View file @ b8db2e1f
......@@ -5,11 +5,41 @@
#+STARTUP: overview indent
#+OPTIONS: num:nil toc:t
If you have never used git with Rstudio, *we strongly advise that you
follow 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. Alternatively, you
may want to watch this video:
#+BEGIN_EXPORT html
<iframe width="854" height="480" src="https://www.youtube.com/embed/uHYcDQDbMY8" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
#+END_EXPORT
The next sections provide information on how to install Rstudio, Git
(to interact with GitLab), and SSH (to avoid typing your password
every time you synchronize with GitLab).
Finally, you need to 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 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]]
* 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).
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:
......@@ -71,7 +101,7 @@ install.packages("ggplot2")
** 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).
for other distributions (e.g., redhat, fedora).
Run (as root):
#+begin_src sh :results output :exports both
......@@ -84,32 +114,35 @@ apt-get update ; apt-get install git
- [[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.
[[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]]
* Setting up SSH
There are two ways of synchronizing your local repository with GitLab:
through HTTPS or through SSH. The first one does not require any
particular configuration but you will be regularly prompted for your
GitLab password, which can be quite tedious. To avoid this, the best
solution is to set install SSH, to create a pair or private/public
keys, and to upload your SSH public key on GitLab. This section
provides with information on how to do this.
** Installation
*** 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).
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]]
Run (as root):
#+begin_src sh :results output :exports both
apt-get update ; apt-get install openssh-client
#+end_src
*** Mac OSX
You do not have anything to do as it is installed by default.
*** Windows
You should install the [[https://www.ssh.com/ssh/putty/windows/][Putty]] client. Once it is installed, look for
the section on [[https://www.ssh.com/ssh/putty/windows/puttygen][generating an SSH key]].
** Setting up SSH on Framagit
Here are [[https://docs.gitlab.com/ee/ssh/][all the official explanations on how to set up your SSH key
on GitLab]]. Alternatively, you may also want to have a look at this
video:
#+BEGIN_EXPORT html
<iframe width="560" height="315" src="https://www.youtube.com/embed/54mxyLo3Mqk" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
#+END_EXPORT
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