JulesDommartin/proglit

Literate Programming

Literate Programming Course

Welcome to the Literate Programming public repository, part of the Miage L3.

Presentations

• General Introduction - Course overview, goals, references and reproducibility
• Literate Programming - Literate Programming Motivation & RStudio Case Study
• Data Representation - Checklist for good graphics (Slides for Discussion)

TD Specifications

TD1: Setup

1. Download and Install git and RStudio (take the free version)

   • Git: https://git-scm.com/downloads
     • Understand git and Tutorial: https://try.github.io/
   • RStudio: https://www.rstudio.com/products/rstudio/download/

2. Create a github account

   • https://github.com/join
     • Use as login something that uniquely identify yourself in Miage L3.
   • Login with your new account in the http://github.com/

3. Add your public SSH key

   • Add it here: https://github.com/settings/keys
   • Tutorial: https://help.github.com/articles/connecting-to-github-with-ssh/

4. Fork the reference repository

   • Fork this repository: https://github.com/schnorr/proglitt
     • Please, use the Fork button in the web interface
   • Tutorial: https://help.github.com/articles/fork-a-repo/

5. Clone your forked repository locally

   • git clone git@github.com:LOGIN/proglitt.git
   • Tutorial: https://help.github.com/articles/cloning-a-repository/

6. Create your first commit, then push it to github

   • Create a file AUTHOR.txt with your name
   • Then, run git add AUTHOR.txt
   • Commit it locally using git commit -m "my first commit"
   • Push to github with git push origin master

7. Add Prof. Schnorr's remote

   Do in your local repository, the one that you've cloned, the following commands:

   • Run git remote add schnorr git@github.com:schnorr/proglitt.git
   • Check for updates: git fetch schnorr master
   • Merge them locally: git pull schnorr master (pull is equivalent to fetch+merge commands)
   • Push then to your github repository: git push origin master

   Repeat the last two commands to keep your github repository updated.

   This is necessary to keep yourself up to date with latest TD updates.

Congratulations, you're done for the TD1.

TD2: Critical view for plots

1. Create a directory TD2 in your local repository

   • Run mkdir TD2
   • You are going to put your TD2 on that directory

2. Select a plot

   • Select any plot you have seen in journals/articles/...
   • Create a text with your critical view on that plot
     • Is the plot right? What about the axes, are they explicit?
     • Are the scales correct? Is the origin there?
     • What about the colors, shapes of the points?

3. Commit the plot you have selected and your critical view to the TD2 directory

   Suppose your critical view is on the file myTD2.txt and the plot is mySelectedPlot.pdf, do:

   • cd TD2
   • git add myTD2.txt mySelectedPlot.pdf
   • git commit -m "my TD2 has been completed"

Congratulations, you're done for the TD2.

TD3: Using RStudio for running a Statistical Analysis

See the Specification for the TD3. You need to repeat the analysis that has been presented for one of the provided data sets: ping-pong measurements or the iteration duration of a geophysics application. You need to use RStudio to modify the given file, writing in your data interpretation of the results, and generating a PDF file at running knitr in the document (through the appropriate feature in RStudio).

TD4: Forthcoming

Contact Information

If you encounter any problem, please contact the professors by e-mail:

• Jean-Marc Vincent (jean-marc.vincent@imag.fr)
• Lucas Mello Schnorr (schnorr@inf.ufrgs.br)