Module 3/exo 2: mise à jour et version anglaise

Ce sont en fait des modèles assez universels.

module3/exo2/exercice_R_en.org

+#+TITLE:  Your title
+#+AUTHOR: Your name
+#+DATE:   Today's date
+#+LANGUAGE: en
+# #+PROPERTY: header-args :eval never-export
+
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
+#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
+#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
+
+* Some explanations
+
+This is an org-mode document with code examples in R.  Once opened in
+Emacs, this document can easily be exported to HTML, PDF, and Office
+formats. For more information on org-mode, see
+https://orgmode.org/guide/.
+
+When you type the shortcut =C-c C-e h o=, this document will be
+exported as HTML. All the code in it will be re-executed, and the
+results will be retrieved and included into the exported document. If
+you do not want to re-execute all code each time, you can delete the #
+and the space before ~#+PROPERTY:~ in the header of this document.
+
+Like we showed in the video, R code is included as follows (and is
+exxecuted by typing ~C-c C-c~):
+
+#+begin_src R :results output :exports both
+print("Hello world!")
+#+end_src
+
+#+RESULTS:
+: [1] "Hello world!"
+
+And now the same but in an R session. This is the most frequent
+situation, because R is really an interactive language. With a
+session, R's state, i.e. the values of all the variables, remains
+persistent from one code block to the next. The code is still executed
+using ~C-c C-c~.
+
+#+begin_src R :results output :session *R* :exports both
+summary(cars)
+#+end_src
+
+#+RESULTS:
+:      speed           dist       
+:  Min.   : 4.0   Min.   :  2.00  
+:  1st Qu.:12.0   1st Qu.: 26.00  
+:  Median :15.0   Median : 36.00  
+:  Mean   :15.4   Mean   : 42.98  
+:  3rd Qu.:19.0   3rd Qu.: 56.00  
+:  Max.   :25.0   Max.   :120.00
+
+Finally, an example for graphical output:
+#+begin_src R :results output graphics :file "./cars.png" :exports results :width 600 :height 400 :session *R* 
+plot(cars)
+#+end_src
+
+#+RESULTS:
+[[file:./cars.png]]
+
+Note the parameter ~:exports results~, which indicates that the code
+will not appear in the exported document. We recommend that in the
+context of this MOOC, you always leave this parameter setting as
+~:exports both~, because we want your analyses to be perfectly
+transparent and reproducible.
+
+Watch out: the figure generated by the code block is /not/ stored in
+the org document. It's a plain file, here named ~cars.png~. You have
+to commit it explicitly if you want your analysis to be legible and
+understandable on GitLab.
+
+Finally, don't forget that we provide in the resource section of this
+MOOC a configuration with a few keyboard shortcuts that allow you to
+quickly create code blocks in R by typing ~<r~ or ~<R~ followed by
+~Tab~.
+
+Now it's your turn! You can delete all this information and replace it
+by your computational document.

module3/exo2/exercice_R.org → module3/exo2/exercice_R_fr.org

@@ -3,7 +3,6 @@
 #+DATE:   La date du jour
 #+LANGUAGE: fr
 # #+PROPERTY: header-args :eval never-export
-# #### :session  :exports both
 
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
@@ -36,7 +35,7 @@ print("Hello world!")
 #+RESULTS:
 : [1] "Hello world!"
 
-Voici la même chose, mais avec une session python (c'est le cas le
+Voici la même chose, mais avec une session R (c'est le cas le
 plus courant, R étant vraiment un langage interactif), donc une
 persistance d'un bloc à l'autre (et on l'exécute toujours en faisant
 ~C-c C-c~).
@@ -78,9 +77,8 @@ forcément de fichier de départ, ça sera à vous de le créer, par
 exemple en repartant de ce document et de le commiter vers
 gitlab. N'oubliez pas que nous vous fournissons dans les ressources de
 ce MOOC une configuration avec un certain nombre de raccourcis
-claviers permettant de créer rapidement les blocs de code python (en
+claviers permettant de créer rapidement les blocs de code R (en
 faisant ~<r~ ou ~<R~ suivi de ~Tab~).
 
 Maintenant, à vous de jouer! Vous pouvez effacer toutes ces
-informations pour essayer de reproduire le document sur le calcul de
-$\pi$.
+informations et les remplacer par votre document computationnel.

module3/exo2/exercice_en.Rmd

+---
+title: "Your title"
+author: "Your name"
+date: "Today's date"
+output: html_document
+---
+
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## Some explanations
+
+This is an R Markdown document that you can easily export to HTML, PDF, and MS Word formats. For more information on R Markdown, see <http://rmarkdown.rstudio.com>.
+
+When you click on the button **Knit**, the document will be compiled in order to re-execute the R code and to include the results into the final document. As we have shown in the video, R code is inserted as follows:
+
+```{r cars}
+summary(cars)
+```
+
+It is also straightforward to include figures. For example:
+
+```{r pressure, echo=FALSE}
+plot(pressure)
+```
+
+Note the parameter `echo = FALSE` that indicates that the code will not appear in the final version of the document. We recommend not to use this parameter in the context of this MOOC, because we want your data analyses to be perfectly transparent and reproducible.
+
+Since the results are not stored in Rmd files, you should generate an HTML or PDF version of your exercises and commit them. Otherwise reading and checking your analysis will be difficult for anyone else but you.
+
+Now it's your turn! You can delete all this information and replace it by your computational document.

module3/exo2/exercice.Rmd → module3/exo2/exercice_fr.Rmd

@@ -29,6 +29,5 @@ plot(pressure)
 Vous remarquerez le paramètre `echo = FALSE` qui indique que le code ne doit pas apparaître dans la version finale du document. Nous vous recommandons dans le cadre de ce MOOC de ne pas utiliser ce paramètre car l'objectif est que vos analyses de données soient parfaitement transparentes pour être reproductibles. 
 
 Comme les résultats ne sont pas stockés dans les fichiers Rmd, pour faciliter la relecture de vos analyses par d'autres personnes, vous aurez donc intérêt à générer un HTML ou un PDF et à le commiter.
-Enfin, pour les prochains exercices, nous ne vous fournirons pas forcément de fichier de départ, ça sera à vous de le créer à partir de Rstudio et de le commiter vers gitlab.
 
-Maintenant, à vous de jouer! Vous pouvez effacer toutes ces informations pour essayer de reproduire le document sur le calcul de $\pi$.
+Maintenant, à vous de jouer! Vous pouvez effacer toutes ces informations et les remplacer par votre document computationnel.

module3/exo2/exercice_fr.ipynb

+{
+ "cells": [],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
+

module3/exo2/exercice_python_en.org

+#+TITLE:  Your title
+#+AUTHOR: Your name
+#+DATE:   Today's date
+#+LANGUAGE: en
+# #+PROPERTY: header-args :eval never-export
+
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
+#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
+#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
+
+* Some explanations
+
+This is an org-mode document with code examples in R.  Once opened in
+Emacs, this document can easily be exported to HTML, PDF, and Office
+formats. For more information on org-mode, see
+https://orgmode.org/guide/.
+
+When you type the shortcut =C-c C-e h o=, this document will be
+exported as HTML. All the code in it will be re-executed, and the
+results will be retrieved and included into the exported document. If
+you do not want to re-execute all code each time, you can delete the #
+and the space before ~#+PROPERTY:~ in the header of this document.
+
+Like we showed in the video, Python code is included as follows (and
+is exxecuted by typing ~C-c C-c~):
+
+#+begin_src python :results output :exports both
+print("Hello world!")
+#+end_src
+
+#+RESULTS:
+: Hello world!
+
+And now the same but in an Python session. With a session, Python's
+state, i.e. the values of all the variables, remains persistent from
+one code block to the next. The code is still executed using ~C-c
+C-c~.
+
+#+begin_src python :results output :session :exports both
+import numpy
+x=numpy.linspace(-15,15)
+print(x)
+#+end_src
+
+#+RESULTS:
+#+begin_example
+[-15.         -14.3877551  -13.7755102  -13.16326531 -12.55102041
+ -11.93877551 -11.32653061 -10.71428571 -10.10204082  -9.48979592
+  -8.87755102  -8.26530612  -7.65306122  -7.04081633  -6.42857143
+  -5.81632653  -5.20408163  -4.59183673  -3.97959184  -3.36734694
+  -2.75510204  -2.14285714  -1.53061224  -0.91836735  -0.30612245
+   0.30612245   0.91836735   1.53061224   2.14285714   2.75510204
+   3.36734694   3.97959184   4.59183673   5.20408163   5.81632653
+   6.42857143   7.04081633   7.65306122   8.26530612   8.87755102
+   9.48979592  10.10204082  10.71428571  11.32653061  11.93877551
+  12.55102041  13.16326531  13.7755102   14.3877551   15.        ]
+#+end_example
+
+Finally, an example for graphical output:
+#+begin_src python :results output file :session :var matplot_lib_filename="./cosxsx.png" :exports results
+import matplotlib.pyplot as plt
+
+plt.figure(figsize=(10,5))
+plt.plot(x,numpy.cos(x)/x)
+plt.tight_layout()
+
+plt.savefig(matplot_lib_filename)
+print(matplot_lib_filename)
+#+end_src
+
+#+RESULTS:
+[[file:./cosxsx.png]]
+
+Note the parameter ~:exports results~, which indicates that the code
+will not appear in the exported document. We recommend that in the
+context of this MOOC, you always leave this parameter setting as
+~:exports both~, because we want your analyses to be perfectly
+transparent and reproducible.
+
+Watch out: the figure generated by the code block is /not/ stored in
+the org document. It's a plain file, here named ~cosxsx.png~. You have
+to commit it explicitly if you want your analysis to be legible and
+understandable on GitLab.
+
+Finally, don't forget that we provide in the resource section of this
+MOOC a configuration with a few keyboard shortcuts that allow you to
+quickly create code blocks in Python by typing ~<p~, ~<P~ or ~<PP~
+followed by ~Tab~.
+
+Now it's your turn! You can delete all this information and replace it
+by your computational document.

module3/exo2/exercice_python.org → module3/exo2/exercice_python_fr.org

@@ -3,7 +3,6 @@
 #+DATE:   La date du jour
 #+LANGUAGE: fr
 # #+PROPERTY: header-args :eval never-export
-# #### :session  :exports both
 
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
@@ -85,14 +84,10 @@ org. C'est un fichier ordinaire, ici nommé ~cosxsx.png~. N'oubliez pas
 de le committer si vous voulez que votre analyse soit lisible et
 compréhensible sur GitLab.
 
-Enfin, pour les prochains exercices, nous ne vous fournirons pas
-forcément de fichier de départ, ça sera à vous de le créer, par
-exemple en repartant de ce document et de le commiter vers
-gitlab. N'oubliez pas que nous vous fournissons dans les ressources de
+Enfin, n'oubliez pas que nous vous fournissons dans les ressources de
 ce MOOC une configuration avec un certain nombre de raccourcis
 claviers permettant de créer rapidement les blocs de code python (en
 faisant ~<p~, ~<P~ ou ~<PP~ suivi de ~Tab~).
 
 Maintenant, à vous de jouer! Vous pouvez effacer toutes ces
-informations pour essayer de reproduire le document sur le calcul de
-$\pi$.
+informations et les remplacer par votre document computationnel.