diff --git a/module2/exo3/exercice_python_en.org b/module2/exo3/exercice_python_en.org
index 5782f493934678ba782fb65634a4d86e5f3adefc..a57a8f86b66df792803688893437be5a8cdb27a1 100644
--- a/module2/exo3/exercice_python_en.org
+++ b/module2/exo3/exercice_python_en.org
@@ -11,84 +11,35 @@
#+HTML_HEAD:
#+HTML_HEAD:
-* 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!")
+#+begin_src python :results file :session :var matplot_lib_filename=(org-babel-temp-file "figure" ".png") :exports both
+import numpy as np
+import matplotlib.pyplot as plt
+l= [14.0, 7.6, 11.2, 12.8, 12.5, 9.9, 14.9, 9.4, 16.9, 10.2, 14.9, 18.1, 7.3, 9.8, 10.9,12.2, 9.9, 2.9, 2.8, 15.4, 15.7, 9.7, 13.1, 13.2, 12.3, 11.7, 16.0, 12.4, 17.9, 12.2, 16.2, 18.7, 8.9, 11.9, 12.1, 14.6, 12.1, 4.7, 3.9, 16.9, 16.8, 11.3, 14.4, 15.7, 14.0, 13.6, 18.0, 13.6, 19.9, 13.7, 17.0, 20.5, 9.9, 12.5, 13.2, 16.1, 13.5, 6.3, 6.4, 17.6, 19.1, 12.8, 15.5, 16.3, 15.2, 14.6, 19.1, 14.4, 21.4, 15.1, 19.6, 21.7, 11.3, 15.0, 14.3, 16.8, 14.0, 6.8, 8.2, 19.9, 20.4, 14.6, 16.4, 18.7, 16.8, 15.8, 20.4, 15.8, 22.4, 16.2, 20.3, 23.4, 12.1, 15.5, 15.4, 18.4, 15.7, 10.2, 8.9, 21.0]
+print(len(l))
+x=numpy.linspace(0,100,100)
+plt.figure(figsize=(10,5))
+plt.plot(x,l)
+plt.savefig(matplot_lib_filename)
+matplot_lib_filename
#+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~.
+[[file:/tmp/babel-XsHjUo/figure3nkNUU.png]]
-#+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
+#+begin_src python :results file :session :var matplot_lib_file=(org-babel-temp-file "figure2" ".png") :exports both
+import numpy as np
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)
+print(len(l))
+num_bins = 10
+n, bins, patches = plt.hist(l,num_bins, facecolor = 'blue', alpha = 0.5, edgecolor= 'black')
+plt.savefig(matplot_lib_file)
+matplot_lib_file
#+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 ~|z|)
-(Intercept) -1.389528 3.195752 -0.435 0.664
-Temperature 0.001416 0.049773 0.028 0.977
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 5.08498 3.05247 1.666 0.0957 .
+Temperature -0.11560 0.04702 -2.458 0.0140 *
+---
+codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
- Null deviance: 1.3347 on 6 degrees of freedom
-Residual deviance: 1.3339 on 5 degrees of freedom
-AIC: 18.894
+ Null deviance: 24.230 on 22 degrees of freedom
+Residual deviance: 18.086 on 21 degrees of freedom
+AIC: 35.647
-Number of Fisher Scoring iterations: 4
+Number of Fisher Scoring iterations: 5
#+end_example
L'estimateur le plus probable du paramètre de température est 0.001416
diff --git a/module3/exo1/analyse-syndrome-grippal.org b/module3/exo1/analyse-syndrome-grippal.org
index 1720b70df3a93009c79592b68d1dcf57a53f6341..6db4cbf0ad3d45f2d2f923fa9869a79a471f2b83 100644
--- a/module3/exo1/analyse-syndrome-grippal.org
+++ b/module3/exo1/analyse-syndrome-grippal.org
@@ -80,6 +80,47 @@ Regardons ce que nous avons obtenu:
table[:5]
#+END_SRC
+** Utilisation de données locales
+Dans le cas ou internet est indisponible, ou si le jeu de données
+fourni en ligne est susceptible d’être modifié, mieux vaut travailler
+sur des données téléchargées, en local.
+
+On vérifie que le jeu de données n’existe pas déja
+#+begin_src shell :session *shell* :results output :exports both
+cd /home/lcs/Documents/césure/mooc-rr/module3/exo1
+ls
+#+end_src
+
+#+RESULTS:
+:
+: analyse-syndrome-grippal.ipynb incidence-PAY-3.csv
+: analyse-syndrome-grippal.org#' influenza-like-illness-analysis.ipynb
+: analyse-syndrome-grippal.org influenza-like-illness-analysis.org
+: analyse-syndrome-grippal.Rmd influenza-like-illness-analysis.Rmd
+
+
+
+#+BEGIN_SRC python :results silent :var data_url=data-url
+#import panda as pd
+#data = pd.read_csv('incidence-PAY-3.csv',header = 1)
+
+import csv
+with open('incidence-PAY-3.csv') as csv_file:
+ csv_read=csv.reader(csv_file, delimiter=',')
+
+
+lines = data.decode('latin-1').strip().split('\n')
+data_lines = lines[1:]
+table = [line.split(',') for line in data_lines]
+#+END_SRC
+
+Regardons ce que nous avons obtenu:
+#+BEGIN_SRC python :results value
+table[:5]
+#+END_SRC
+
+#+RESULTS:
+
** Recherche de données manquantes
Il y a malheureusement beaucoup de façon d'indiquer l'absence d'un point de données. Nous testons ici seulement pour la présence de champs vides. Il faudrait aussi rechercher des valeurs non-numériques dans les colonnes à priori numériques. Nous ne le faisons pas ici, mais une vérification ultérieure capterait des telles anomalies.
@@ -94,6 +135,13 @@ for row in table:
valid_table.append(row)
#+END_SRC
+#+RESULTS:
+: Traceback (most recent call last):
+: File "", line 1, in
+: File "/tmp/babel-XsHjUo/python-WeKugl", line 2, in
+: for row in table:
+: NameError: name 'table' is not defined
+
** Extraction des colonnes utilisées
Il y a deux colonnes qui nous intéressent: la première (~"week"~) et la troisième (~"inc"~). Nous vérifions leurs noms dans l'en-tête, que nous effaçons par la suite. Enfin, nous créons un tableau avec les deux colonnes pour le traitement suivant.
#+BEGIN_SRC python :results silent