# This is an <h1> tag ## This is an <h2> tag @@ -49,9 +49,9 @@ H. Steiger.
*This text will be italic* _This will also be italic_ @@ -64,13 +64,13 @@ _You **can** combine them_
* Item 1 * Item 2 @@ -79,9 +79,9 @@ _You **can** combine them_
1. Item 1 1. Item 2 @@ -92,27 +92,27 @@ _You **can** combine them_
 Format: 
http://github.com - automatic! [GitHub](http://github.com)
As Kanye West said: @@ -121,9 +121,9 @@ As Kanye West said:
I think you should use an `<addr>` element here instead. @@ -131,9 +131,9 @@ I think you should use an
Equations can be formatted inline or as displayed formulas. 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.
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:
If your distribution is older than this, well, it may be a good time @@ -123,26 +123,26 @@ which is now deprecated.
+
Option 1: Install the .dmg file from Vincent Goulet:
https://vigou3.github.io/emacs-modified-macos/. It ships with recent
versions:
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…
+
Option 2: If you already use brew, simply do the following
Install the .exe file from Vincent Goulet:
https://vigou3.github.io/emacs-modified-windows/. It ships with recent
versions:
Emacs comes with very basic default configuration and it appears like everyone has its own taste. You will for example find here several @@ -189,9 +189,9 @@ adding a few org-mode specific configurations.
The procedure we propose will wipe your already existing custom emacs configuration if you already have one. You should thus beforehand make @@ -212,9 +212,9 @@ rr_org/journal.org
Create an org/ directory in the top of your home:
Copy rr_org/init.el in your ~/.emacs.d/ directory.
emacs -q -l rr_org/init.el
Open a new instance of Emacs and open a foo.org file. Copy the
following lines in this file:
@@ -278,9 +278,9 @@ is demonstrated in the first entr
In step 1, you were told to create an journal in
~org/journal.org. First you probably want to make sure this file is
@@ -292,57 +292,57 @@ forums.
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:
For those of you who prefer video explanations, here is a Youtube channel with many step by step emacs tutorials.
Company-mode 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: http://company-mode.g
Magit 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:
Remember, you need a working LaTeX and R environment. If you can't
open a terminal and run the commands R and pdflatex, you will not be
diff --git a/module2/ressources/jupyter.html b/module2/ressources/jupyter.html
index 4d7aa2ee5eab90967b2e6296f1d6ac7108cc42ce..b7607f331b4621994fc256ca42eff8ccebcee52a 100644
--- a/module2/ressources/jupyter.html
+++ b/module2/ressources/jupyter.html
@@ -4,31 +4,31 @@
This section needs some love. @@ -45,13 +45,13 @@ and to share your notebook with others.
The following webpage lists several Jupyter tricks (in particular, it
illustrates many Ipython magic commands) that should improve your
@@ -61,9 +61,9 @@ now).
The best solution to this is to install rpy2. On my machine, I have
installed the python3-rpy2 debian package with apt-get install. An
@@ -78,14 +78,14 @@ with
Then you'll be able to use both languages in the same notebook by:
+
Loading rpy2:
%load_ext rpy2.ipython
+
Using the %R Ipython magic:
Obviously, you can convert to html or pdf using the using the File >
Download as > HTML (or PDF) menu option. This can also be done from
@@ -134,13 +134,13 @@ taste.
Here is what you should install:
@@ -171,16 +171,16 @@ The ipython notebook can then be run with the following command:If you also want to have the R kernel in jupyter, follow these instructions.
-Alternatively, you can install rpy2 (see the Running R and Python in
+Alternatively, you can install rpy2 (see the Running R and Python in
the same notebook section).
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
Here is our jupyter extension that allows to git push/pull from the notebooks: @@ -217,14 +217,14 @@ jupyter nbextension enable nb-git
Here are two interesting extensions that can improve readability:
+
+
Benoit may give a few hints on this. diff --git a/module2/ressources/rstudio.html b/module2/ressources/rstudio.html index a7dde5fde36c2eac3aaabe7b656d257a3924ffd9..ea0701d582935ca2e41bb9245d6c318edd346d6b 100644 --- a/module2/ressources/rstudio.html +++ b/module2/ressources/rstudio.html @@ -4,36 +4,36 @@
Table of Contents
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:
If your distribution is older than this, well, it may be a good time @@ -55,9 +55,9 @@ for upgrading…
Beforehand, you need to install the R language and convenient packages by running (as root): @@ -90,9 +90,9 @@ to run (as root):
Rstudio is unfortunately not packaged within debian so the easiest is
to download the corresponding debian package on the Rstudio webpage
@@ -110,9 +110,9 @@ sudo apt-get update ; sudo apt-get -f install
-
Some instructions on installing R and knitr must be missing. This
@@ -136,13 +136,13 @@ install.packages("ggplot2")
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):
+
We may want to redo a screencast in French for this
@@ -197,26 +197,26 @@ Alternatively, we can point to:
http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/
The Rstudio team has created a lot of good material and tutorials. You
should definitively look at the Cheat sheets webpage. In particular
you want to have look at the ones on:
@@ -224,10 +224,10 @@ In case it helps, here are some (sometimes outdated) French versions
of these documents:
Mac OSX and Windows
-Mac OSX and Windows
+
Installing Git
-Installing Git
+Linux (debian, ubuntu)
-Linux (debian, ubuntu)
+Mac OSX and Windows
-Mac OSX and Windows
+
-
-
@@ -180,16 +180,16 @@ Rstudio):
Rstudio and git/github/gitlab
-Rstudio and git/github/gitlab
+
-
-
Cheat Sheets
-Cheat Sheets
+
-
