<h4id="orge575f92">Step 0: Backup and download our configuration</h4>
<divclass="outline-text-4"id="text-orge575f92">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make
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@@ -200,7 +208,7 @@ exists).
</p>
<p>
Then download <ahref="rr_org_archive.tgz">this archive</a> and uncompress it. It contains the
Then download <ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/rr_org_archive.tgz">this archive</a> and uncompress it. It contains the
following files and we will refer to them in the following:
<h4id="org94b4862">Step 1: Prepare your journal</h4>
<divclass="outline-text-4"id="text-org94b4862">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
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@@ -226,14 +234,14 @@ Create an <code>org/</code> directory in the top of your home:
Then copy <code>rr_org/journal.org</code> file in your <code>~/org/</code> directory. This
file will be your laboratory notebook and all the notes you will
capture with <code>C-c c</code> will go automatically go in this file. The first
entry of this notebook is populated with <ahref="rr_org/journal.html#MissingReference">many emacs shortcuts</a> that you
entry of this notebook is populated with <ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">many emacs shortcuts</a> that you
<h4id="orgeadfe2f">Step 3: Check whether the installation is working or not</h4>
<divclass="outline-text-4"id="text-orgeadfe2f">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
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@@ -274,13 +282,13 @@ worked.
In the video, we already have demonstrated the main features and
shortcuts of emacs/org-mode that will help you maintain a document and
benefit from literate programming. The list of features and shortcuts
is demonstrated in the <ahref="rr_org/journal.html#MissingReference">first entry of your labbook</a>.
is demonstrated in the <ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">first entry of your labbook</a>.
<h3id="orgb7bc421"><spanclass="todo TODO">TODO</span> A stub of replicable article</h3>
<divclass="outline-text-3"id="text-orgb7bc421">
<blockquote>
<p>
There will be a mini video illustrating these steps at some point
</p>
</blockquote>
<p>
Remember, you need a working LaTeX and R environment. If you can't
open a terminal and run the commands <code>R</code>, <code>pdflatex</code>, and <code>python</code>, you will not be
able to generate this document. When being compiled, the article downloads the
corresponding LaTeX packages so you also need to have a working <code>wget</code>
command (alternatively, it uses <code>curl</code>). Once downloaded, you may still read the
source (<ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org">article.org</a>) and understand how it works though.
</p>
<p>
Download the following <ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article/replicable_article.tgz">archive</a> and untar it.
</p>
<p>
and simply <code>make</code> to generate the
article. You should then be able to open the <ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf">resulting article</a>. This
and export it to pdf with the following shortcut: <code>C-c C-e l o</code>
</p>
<p>
If it still doesn't work and emacs complains about not finding ESS, it
may be because you installed ESS in your home instead of
system-wide. In that case, try to remove the <code>-q</code> in the previous
command line to load your personal emacs configuration.
</p>
<p>
Finally, when you'll be tired of always reexecuting all the source
code when exporting, just look for the following line in <ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org">article.org</a>:
<listyle="margin-bottom:0;"><ahref="org/journal.html#MissingReference">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
<listyle="margin-bottom:0;">Two graphical cheat-sheats by Sacha Hua on <ahref="http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png">how to learn emacs</a> and on
<ahref="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>
<listyle="margin-bottom:0;"><ahref="org/journal.html#MissingReference">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
<listyle="margin-bottom:0;"><ahref="https://orgmode.org/worg/dev/org-syntax.html">The official description of the org-mode syntax</a> and a <ahref="https://gist.github.com/hoeltgman/3825415">relatively concise description of the org-mode syntax</a>.</li>
<listyle="margin-bottom:0;"><ahref="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</a></li>
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@@ -374,66 +450,4 @@ you should follow the instructions from here:
