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module2/exo4/exercice.ipynb deleted 100644 → 0
View file @ 5424c37c
{
"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
}
module2/exo4/exercice_R_en.org deleted 100644 → 0
View file @ 5424c37c
#+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.
module2/exo4/exercice_R_fr.org deleted 100644 → 0
View file @ 5424c37c
#+TITLE: Votre titre
#+AUTHOR: Votre nom
#+DATE: La date du jour
#+LANGUAGE: fr
# #+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>
* Quelques explications
Ceci est un document org-mode avec quelques exemples de code
R. Une fois ouvert dans emacs, ce document peut aisément être
exporté au format HTML, PDF, et Office. Pour plus de détails sur
org-mode vous pouvez consulter https://orgmode.org/guide/.
Lorsque vous utiliserez le raccourci =C-c C-e h o=, ce document sera
compilé en html. Tout le code contenu sera ré-exécuté, les résultats
récupérés et inclus dans un document final. Si vous ne souhaitez pas
ré-exécuter tout le code à chaque fois, il vous suffit de supprimer
le # et l'espace qui sont devant le ~#+PROPERTY:~ au début de ce
document.
Comme nous vous l'avons montré dans la vidéo, on inclut du code
R de la façon suivante (et on l'exécute en faisant ~C-c C-c~):
#+begin_src R :results output :exports both
print("Hello world!")
#+end_src
#+RESULTS:
: [1] "Hello world!"
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~).
#+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
Et enfin, voici un exemple de sortie graphique:
#+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]]
Vous remarquerez le paramètre ~:exports results~ 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 changer ce paramètre
(indiquer ~both~) car l'objectif est que vos analyses de données soient
parfaitement transparentes pour être reproductibles.
Attention, la figure ainsi générée n'est pas stockée dans le document
org. C'est un fichier ordinaire, ici nommé ~cars.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
ce MOOC une configuration avec un certain nombre de raccourcis
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 et les remplacer par votre document computationnel.
module2/exo4/exercice_en.Rmd deleted 100644 → 0
View file @ 5424c37c
---
title: "Your title"
author: "Your name"
date: "Today's date"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Some explanations
This is an R Markdown document that you can easily export to HTML, PDF, and MS Word formats. For more information on R Markdown, see <http://rmarkdown.rstudio.com>.
When you click on the button **Knit**, the document will be compiled in order to re-execute the R code and to include the results into the final document. As we have shown in the video, R code is inserted as follows:
```{r cars}
summary(cars)
```
It is also straightforward to include figures. For example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note the parameter `echo = FALSE` that indicates that the code will not appear in the final version of the document. We recommend not to use this parameter in the context of this MOOC, because we want your data analyses to be perfectly transparent and reproducible.
Since the results are not stored in Rmd files, you should generate an HTML or PDF version of your exercises and commit them. Otherwise reading and checking your analysis will be difficult for anyone else but you.
Now it's your turn! You can delete all this information and replace it by your computational document.
module2/exo4/exercice_en.ipynb deleted 100644 → 0
View file @ 5424c37c
{
"cells": [],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
module2/exo4/exercice_fr.Rmd deleted 100644 → 0
View file @ 5424c37c
---
title: "Votre titre"
author: "Votre nom"
date: "La date du jour"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Quelques explications
Ceci est un document R markdown que vous pouvez aisément exporter au format HTML, PDF, et MS Word. Pour plus de détails sur R Markdown consultez <http://rmarkdown.rstudio.com>.
Lorsque vous cliquerez sur le bouton **Knit** ce document sera compilé afin de ré-exécuter le code R et d'inclure les résultats dans un document final. Comme nous vous l'avons montré dans la vidéo, on inclue du code R de la façon suivante:
```{r cars}
summary(cars)
```
Et on peut aussi aisément inclure des figures. Par exemple:
```{r pressure, echo=FALSE}
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.
Maintenant, à vous de jouer! Vous pouvez effacer toutes ces informations et les remplacer par votre document computationnel.
module2/exo4/exercice_fr.ipynb deleted 100644 → 0
View file @ 5424c37c
{
"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
}
module2/exo4/exercice_python_en.org deleted 100644 → 0
View file @ 5424c37c
#+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.
module2/exo4/exercice_python_fr.org deleted 100644 → 0
View file @ 5424c37c
#+TITLE: Votre titre
#+AUTHOR: Votre nom
#+DATE: La date du jour
#+LANGUAGE: fr
# #+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>
* Quelques explications
Ceci est un document org-mode avec quelques exemples de code
python. Une fois ouvert dans emacs, ce document peut aisément être
exporté au format HTML, PDF, et Office. Pour plus de détails sur
org-mode vous pouvez consulter https://orgmode.org/guide/.
Lorsque vous utiliserez le raccourci =C-c C-e h o=, ce document sera
compilé en html. Tout le code contenu sera ré-exécuté, les résultats
récupérés et inclus dans un document final. Si vous ne souhaitez pas
ré-exécuter tout le code à chaque fois, il vous suffit de supprimer
le # et l'espace qui sont devant le ~#+PROPERTY:~ au début de ce
document.
Comme nous vous l'avons montré dans la vidéo, on inclue du code
python de la façon suivante (et on l'exécute en faisant ~C-c C-c~):
#+begin_src python :results output :exports both
print("Hello world!")
#+end_src
#+RESULTS:
: Hello world!
Voici la même chose, mais avec une session python, donc une
persistance d'un bloc à l'autre (et on l'exécute toujours en faisant
~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
Et enfin, voici un exemple de sortie graphique:
#+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]]
Vous remarquerez le paramètre ~:exports results~ 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 changer ce paramètre
(indiquer ~both~) car l'objectif est que vos analyses de données soient
parfaitement transparentes pour être reproductibles.
Attention, la figure ainsi générée n'est pas stockée dans le document
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, 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 et les remplacer par votre document computationnel.
module2/exo4/portugal_covid19.csv 0 → 100644
View file @ 276af950
Day,ConfirmedCases,Hospital,ICU,Deaths,Recoveries,Report
2020-03-03,4,0,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-1.pdf
2020-03-04,6,0,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-2.pdf
2020-03-05,9,9,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-3.pdf
2020-03-06,13,13,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-4.pdf
2020-03-07,21,21,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-5.pdf
2020-03-08,30,30,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-6.pdf
2020-03-09,39,38,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-7.pdf
2020-03-10,41,40,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-8.pdf
2020-03-11,59,57,0,0,0,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-9.pdf
2020-03-12,78,69,0,0,1,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-10.pdf
2020-03-13,112,107,0,0,1,https://covid19.min-saude.pt/wp-content/uploads/2020/03/Relato%CC%81rio-de-Situac%CC%A7a%CC%83o-11.pdf
2020-03-14,169,114,10,0,1,https://covid19.min-saude.pt/wp-content/uploads/2020/03/12_DGS_boletim_202003143.pdf
2020-03-15,245,139,9,0,2,https://covid19.min-saude.pt/wp-content/uploads/2020/03/DGS_boletim_20200315_3.pdf
2020-03-16,331,139,18,1,3,https://www.dgs.pt/em-destaque/relatorio-de-situacao-n-014-16032020-pdf
2020-03-17,448,206,17,1,3,https://www.dgs.pt/em-destaque/relatorio-de-situacao-n-015-17032020-pdf
2020-03-18,642,89,20,2,3,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026029.pdf
2020-03-19,785,89,20,3,3,https://covid19.min-saude.pt/wp-content/uploads/2020/03/17_DGS_boletim_20200319.pdf.pdf
2020-03-20,1020,126,26,6,5,https://covid19.min-saude.pt/wp-content/uploads/2020/03/18_DGS_boletim_20200320-1.pdf
2020-03-21,1280,156,35,12,5,https://covid19.min-saude.pt/wp-content/uploads/2020/03/19_DGS_boletim_20200321.pdf
2020-03-22,1600,169,41,14,5,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026051.pdf
2020-03-23,2060,201,47,23,14,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026056.pdf
2020-03-24,2362,203,48,33,22,https://covid19.min-saude.pt/wp-content/uploads/2020/03/22_DGS_boletim_20200324_3.pdf
2020-03-25,2995,276,61,43,22,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026070.pdf
2020-03-26,3544,191,61,60,43,https://www.dgs.pt/em-destaque/relatorio-de-situacao-n-024-26032020-pdf
2020-03-27,4268,354,71,76,43,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026082.pdf
2020-03-28,5170,418,89,100,43,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026084.pdf
2020-03-29,5962,486,136,119,43,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026088.pdf
2020-03-30,6408,571,164,140,43,https://covid19.min-saude.pt/wp-content/uploads/2020/03/i026097.pdf
2020-03-31,7443,627,188,160,43,https://covid19.min-saude.pt/wp-content/uploads/2020/03/29_DGS_boletim_20200331.pdf
2020-04-01,8251,726,230,187,43,https://covid19.min-saude.pt/wp-content/uploads/2020/04/i026123.pdf
2020-04-02,9034,1042,240,209,68,https://covid19.min-saude.pt/wp-content/uploads/2020/04/31_DGS_boletim_20200402.pdf
2020-04-03,9886,1058,245,246,68,https://covid19.min-saude.pt/wp-content/uploads/2020/04/32_DGS_boletim_20200403.pdf
2020-04-04,10524,1075,251,266,75,https://covid19.min-saude.pt/wp-content/uploads/2020/04/33_DGS_boletim_20200404.pdf
2020-04-05,11278,1084,267,295,75,https://covid19.min-saude.pt/wp-content/uploads/2020/04/34_DGS_boletim_20200405.pdf
2020-04-06,11730,1099,270,311,140,https://covid19.min-saude.pt/wp-content/uploads/2020/04/34_DGS_boletim_20200406.pdf
2020-04-07,12442,1180,271,345,184,https://covid19.min-saude.pt/wp-content/uploads/2020/04/36_DGS_boletim_20200407_2.pdf
2020-04-08,13141,1211,245,380,196,https://covid19.min-saude.pt/wp-content/uploads/2020/04/37_DGS_boletim_20200408.pdf
2020-04-09,13956,1173,241,409,205,https://covid19.min-saude.pt/wp-content/uploads/2020/04/38_DGS_boletim_20200409_VERSA%CC%83O-FINAL.pdf
2020-04-10,15472,1179,226,435,233,https://covid19.min-saude.pt/wp-content/uploads/2020/04/39_DGS_boletim_20200410.pdf
2020-04-11,15987,1175,233,470,266,https://covid19.min-saude.pt/wp-content/uploads/2020/04/40_DGS_boletim_20200411.pdf
2020-04-12,16585,1177,228,504,277,https://covid19.min-saude.pt/wp-content/uploads/2020/04/41_DGS_boletim_20200412.pdf
2020-04-13,16934,1187,188,535,277,https://covid19.min-saude.pt/wp-content/uploads/2020/04/42_DGS_boletim_20200413-DGS-259.pdf
2020-04-14,17448,1227,218,567,347,https://covid19.min-saude.pt/wp-content/uploads/2020/04/43_DGS_boletim_20200414.pdf
2020-04-15,18091,1200,208,599,383,https://covid19.min-saude.pt/wp-content/uploads/2020/04/44_DGS_boletim_20200415.pdf
2020-04-16,18841,1302,229,629,493,https://covid19.min-saude.pt/wp-content/uploads/2020/04/45_DGS_boletim_20200416-FINAL.pdf
2020-04-17,19022,1284,222,657,519,https://covid19.min-saude.pt/wp-content/uploads/2020/04/46_DGS_boletim_20200417.pdf
2020-04-18,19685,1253,228,687,610,https://covid19.min-saude.pt/wp-content/uploads/2020/04/47_DGS_boletim_20200418.pdf
2020-04-19,20206,1243,224,714,610,https://covid19.min-saude.pt/wp-content/uploads/2020/04/48_DGS_boletim_20200419.pdf
2020-04-20,20863,1208,215,735,610,https://covid19.min-saude.pt/wp-content/uploads/2020/04/49_DGS_boletim_202004201.pdf
2020-04-21,21379,1172,213,762,917,https://covid19.min-saude.pt/wp-content/uploads/2020/04/50_DGS_boletim_20200421.pdf
2020-04-22,21983,1146,207,785,1143,https://covid19.min-saude.pt/wp-content/uploads/2020/04/51_DGS_boletim_20200422.pdf
2020-04-23,22353,1095,204,820,1201,https://covid19.min-saude.pt/wp-content/uploads/2020/04/52_DGS_boletim_20200423.pdf
2020-04-24,22797,1068,188,854,1228,https://covid19.min-saude.pt/wp-content/uploads/2020/04/53_DGS_boletim_20200424.pdf
2020-04-25,23392,1040,186,880,1277,https://covid19.min-saude.pt/wp-content/uploads/2020/04/54_DGS_boletim_20200425.pdf
2020-04-26,23864,1005,182,903,1329,https://covid19.min-saude.pt/wp-content/uploads/2020/04/55_DGS_boletim_20200426.pdf
2020-04-27,24027,995,176,928,1357,https://covid19.min-saude.pt/wp-content/uploads/2020/04/56_DGS_boletim_20200427.pdf
2020-04-28,24322,936,172,948,1389,https://covid19.min-saude.pt/wp-content/uploads/2020/04/57_DGS_boletim_20200428.pdf
2020-04-29,24505,980,169,973,1470,https://covid19.min-saude.pt/wp-content/uploads/2020/04/58_DGS_boletim_20200429.pdf
2020-04-30,25056,968,172,989,1519,https://covid19.min-saude.pt/wp-content/uploads/2020/04/59_DGS_boletim_20200430V2.pdf
2020-05-01,25351,892,154,1007,1647,https://covid19.min-saude.pt/wp-content/uploads/2020/05/60_DGS_boletim_20200501.pdf
2020-05-02,25190,855,150,1023,1671,https://covid19.min-saude.pt/wp-content/uploads/2020/05/61_DGS_boletim_20200502_V2.pdf
module2/exo4/portugal_covid19.org 0 → 100644
View file @ 276af950
#+TITLE: Analysis of Portugal COVID-19 Numbers
#+AUTHOR: Alexandre D. Jesus
#+DATE: 2020-05-02
#+LANGUAGE: en
* Preparation
Load the csv
#+BEGIN_SRC R :results output :exports both :session *R*
dat <- read.csv("portugal_covid19.csv", head = T)
dat$Day <- as.Date(dat$Day)
summary(dat)
#+END_SRC
#+RESULTS:
#+begin_example
Day ConfirmedCases Hospital ICU
Min. :2020-03-03 Min. : 4 Min. : 0.0 Min. : 0.0
1st Qu.:2020-03-18 1st Qu.: 642 1st Qu.: 139.0 1st Qu.: 20.0
Median :2020-04-02 Median : 9034 Median : 855.0 Median :169.0
Mean :2020-04-02 Mean :10340 Mean : 658.6 Mean :129.7
3rd Qu.:2020-04-17 3rd Qu.:19022 3rd Qu.:1146.0 3rd Qu.:222.0
Max. :2020-05-02 Max. :25351 Max. :1302.0 Max. :271.0
Deaths Recoveries Report
Min. : 0.0 Min. : 0.0 Length:61
1st Qu.: 2.0 1st Qu.: 3.0 Class :character
Median : 209.0 Median : 68.0 Mode :character
Mean : 341.7 Mean : 363.5
3rd Qu.: 657.0 3rd Qu.: 519.0
Max. :1023.0 Max. :1671.0
#+end_example
Download the DGS reports for posterity, using the following shell
script. Note that only the missing files are downloaded
#+BEGIN_SRC sh
REPORTSDIR=./reports
mkdir -p $REPORTSDIR
for row in $(tail -n +2 portugal.csv); do
day=$(echo "$row" | cut -d, -f1)
link=$(echo "$row" | cut -d, -f7)
outf=${REPORTSDIR}/${day}.pdf
if [ ! -f "$outf" ]; then
echo "Missing file $outf. Downloading..."
wget -q "$link" -O "$outf"
fi
done
#+END_SRC
#+RESULTS:
For each of the columns "ConfirmedCases", "Hospital", "ICU", "Deaths",
and "Recoveries", we process a per day statistic.
#+BEGIN_SRC R :results output :exports both :session *R*
diffvec <- function(x) {
if(length(x) == 0) { return(c()) }
res <- c(0)
if(length(x) == 1) { return(res) }
for(i in 2:length(x)) {
res <- c(res, x[i] - x[i-1])
}
return(res)
}
dat$ConfirmedCasesPerDay <- diffvec(dat$ConfirmedCases)
dat$HospitalPerDay <- diffvec(dat$Hospital)
dat$ICUPerDay <- diffvec(dat$ICU)
dat$DeathsPerDay <- diffvec(dat$Deaths)
dat$RecoveriesPerDay <- diffvec(dat$Recoveries)
summary(dat)
#+END_SRC
#+RESULTS:
#+begin_example
Day ConfirmedCases Hospital ICU
Min. :2020-03-03 Min. : 4 Min. : 0.0 Min. : 0.0
1st Qu.:2020-03-18 1st Qu.: 642 1st Qu.: 139.0 1st Qu.: 20.0
Median :2020-04-02 Median : 9034 Median : 855.0 Median :169.0
Mean :2020-04-02 Mean :10340 Mean : 658.6 Mean :129.7
3rd Qu.:2020-04-17 3rd Qu.:19022 3rd Qu.:1146.0 3rd Qu.:222.0
Max. :2020-05-02 Max. :25351 Max. :1302.0 Max. :271.0
Deaths Recoveries Report ConfirmedCasesPerDay
Min. : 0.0 Min. : 0.0 Length:61 Min. :-161.0
1st Qu.: 2.0 1st Qu.: 3.0 Class :character 1st Qu.: 117.0
Median : 209.0 Median : 68.0 Mode :character Median : 446.0
Mean : 341.7 Mean : 363.5 Mean : 412.9
3rd Qu.: 657.0 3rd Qu.: 519.0 3rd Qu.: 643.0
Max. :1023.0 Max. :1671.0 Max. :1516.0
HospitalPerDay ICUPerDay DeathsPerDay RecoveriesPerDay
Min. :-117.00 Min. :-40.000 Min. : 0.00 Min. : 0.00
1st Qu.: -18.00 1st Qu.: -4.000 1st Qu.: 1.00 1st Qu.: 0.00
Median : 8.00 Median : 0.000 Median :20.00 Median : 1.00
Mean : 14.02 Mean : 2.459 Mean :16.77 Mean : 27.39
3rd Qu.: 32.00 3rd Qu.: 6.000 3rd Qu.:27.00 3rd Qu.: 32.00
Max. : 316.00 Max. : 47.000 Max. :37.00 Max. :307.00
#+end_example
Now we will make the plots for each of these statistics. But first we
create the figures directory.
#+BEGIN_SRC bash
mkdir -p ./figures
#+END_SRC
#+RESULTS:
* Confirmed Cases
Let's start by plotting the number of confirmed cases
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/confirmed_cases.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = ConfirmedCases)) +
geom_line() +
theme_bw() +
ylab("Cumulative Confirmed Cases") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/confirmed_cases.png]]
And the cases per day
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/confirmed_cases_per_day.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = ConfirmedCasesPerDay)) +
geom_line() +
theme_bw() +
ylab("Confirmed Cases") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/confirmed_cases_per_day.png]]
* Hospital
Now we plot the number of cases in the hospital at each day
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/hospital.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = Hospital)) +
geom_line() +
theme_bw() +
ylab("Cases in the hospital") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/hospital.png]]
And the variation per day
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/hospital_per_day.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = HospitalPerDay)) +
geom_line() +
theme_bw() +
ylab("Variation in the number of cases in the hospital") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/hospital_per_day.png]]
* ICU
We do the same for the cases in the ICU
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/icu.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = Hospital)) +
geom_line() +
theme_bw() +
ylab("Cases in the ICU") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/icu.png]]
And the variation per day
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/icu_per_day.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = HospitalPerDay)) +
geom_line() +
theme_bw() +
ylab("Variation in the number of cases in the ICU") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/icu_per_day.png]]
* Deaths
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/deaths.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = Deaths)) +
geom_line() +
theme_bw() +
ylab("Cumulative deaths") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/deaths.png]]
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/deaths_per_day.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = DeathsPerDay)) +
geom_line() +
theme_bw() +
ylab("Deaths per day") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/deaths_per_day.png]]
* Recoveries
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/recoveries.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = Recoveries)) +
geom_line() +
theme_bw() +
ylab("Cumulative recoveries") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/recoveries.png]]
#+BEGIN_SRC R :results output graphics :exports both :file ./figures/recoveries_per_day.png :width 600 :height 400 :session *R*
library(ggplot2)
ggplot(dat, aes(x = Day, y = RecoveriesPerDay)) +
geom_line() +
theme_bw() +
ylab("Recoveries per day") +
theme(axis.text.x=element_text(angle=60, hjust=1))
#+END_SRC
#+RESULTS:
[[file:./figures/recoveries_per_day.png]]
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