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module1/ressources/introduction_to_markdown.html
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......@@ -4,26 +4,26 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge7765d4">Syntaxe</a>
<li style="margin-bottom:0;"><a href="#org8de79b7">Syntaxe</a>
<ul>
<li><a href="#orgfa68a29">Headers</a></li>
<li><a href="#org8efa22f">Emphasis</a></li>
<li><a href="#orge264e14">Lists</a>
<li style="margin-bottom:0;"><a href="#orgd0cd01a">Headers</a></li>
<li style="margin-bottom:0;"><a href="#org0a02e8a">Emphasis</a></li>
<li style="margin-bottom:0;"><a href="#org5ba3da0">Lists</a>
<ul>
<li><a href="#org8aff08d">Unordered</a></li>
<li><a href="#org4acaa77">Ordered</a></li>
<li style="margin-bottom:0;"><a href="#orgf404e08">Unordered</a></li>
<li style="margin-bottom:0;"><a href="#orga07db10">Ordered</a></li>
</ul>
</li>
<li><a href="#orgb7930f3">Images</a></li>
<li><a href="#orgef25979">Links</a></li>
<li><a href="#org075cffa">Blockquotes</a></li>
<li><a href="#orgfd6d212">Inline code</a></li>
<li style="margin-bottom:0;"><a href="#orgea33b61">Images</a></li>
<li style="margin-bottom:0;"><a href="#org45306c5">Links</a></li>
<li style="margin-bottom:0;"><a href="#org8cf7f47">Blockquotes</a></li>
<li style="margin-bottom:0;"><a href="#org5cc4188">Inline code</a></li>
</ul>
</li>
<li><a href="#orgec971b4">Écrire des Maths</a>
<li style="margin-bottom:0;"><a href="#orgf5d12d0">Écrire des Maths</a>
<ul>
<li><a href="#org71635d1">Lettres grecques</a></li>
<li><a href="#org08d8b82">Operators</a></li>
<li style="margin-bottom:0;"><a href="#orgd3d090f">Lettres grecques</a></li>
<li style="margin-bottom:0;"><a href="#org4cbab17">Operators</a></li>
</ul>
</li>
</ul>
......@@ -34,13 +34,13 @@ Voici un aperçu rapide de la syntaxe Markdown repris d'une
<a href="https://guides.github.com/features/mastering-markdown/">présentation de Github</a> ainsi que de celles d'<a href="http://csrgxtu.github.io/2015/03/20/Writing-Mathematic-Fomulars-in-Markdown/">Archer Reilly</a> et de <a href="http://www.statpower.net/Content/310/R%20Stuff/SampleMarkdown.html">James
H. Steiger</a>.
</p>
<div id="outline-container-orge7765d4" class="outline-2">
<h2 id="orge7765d4">Syntaxe</h2>
<div class="outline-text-2" id="text-orge7765d4">
<div id="outline-container-org8de79b7" class="outline-2">
<h2 id="org8de79b7">Syntaxe</h2>
<div class="outline-text-2" id="text-org8de79b7">
</div>
<div id="outline-container-orgfa68a29" class="outline-3">
<h3 id="orgfa68a29">Headers</h3>
<div class="outline-text-3" id="text-orgfa68a29">
<div id="outline-container-orgd0cd01a" class="outline-3">
<h3 id="orgd0cd01a">Headers</h3>
<div class="outline-text-3" id="text-orgd0cd01a">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
# This is an &lt;h1&gt; tag
## This is an &lt;h2&gt; tag
......@@ -49,9 +49,9 @@ H. Steiger</a>.
</div>
</div>
<div id="outline-container-org8efa22f" class="outline-3">
<h3 id="org8efa22f">Emphasis</h3>
<div class="outline-text-3" id="text-org8efa22f">
<div id="outline-container-org0a02e8a" class="outline-3">
<h3 id="org0a02e8a">Emphasis</h3>
<div class="outline-text-3" id="text-org0a02e8a">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
*This text will be italic*
_This will also be italic_
......@@ -64,13 +64,13 @@ _You **can** combine them_
</div>
</div>
<div id="outline-container-orge264e14" class="outline-3">
<h3 id="orge264e14">Lists</h3>
<div class="outline-text-3" id="text-orge264e14">
<div id="outline-container-org5ba3da0" class="outline-3">
<h3 id="org5ba3da0">Lists</h3>
<div class="outline-text-3" id="text-org5ba3da0">
</div>
<div id="outline-container-org8aff08d" class="outline-4">
<h4 id="org8aff08d">Unordered</h4>
<div class="outline-text-4" id="text-org8aff08d">
<div id="outline-container-orgf404e08" class="outline-4">
<h4 id="orgf404e08">Unordered</h4>
<div class="outline-text-4" id="text-orgf404e08">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
* Item 1
* Item 2
......@@ -79,9 +79,9 @@ _You **can** combine them_
</pre>
</div>
</div>
<div id="outline-container-org4acaa77" class="outline-4">
<h4 id="org4acaa77">Ordered</h4>
<div class="outline-text-4" id="text-org4acaa77">
<div id="outline-container-orga07db10" class="outline-4">
<h4 id="orga07db10">Ordered</h4>
<div class="outline-text-4" id="text-orga07db10">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
1. Item 1
1. Item 2
......@@ -92,27 +92,27 @@ _You **can** combine them_
</div>
</div>
</div>
<div id="outline-container-orgb7930f3" class="outline-3">
<h3 id="orgb7930f3">Images</h3>
<div class="outline-text-3" id="text-orgb7930f3">
<div id="outline-container-orgea33b61" class="outline-3">
<h3 id="orgea33b61">Images</h3>
<div class="outline-text-3" id="text-orgea33b61">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
![GitHub Logo](/images/logo.png)
Format: ![Alt Text](url)
</pre>
</div>
</div>
<div id="outline-container-orgef25979" class="outline-3">
<h3 id="orgef25979">Links</h3>
<div class="outline-text-3" id="text-orgef25979">
<div id="outline-container-org45306c5" class="outline-3">
<h3 id="org45306c5">Links</h3>
<div class="outline-text-3" id="text-org45306c5">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
http://github.com - automatic!
[GitHub](http://github.com)
</pre>
</div>
</div>
<div id="outline-container-org075cffa" class="outline-3">
<h3 id="org075cffa">Blockquotes</h3>
<div class="outline-text-3" id="text-org075cffa">
<div id="outline-container-org8cf7f47" class="outline-3">
<h3 id="org8cf7f47">Blockquotes</h3>
<div class="outline-text-3" id="text-org8cf7f47">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
As Kanye West said:
......@@ -121,9 +121,9 @@ As Kanye West said:
</pre>
</div>
</div>
<div id="outline-container-orgfd6d212" class="outline-3">
<h3 id="orgfd6d212">Inline code</h3>
<div class="outline-text-3" id="text-orgfd6d212">
<div id="outline-container-org5cc4188" class="outline-3">
<h3 id="org5cc4188">Inline code</h3>
<div class="outline-text-3" id="text-org5cc4188">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
I think you should use an
`&lt;addr&gt;` element here instead.
......@@ -131,9 +131,9 @@ I think you should use an
</div>
</div>
</div>
<div id="outline-container-orgec971b4" class="outline-2">
<h2 id="orgec971b4">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgec971b4">
<div id="outline-container-orgf5d12d0" class="outline-2">
<h2 id="orgf5d12d0">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgf5d12d0">
<p>
Equations can be formatted <b>inline</b> or as <b>displayed formulas</b>. In the
latter case, they are centered and set off from the main text. In the
......@@ -177,9 +177,9 @@ This summation expression is in display form.
</p>
</div>
<div id="outline-container-org71635d1" class="outline-3">
<h3 id="org71635d1">Lettres grecques</h3>
<div class="outline-text-3" id="text-org71635d1">
<div id="outline-container-orgd3d090f" class="outline-3">
<h3 id="orgd3d090f">Lettres grecques</h3>
<div class="outline-text-3" id="text-orgd3d090f">
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
......@@ -223,8 +223,8 @@ This summation expression is in display form.
</table>
</div>
</div>
<div id="outline-container-org08d8b82" class="outline-3">
<h3 id="org08d8b82">Operators</h3>
<div id="outline-container-org4cbab17" class="outline-3">
<h3 id="org4cbab17">Operators</h3>
</div>
</div>
</div>
module2/ressources/emacs_orgmode.html
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......@@ -4,64 +4,64 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9fae67d">Installing emacs, org-mode, ess, and auctex.</a>
<li style="margin-bottom:0;"><a href="#orgf0788f0">Installing emacs, org-mode, ess, and auctex.</a>
<ul>
<li><a href="#org7e26f43">OS-specific installation procedure</a>
<li style="margin-bottom:0;"><a href="#org8412fbd">OS-specific installation procedure</a>
<ul>
<li><a href="#orga1850db">Linux (Debian, Ubuntu)</a></li>
<li><a href="#org7e15d03">Mac OS X</a></li>
<li><a href="#org2955a3d">Windows</a></li>
<li style="margin-bottom:0;"><a href="#org6c162ce">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org61fb10d">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org6345a15">Windows</a></li>
</ul>
</li>
<li><a href="#org796e741">A simple "<i>reproducible research</i>" emacs configuration</a>
<li style="margin-bottom:0;"><a href="#org39100b1">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul>
<li><a href="#orgc87137c">Step 0: Backup and download our configuration</a></li>
<li><a href="#org0433a0a">Step 1: Prepare your journal</a></li>
<li><a href="#orgaf628c4">Step 2: Set up Emacs configuration</a></li>
<li><a href="#org76a0967">Step 3: Check whether the installation is working or not</a></li>
<li><a href="#org1b44bc8">Step 4: Open and play with your journal:</a></li>
<li style="margin-bottom:0;"><a href="#orgead59ff">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org45cc743">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org12df21d">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org1fbd541">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#org528bb3d">Step 4: Open and play with your journal:</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org5233724">Emacs Tips and tricks</a>
<li style="margin-bottom:0;"><a href="#orgf3207a2">Emacs Tips and tricks</a>
<ul>
<li><a href="#orgcf5a5b2">Cheat-sheets</a>
<li style="margin-bottom:0;"><a href="#org63f18b5">Cheat-sheets</a>
<ul>
<li><a href="#orgcb4078f">Emacs</a></li>
<li><a href="#orgde1963f">Org-mode</a></li>
<li style="margin-bottom:0;"><a href="#org22fe63d">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org4d46779">Org-mode</a></li>
</ul>
</li>
<li><a href="#orgc2d812a">Video tutorials</a></li>
<li><a href="#org6c3b81d">Additional useful emacs packages</a>
<li style="margin-bottom:0;"><a href="#orgefcfd8e">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org4a1463b">Additional useful emacs packages</a>
<ul>
<li><a href="#org2b1ba15">Company-mode</a></li>
<li><a href="#org5a154db">Magit</a></li>
<li style="margin-bottom:0;"><a href="#orgf784a61">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org57b6a55">Magit</a></li>
</ul>
</li>
<li><a href="#org00ecde8">Other resources</a></li>
<li style="margin-bottom:0;"><a href="#org84da85a">Other resources</a></li>
</ul>
</li>
<li><a href="#org0e133ea">A replicable article</a>
<li style="margin-bottom:0;"><a href="#org1a26eb1">A replicable article</a>
<ul>
<li><a href="#orgf3a84c7">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#org33696b8">A stub of replicable article</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org9fae67d" class="outline-2">
<h2 id="org9fae67d">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org9fae67d">
<div id="outline-container-orgf0788f0" class="outline-2">
<h2 id="orgf0788f0">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-orgf0788f0">
</div>
<div id="outline-container-org7e26f43" class="outline-3">
<h3 id="org7e26f43">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-org7e26f43">
<div id="outline-container-org8412fbd" class="outline-3">
<h3 id="org8412fbd">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-org8412fbd">
</div>
<div id="outline-container-orga1850db" class="outline-4">
<h4 id="orga1850db">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-orga1850db">
<div id="outline-container-org6c162ce" class="outline-4">
<h4 id="org6c162ce">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-org6c162ce">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -73,9 +73,9 @@ Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode:
</p>
<ul class="org-ul">
<li>Debian (stretch) ships with <a href="https://packages.debian.org/stretch/emacs25">emacs 25.1</a> and <a href="https://packages.debian.org/stretch/org-mode">org-mode 9.0.3</a></li>
<li>Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/bionic/org-mode">org-mode 9.1.6</a></li>
<li>Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/artful/org-mode">org-mode 9.0.9</a></li>
<li style="margin-bottom:0;">Debian (stretch) ships with <a href="https://packages.debian.org/stretch/emacs25">emacs 25.1</a> and <a href="https://packages.debian.org/stretch/org-mode">org-mode 9.0.3</a></li>
<li style="margin-bottom:0;">Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/bionic/org-mode">org-mode 9.1.6</a></li>
<li style="margin-bottom:0;">Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/artful/org-mode">org-mode 9.0.9</a></li>
</ul>
<p>
If your distribution is older than this, well, it may be a good time
......@@ -123,26 +123,26 @@ which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-org7e15d03" class="outline-4">
<h4 id="org7e15d03">Mac OS X</h4>
<div class="outline-text-4" id="text-org7e15d03">
<div id="outline-container-org61fb10d" class="outline-4">
<h4 id="org61fb10d">Mac OS X</h4>
<div class="outline-text-4" id="text-org61fb10d">
<ul class="org-ul">
<li><p>
<li style="margin-bottom:0;"><p>
<b>Option 1</b>: Install the <code>.dmg</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>:
<a href="https://vigou3.github.io/emacs-modified-macos/">https://vigou3.github.io/emacs-modified-macos/</a>. It ships with recent
versions:
</p>
<ul class="org-ul">
<li>Emacs 26.1</li>
<li>Org-mode 9.1.13</li>
<li>ESS 17.11</li>
<li style="margin-bottom:0;">Emacs 26.1</li>
<li style="margin-bottom:0;">Org-mode 9.1.13</li>
<li style="margin-bottom:0;">ESS 17.11</li>
</ul>
<p>
In that case you may have several versions of emacs installed on
your machine and launching emacs from a terminal may not run the one
you just installed. If anyone know how to get rid of this&#x2026;
</p></li>
<li><p>
<li style="margin-bottom:0;"><p>
<b>Option 2</b>: If you already use <code>brew</code>, simply do the following
</p>
<div class="org-src-container">
......@@ -158,25 +158,25 @@ brew install wget
</ul>
</div>
</div>
<div id="outline-container-org2955a3d" class="outline-4">
<h4 id="org2955a3d">Windows</h4>
<div class="outline-text-4" id="text-org2955a3d">
<div id="outline-container-org6345a15" class="outline-4">
<h4 id="org6345a15">Windows</h4>
<div class="outline-text-4" id="text-org6345a15">
<p>
Install the <code>.exe</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>:
<a href="https://vigou3.github.io/emacs-modified-windows/">https://vigou3.github.io/emacs-modified-windows/</a>. It ships with recent
versions:
</p>
<ul class="org-ul">
<li>Emacs 26.1</li>
<li>Org-mode 9.1.13</li>
<li>ESS 17.11</li>
<li style="margin-bottom:0;">Emacs 26.1</li>
<li style="margin-bottom:0;">Org-mode 9.1.13</li>
<li style="margin-bottom:0;">ESS 17.11</li>
</ul>
</div>
</div>
</div>
<div id="outline-container-org796e741" class="outline-3">
<h3 id="org796e741">A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-org796e741">
<div id="outline-container-org39100b1" class="outline-3">
<h3 id="org39100b1">A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-org39100b1">
<p>
Emacs comes with very basic default configuration and it appears like
everyone has its own taste. You will for example find <a href="https://www.emacswiki.org/emacs/StarterKits">here</a> several
......@@ -189,9 +189,9 @@ adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-orgc87137c" class="outline-4">
<h4 id="orgc87137c">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-orgc87137c">
<div id="outline-container-orgead59ff" class="outline-4">
<h4 id="orgead59ff">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-orgead59ff">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make
......@@ -212,9 +212,9 @@ rr_org/journal.org
</div>
</div>
<div id="outline-container-org0433a0a" class="outline-4">
<h4 id="org0433a0a">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-org0433a0a">
<div id="outline-container-org45cc743" class="outline-4">
<h4 id="org45cc743">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-org45cc743">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
......@@ -231,9 +231,9 @@ should give a try.
</p>
</div>
</div>
<div id="outline-container-orgaf628c4" class="outline-4">
<h4 id="orgaf628c4">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-orgaf628c4">
<div id="outline-container-org12df21d" class="outline-4">
<h4 id="org12df21d">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-org12df21d">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
......@@ -245,9 +245,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p>
</div>
</div>
<div id="outline-container-org76a0967" class="outline-4">
<h4 id="org76a0967">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-org76a0967">
<div id="outline-container-org1fbd541" class="outline-4">
<h4 id="org1fbd541">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-org1fbd541">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
......@@ -278,9 +278,9 @@ is demonstrated in the <a href="rr_org/journal.html#MissingReference">first entr
</p>
</div>
</div>
<div id="outline-container-org1b44bc8" class="outline-4">
<h4 id="org1b44bc8">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-org1b44bc8">
<div id="outline-container-org528bb3d" class="outline-4">
<h4 id="org528bb3d">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-org528bb3d">
<p>
In step 1, you were told to create an journal in
<code>~org/journal.org</code>. First you probably want to make sure this file is
......@@ -292,57 +292,57 @@ forums.
</div>
</div>
</div>
<div id="outline-container-org5233724" class="outline-2">
<h2 id="org5233724">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-org5233724">
<div id="outline-container-orgf3207a2" class="outline-2">
<h2 id="orgf3207a2">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orgf3207a2">
</div>
<div id="outline-container-orgcf5a5b2" class="outline-3">
<h3 id="orgcf5a5b2">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orgcf5a5b2">
<div id="outline-container-org63f18b5" class="outline-3">
<h3 id="org63f18b5">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org63f18b5">
<p>
Learning emacs and org-mode can be difficult as there is an inordinate
amount of shortcuts. Many people have thus come up with
cheat-sheats. Here is a selection in case it helps:
</p>
</div>
<div id="outline-container-orgcb4078f" class="outline-4">
<h4 id="orgcb4078f">Emacs</h4>
<div class="outline-text-4" id="text-orgcb4078f">
<div id="outline-container-org22fe63d" class="outline-4">
<h4 id="org22fe63d">Emacs</h4>
<div class="outline-text-4" id="text-org22fe63d">
<ul class="org-ul">
<li><a href="org/journal.html#MissingReference">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<li><a href="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
<li>Two graphical cheat-sheats by Sacha Hua on <a href="http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png">how to learn emacs</a> and on
<li style="margin-bottom:0;"><a href="org/journal.html#MissingReference">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<li style="margin-bottom:0;"><a href="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
<li style="margin-bottom:0;">Two graphical cheat-sheats by Sacha Hua on <a href="http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png">how to learn emacs</a> and on
<a href="http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png">how to learn emacs shortcuts</a>.</li>
</ul>
</div>
</div>
<div id="outline-container-orgde1963f" class="outline-4">
<h4 id="orgde1963f">Org-mode</h4>
<div class="outline-text-4" id="text-orgde1963f">
<div id="outline-container-org4d46779" class="outline-4">
<h4 id="org4d46779">Org-mode</h4>
<div class="outline-text-4" id="text-org4d46779">
<ul class="org-ul">
<li><a href="org/journal.html#MissingReference">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<li><a href="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
<li><a href="https://orgmode.org/worg/dev/org-syntax.html">The official description of the org-mode syntax</a> and a <a href="https://gist.github.com/hoeltgman/3825415">relatively concise description of the org-mode syntax</a>.</li>
<li style="margin-bottom:0;"><a href="org/journal.html#MissingReference">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<li style="margin-bottom:0;"><a href="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
<li style="margin-bottom:0;"><a href="https://orgmode.org/worg/dev/org-syntax.html">The official description of the org-mode syntax</a> and a <a href="https://gist.github.com/hoeltgman/3825415">relatively concise description of the org-mode syntax</a>.</li>
</ul>
</div>
</div>
</div>
<div id="outline-container-orgc2d812a" class="outline-3">
<h3 id="orgc2d812a">Video tutorials</h3>
<div class="outline-text-3" id="text-orgc2d812a">
<div id="outline-container-orgefcfd8e" class="outline-3">
<h3 id="orgefcfd8e">Video tutorials</h3>
<div class="outline-text-3" id="text-orgefcfd8e">
<p>
For those of you who prefer video explanations, here is a <a href="https://www.youtube.com/playlist?list=PL9KxKa8NpFxIcNQa9js7dQQIHc81b0-Xg">Youtube
channel with many step by step emacs tutorials</a>.
</p>
</div>
</div>
<div id="outline-container-org6c3b81d" class="outline-3">
<h3 id="org6c3b81d">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org6c3b81d">
<div id="outline-container-org4a1463b" class="outline-3">
<h3 id="org4a1463b">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org4a1463b">
</div>
<div id="outline-container-org2b1ba15" class="outline-4">
<h4 id="org2b1ba15">Company-mode</h4>
<div class="outline-text-4" id="text-org2b1ba15">
<div id="outline-container-orgf784a61" class="outline-4">
<h4 id="orgf784a61">Company-mode</h4>
<div class="outline-text-4" id="text-orgf784a61">
<p>
<a href="http://company-mode.github.io/">Company-mode</a> is a text completion framework for Emacs. It allows to
have smart completion in emacs for the most common languages. If you
......@@ -351,9 +351,9 @@ official webpage: <a href="http://company-mode.github.io/">http://company-mode.g
</p>
</div>
</div>
<div id="outline-container-org5a154db" class="outline-4">
<h4 id="org5a154db">Magit</h4>
<div class="outline-text-4" id="text-org5a154db">
<div id="outline-container-org57b6a55" class="outline-4">
<h4 id="org57b6a55">Magit</h4>
<div class="outline-text-4" id="text-org57b6a55">
<p>
<a href="https://magit.vc/">Magit</a> is an emacs interface for Git. It is very powerfull and we use
it on a daily basis but you should definitely understand what git does
......@@ -364,23 +364,23 @@ you should follow the instructions from here:
</div>
</div>
</div>
<div id="outline-container-org00ecde8" class="outline-3">
<h3 id="org00ecde8">Other resources</h3>
<div class="outline-text-3" id="text-org00ecde8">
<div id="outline-container-org84da85a" class="outline-3">
<h3 id="org84da85a">Other resources</h3>
<div class="outline-text-3" id="text-org84da85a">
<ul class="org-ul">
<li><a href="https://orgmode.org/orgguide.pdf">The compact Org-mode Guide</a></li>
<li><a href="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</a></li>
<li style="margin-bottom:0;"><a href="https://orgmode.org/orgguide.pdf">The compact Org-mode Guide</a></li>
<li style="margin-bottom:0;"><a href="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</a></li>
</ul>
</div>
</div>
</div>
<div id="outline-container-org0e133ea" class="outline-2">
<h2 id="org0e133ea">A replicable article</h2>
<div class="outline-text-2" id="text-org0e133ea">
<div id="outline-container-org1a26eb1" class="outline-2">
<h2 id="org1a26eb1">A replicable article</h2>
<div class="outline-text-2" id="text-org1a26eb1">
</div>
<div id="outline-container-orgf3a84c7" class="outline-3">
<h3 id="orgf3a84c7">A stub of replicable article</h3>
<div class="outline-text-3" id="text-orgf3a84c7">
<div id="outline-container-org33696b8" class="outline-3">
<h3 id="org33696b8">A stub of replicable article</h3>
<div class="outline-text-3" id="text-org33696b8">
<p>
Remember, you need a working LaTeX and R environment. If you can't
open a terminal and run the commands <code>R</code> and <code>pdflatex</code>, you will not be
......
module2/ressources/jupyter.html
View file @ 1b527eda
......@@ -4,31 +4,31 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org877f03b">Interacting with gitlab</a></li>
<li><a href="#org16a59c6">Additional Jupyter resources or tricks</a>
<li style="margin-bottom:0;"><a href="#orgc72397d">Interacting with gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org186a10f">Additional Jupyter resources or tricks</a>
<ul>
<li><a href="#org21ed683">Tips and tricks</a></li>
<li><a href="#org81cf6e7">Running R and Python in the same notebook</a></li>
<li><a href="#orgff572f3">Exporting a notebook</a></li>
<li style="margin-bottom:0;"><a href="#org9d17f16">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#org3c5eb3e">Running R and Python in the same notebook</a></li>
<li style="margin-bottom:0;"><a href="#org656a59e">Exporting a notebook</a></li>
</ul>
</li>
<li><a href="#org3bb44ad">Installing jupyter or jupyter hub on your own machine</a>
<li style="margin-bottom:0;"><a href="#org2b24a9c">Installing jupyter or jupyter hub on your own machine</a>
<ul>
<li><a href="#org7acfd0d">Installing jupyter</a></li>
<li><a href="#org4236b75">Using R</a></li>
<li><a href="#org04ec93e">Exporting your notebooks with latex</a></li>
<li><a href="#orgd9a7f1c">Interacting with gitlab</a></li>
<li><a href="#orgad4d4c4">Interesting extensions to improve notebook readability</a></li>
<li><a href="#orgff424ae">Installing jupyterhub</a></li>
<li style="margin-bottom:0;"><a href="#orgfe13c9b">Installing jupyter</a></li>
<li style="margin-bottom:0;"><a href="#orgaeb7a97">Using R</a></li>
<li style="margin-bottom:0;"><a href="#orgbf7d110">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#orgff388aa">Interacting with gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org77fb4ca">Interesting extensions to improve notebook readability</a></li>
<li style="margin-bottom:0;"><a href="#org364ee89">Installing jupyterhub</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org877f03b" class="outline-2">
<h2 id="org877f03b">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-org877f03b">
<div id="outline-container-orgc72397d" class="outline-2">
<h2 id="orgc72397d">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-orgc72397d">
<blockquote>
<p>
This section needs some love.
......@@ -45,13 +45,13 @@ and to share your notebook with others.
</p>
</div>
</div>
<div id="outline-container-org16a59c6" class="outline-2">
<h2 id="org16a59c6">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org16a59c6">
<div id="outline-container-org186a10f" class="outline-2">
<h2 id="org186a10f">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org186a10f">
</div>
<div id="outline-container-org21ed683" class="outline-3">
<h3 id="org21ed683">Tips and tricks</h3>
<div class="outline-text-3" id="text-org21ed683">
<div id="outline-container-org9d17f16" class="outline-3">
<h3 id="org9d17f16">Tips and tricks</h3>
<div class="outline-text-3" id="text-org9d17f16">
<p>
The following <a href="https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/">webpage</a> lists several Jupyter tricks (in particular, it
illustrates many <code>Ipython magic</code> commands) that should improve your
......@@ -61,9 +61,9 @@ now).
</p>
</div>
</div>
<div id="outline-container-org81cf6e7" class="outline-3">
<h3 id="org81cf6e7">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org81cf6e7">
<div id="outline-container-org3c5eb3e" class="outline-3">
<h3 id="org3c5eb3e">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org3c5eb3e">
<p>
The best solution to this is to install rpy2. On my machine, I have
installed the <code>python3-rpy2</code> debian package with <code>apt-get install</code>. An
......@@ -78,14 +78,14 @@ with
Then you'll be able to use both languages in the same notebook by:
</p>
<ol class="org-ol">
<li><p>
<li style="margin-bottom:0;"><p>
Loading <code>rpy2</code>:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%load_ext rpy2.ipython
</pre>
</div></li>
<li><p>
<li style="margin-bottom:0;"><p>
Using the <code>%R</code> Ipython magic:
</p>
<div class="org-src-container">
......@@ -105,9 +105,9 @@ plot((df)
</ol>
</div>
</div>
<div id="outline-container-orgff572f3" class="outline-3">
<h3 id="orgff572f3">Exporting a notebook</h3>
<div class="outline-text-3" id="text-orgff572f3">
<div id="outline-container-org656a59e" class="outline-3">
<h3 id="org656a59e">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org656a59e">
<p>
Obviously, you can convert to html or pdf using the using the <code>File &gt;
Download as &gt; HTML</code> (or <code>PDF</code>) menu option. This can also be done from
......@@ -134,13 +134,13 @@ taste.
</div>
</div>
</div>
<div id="outline-container-org3bb44ad" class="outline-2">
<h2 id="org3bb44ad">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-org3bb44ad">
<div id="outline-container-org2b24a9c" class="outline-2">
<h2 id="org2b24a9c">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-org2b24a9c">
</div>
<div id="outline-container-org7acfd0d" class="outline-3">
<h3 id="org7acfd0d">Installing jupyter</h3>
<div class="outline-text-3" id="text-org7acfd0d">
<div id="outline-container-orgfe13c9b" class="outline-3">
<h3 id="orgfe13c9b">Installing jupyter</h3>
<div class="outline-text-3" id="text-orgfe13c9b">
<p>
Here is what you should install:
</p>
......@@ -171,16 +171,16 @@ The ipython notebook can then be run with the following command:
</div>
</div>
</div>
<div id="outline-container-org4236b75" class="outline-3">
<h3 id="org4236b75">Using R</h3>
<div class="outline-text-3" id="text-org4236b75">
<div id="outline-container-orgaeb7a97" class="outline-3">
<h3 id="orgaeb7a97">Using R</h3>
<div class="outline-text-3" id="text-orgaeb7a97">
<p>
If you also want to have the R kernel in jupyter, follow <a href="https://github.com/IRkernel/IRkernel#installation">these
instructions</a>.
</p>
<p>
Alternatively, you can install <code>rpy2</code> (see the <a href="#org81cf6e7">Running R and Python in
Alternatively, you can install <code>rpy2</code> (see the <a href="#org3c5eb3e">Running R and Python in
the same notebook</a> section).
</p>
<div class="org-src-container">
......@@ -189,9 +189,9 @@ the same notebook</a> section).
</div>
</div>
</div>
<div id="outline-container-org04ec93e" class="outline-3">
<h3 id="org04ec93e">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-org04ec93e">
<div id="outline-container-orgbf7d110" class="outline-3">
<h3 id="orgbf7d110">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgbf7d110">
<p>
Here is what I had to install to make sure the notebook export via
latex works:
......@@ -203,9 +203,9 @@ sudo apt-get install texlive-xetex
</div>
</div>
</div>
<div id="outline-container-orgd9a7f1c" class="outline-3">
<h3 id="orgd9a7f1c">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgd9a7f1c">
<div id="outline-container-orgff388aa" class="outline-3">
<h3 id="orgff388aa">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgff388aa">
<p>
Here is our <a href="https://github.com/brospars/nb-git">jupyter extension that allows to git push/pull from the
notebooks</a>:
......@@ -217,14 +217,14 @@ jupyter nbextension enable nb-git
</div>
</div>
</div>
<div id="outline-container-orgad4d4c4" class="outline-3">
<h3 id="orgad4d4c4">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-orgad4d4c4">
<div id="outline-container-org77fb4ca" class="outline-3">
<h3 id="org77fb4ca">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-org77fb4ca">
<p>
Here are two interesting extensions that can improve readability:
</p>
<ul class="org-ul">
<li><p>
<li style="margin-bottom:0;"><p>
<a href="https://stackoverflow.com/questions/33159518/collapse-cell-in-jupyter-notebook">Code folding</a>
</p>
<div class="org-src-container">
......@@ -232,7 +232,7 @@ Here are two interesting extensions that can improve readability:
<span style="font-weight: bold; font-style: italic;"># </span><span style="font-weight: bold; font-style: italic;">jupyter contrib nbextension install --user # not done yet</span>
</pre>
</div></li>
<li><p>
<li style="margin-bottom:0;"><p>
<a href="https://github.com/kirbs-/hide_code">Hiding code</a>
</p>
<div class="org-src-container">
......@@ -245,9 +245,9 @@ jupyter-serverextension enable --py hide_code
</ul>
</div>
</div>
<div id="outline-container-orgff424ae" class="outline-3">
<h3 id="orgff424ae">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-orgff424ae">
<div id="outline-container-org364ee89" class="outline-3">
<h3 id="org364ee89">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-org364ee89">
<blockquote>
<p>
Benoit may give a few hints on this.
......
module2/ressources/rstudio.html
View file @ 1b527eda
......@@ -4,36 +4,36 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org937177d">Installing Rstudio</a>
<li style="margin-bottom:0;"><a href="#org47ec510">Installing Rstudio</a>
<ul>
<li><a href="#org8f48c7c">Linux (debian, ubuntu)</a>
<li style="margin-bottom:0;"><a href="#org366dd3d">Linux (debian, ubuntu)</a>
<ul>
<li><a href="#orge26d961">Installing R</a></li>
<li><a href="#org8956720">Installing rstudio</a></li>
<li style="margin-bottom:0;"><a href="#orgba71b69">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#orgfe3a4ba">Installing rstudio</a></li>
</ul>
</li>
<li><a href="#org8770e8d">Mac OSX and Windows</a></li>
<li style="margin-bottom:0;"><a href="#orgdf29b54">Mac OSX and Windows</a></li>
</ul>
</li>
<li><a href="#orgc5c6960">Installing Git</a>
<li style="margin-bottom:0;"><a href="#orgd30feb0">Installing Git</a>
<ul>
<li><a href="#org5b86b8a">Linux (debian, ubuntu)</a></li>
<li><a href="#org18d42c3">Mac OSX and Windows</a></li>
<li style="margin-bottom:0;"><a href="#org02fa6c2">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org0611f52">Mac OSX and Windows</a></li>
</ul>
</li>
<li><a href="#org2392c30">Rstudio and git/github/gitlab</a></li>
<li><a href="#org40217fe">Cheat Sheets</a></li>
<li style="margin-bottom:0;"><a href="#orgabc8626">Rstudio and git/github/gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org270116a">Cheat Sheets</a></li>
</ul>
</div>
</div>
<div id="outline-container-org937177d" class="outline-2">
<h2 id="org937177d">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org937177d">
<div id="outline-container-org47ec510" class="outline-2">
<h2 id="org47ec510">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org47ec510">
</div>
<div id="outline-container-org8f48c7c" class="outline-3">
<h3 id="org8f48c7c">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org8f48c7c">
<div id="outline-container-org366dd3d" class="outline-3">
<h3 id="org366dd3d">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org366dd3d">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -45,9 +45,9 @@ Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode:
</p>
<ul class="org-ul">
<li>Debian (stretch) ships with <a href="https://packages.debian.org/stretch/r-base">R 3.3.3-1</a>, <a href="https://packages.debian.org/stretch/r-cran-knitr">knitr 1.15.1</a>, and <a href="https://packages.debian.org/stretch/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li>Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/r-base">R 3.4.4</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-knitr">knitr 1.17</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li>Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/r-base">R 3.4.2</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-knitr">knitr 1.15</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li style="margin-bottom:0;">Debian (stretch) ships with <a href="https://packages.debian.org/stretch/r-base">R 3.3.3-1</a>, <a href="https://packages.debian.org/stretch/r-cran-knitr">knitr 1.15.1</a>, and <a href="https://packages.debian.org/stretch/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li style="margin-bottom:0;">Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/r-base">R 3.4.4</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-knitr">knitr 1.17</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li style="margin-bottom:0;">Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/r-base">R 3.4.2</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-knitr">knitr 1.15</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-ggplot2">ggplot 2.2.1</a></li>
</ul>
<p>
If your distribution is older than this, well, it may be a good time
......@@ -55,9 +55,9 @@ for upgrading&#x2026;
</p>
</div>
<div id="outline-container-orge26d961" class="outline-4">
<h4 id="orge26d961">Installing R</h4>
<div class="outline-text-4" id="text-orge26d961">
<div id="outline-container-orgba71b69" class="outline-4">
<h4 id="orgba71b69">Installing R</h4>
<div class="outline-text-4" id="text-orgba71b69">
<p>
Beforehand, you need to install the R language and convenient packages
by running (as root):
......@@ -90,9 +90,9 @@ to run (as root):
</div>
</div>
<div id="outline-container-org8956720" class="outline-4">
<h4 id="org8956720">Installing rstudio</h4>
<div class="outline-text-4" id="text-org8956720">
<div id="outline-container-orgfe3a4ba" class="outline-4">
<h4 id="orgfe3a4ba">Installing rstudio</h4>
<div class="outline-text-4" id="text-orgfe3a4ba">
<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 +110,9 @@ sudo apt-get update ; sudo apt-get -f install <span style="font-weight: bold; fo
</div>
</div>
</div>
<div id="outline-container-org8770e8d" class="outline-3">
<h3 id="org8770e8d">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org8770e8d">
<div id="outline-container-orgdf29b54" class="outline-3">
<h3 id="orgdf29b54">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-orgdf29b54">
<blockquote>
<p>
Some instructions on installing R and knitr must be missing. This
......@@ -136,13 +136,13 @@ install.packages(<span style="font-style: italic;">"ggplot2"</span>)
</div>
</div>
</div>
<div id="outline-container-orgc5c6960" class="outline-2">
<h2 id="orgc5c6960">Installing Git</h2>
<div class="outline-text-2" id="text-orgc5c6960">
<div id="outline-container-orgd30feb0" class="outline-2">
<h2 id="orgd30feb0">Installing Git</h2>
<div class="outline-text-2" id="text-orgd30feb0">
</div>
<div id="outline-container-org5b86b8a" class="outline-3">
<h3 id="org5b86b8a">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org5b86b8a">
<div id="outline-container-org02fa6c2" class="outline-3">
<h3 id="org02fa6c2">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org02fa6c2">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -158,16 +158,16 @@ Run (as root):
</div>
</div>
</div>
<div id="outline-container-org18d42c3" class="outline-3">
<h3 id="org18d42c3">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org18d42c3">
<div id="outline-container-org0611f52" class="outline-3">
<h3 id="org0611f52">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org0611f52">
<ul class="org-ul">
<li>Download and install Git from the <a href="https://git-scm.com/downloads">Git website</a>.</li>
<li>Optional Git clients (should not be needed if you work within
<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
Rstudio):
<ul class="org-ul">
<li><a href="https://www.sourcetreeapp.com/">SourceTree</a></li>
<li><p>
<li style="margin-bottom:0;"><a href="https://www.sourcetreeapp.com/">SourceTree</a></li>
<li style="margin-bottom:0;"><p>
<a href="https://desktop.github.com/">GitHub Desktop</a>
</p>
<blockquote>
......@@ -180,16 +180,16 @@ Rstudio):
</div>
</div>
</div>
<div id="outline-container-org2392c30" class="outline-2">
<h2 id="org2392c30">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-org2392c30">
<div id="outline-container-orgabc8626" class="outline-2">
<h2 id="orgabc8626">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-orgabc8626">
<blockquote>
<p>
We may want to redo a screencast in French for this
</p>
</blockquote>
<ul class="org-ul">
<li><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>
<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>
......@@ -197,26 +197,26 @@ 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>
</p>
<ul class="org-ul">
<li>Part 1/item 2: Setup Git in RStudio</li>
<li>Part 2 (to adapt to gitlab)</li>
<li>Part 3</li>
<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>
</div>
<div id="outline-container-org40217fe" class="outline-2">
<h2 id="org40217fe">Cheat Sheets</h2>
<div class="outline-text-2" id="text-org40217fe">
<div id="outline-container-org270116a" class="outline-2">
<h2 id="org270116a">Cheat Sheets</h2>
<div class="outline-text-2" id="text-org270116a">
<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:
</p>
<ul class="org-ul">
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf">the Rstudio IDE</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf">R Markdown</a>,</li>
<li>the <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">R Markdown Reference guide</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf">data visualization with ggplot2</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf">data transformation with dplyr</a></li>
<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>
......@@ -224,10 +224,10 @@ In case it helps, here are some (sometimes outdated) French versions
of these documents:
</p>
<ul class="org-ul">
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf">L'IDE Rstudio</a></li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf">Visualisation de données avec ggplot2</a></li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf">Transformation de données avec dplyr</a></li>
<li><a href="https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf">Un court document sur R Markdown</a></li>
<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>
......
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