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Module 2 exercise 3

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module2/exo3/exercice_R_en.org
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#+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
* Data :noexport:
#+Begin_src R :session *R* :exports none
data <- c(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)
#+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
| 14 |
| 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 |
| 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 |
| 13.6 |
| 18 |
| 13.6 |
| 19.9 |
| 13.7 |
| 17 |
| 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 |
| 14.3 |
| 16.8 |
| 14 |
| 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 |
* Line plot
In order to plot with the lines, we need to specify the argument =type=.
#+Begin_src R :results output graphics file :file "./lines.png" :exports results :width 600 :height 400 :session *R*
plot(data, type="l")
#+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
[[file:./lines.png]]
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
* Histogram
For the histogram, we need to use =hist=:
#+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.
#+Begin_src R :results output graphics file :file "./hist.png" :exports results :width 600 :height 400 :session *R*
hist(data)
#+End_src
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.
#+RESULTS:
[[file:./hist.png]]
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