# Reproducible research course logbook 

## Module 1: Laboratory Notebook

### Quiz 01 (4/4)

1.  Why has a European project recently used the logbooks of the Portuguese, Spanish, Dutch and English Indian?

    *Answer*
*     a . To try to reconstitute the ocean climate criss-crossed by the Western navies 

2. What note media are illustrated in the course video "Note-taking concerns everyone" by Christophe Pouzat?

    *Answer*
*      b. Notes in books and manuscripts margins
*      d. Notes on cards and paper slips


3. Why did Leibniz order the construction of a closet ?

    *Answer*
*    b. To store and order notes written on paper slips  

4. For the curious, visit the Darwin Online web sites go to the notebooks and describe how Darwin took his notes.

     *Answer*
*    c. First in notebooks then on cards and paper sheets stored in folders 

### Quiz 02 (2/3)

1. What is the origin of the codex?
      *Answer*
*  a. Initially codices were made of parchment a much stronger (and therefore more durable) material than the papyrus used for scrolls 

    ***correction***
*   c. The Egyptian production of papyrus was not large enough to meet the demand of writers

2. What aspect of Eusebius work is presented in this sequence?
      *Answer*
*   b. His canon tables (cross-references between the Gospel books) 

3. In which line should the keyword "Analysis" go in John Locke's index ?
      *Answer*
*    c. « Aa » 

### Quiz 03 (3/3)

1. What is a text file ?
      *Answer*
*   b. A file made up (stored as) UTF-8 characters 

2. What is a tag ?
      *Answer*
*    c. A character, or series of characters, used to structure a document that will be invisible to the final reader.

3. Markdown is a markup language:
      *Answer*
*    a. "Light" 

### Exercice 01 (1st part): Getting familiar with GitLab
#### Exercice 01-1 : Gitlab Recherche/Search
#### Exercice 01-1 : Gitlab Historique (2/2 points)

### Exercice 01 (2nd part): Getting familiar with Markdown
#### Exercice 01-2 (0.86/1 point)

# Module 2: the showcase behind the scenes: the computational document

## Quiz 07 (3/3 marks)
1. In the studies we have presented to you, what prevents, sometimes for several years, the debate on the relevance of a study?
   *Answer*
* [Correct] has. Unpublished computational procedures
* [False] has. Unpublished computational proceduresb. Pressure from government or industry lobbyists who wish to build on the study in question
* [Correct] vs. Data used in the study was not released
* [False] Experts disagree

2. In the various examples presented (economics, MRI, crystallography), what are the main causes of errors?
   *Answer*
* [Correct] has. Data acquisition (bias, machine calibration, etc.)
* [Correct] b. Computation errorsvs.
* [Correct] Inadequate data processing or statisticsd. 
* [False] It's all about interpretation, error is inevitable.

3. What are the consequences of lack of transparency?
    *Answer*
* [Correct] has. It's difficult to rely on the work of othersb.
* [Correct] Articles contain less information (no details on calculations, experimental protocols, data analysis, etc.) and are therefore easier to readvs. 
* [Correct] It is difficult to verify and reproduce the analyzes presented in the articlesd. 
* [Correct] Two articles may present results that seem to contradict each other, but are both perfectly correct, as the lack of detail prevents the exact conditions of application from being determinede. 
* [False] Hiding the data used in the studies, we "guarantee" a certain anonymity to the people who may appear in these studies

## Quiz 08 (2/3 points)

1. What are the main technical causes behind the difficulties in reproducing someone else's work?
    *Answer*
* [Correct]a. The use of open source software:
* [Correct]b. Lack of documentation on the choices made
* [False] c. Interactive graphical software that hide computation details  
* [False] d. The overload of information because it is very difficult to find what you are looking for
* [Correct]e. Computation errors 
* [Correct]f. Data loss (no backup or no more readable format)

    ***correction***
* [False]a. The use of open source software:
* [Correct]b. Lack of documentation on the choices made
* [Correct] c. Interactive graphical software that hide computation details  
* [False] d. The overload of information because it is very difficult to find what you are looking for
* [Correct]e. Computation errors 
* [Correct]f. Data loss (no backup or no more readable format)

2. Which solutions are mentioned
    *Answer*
* [Correct]a. Using a laboratory notebook 
* [False] b. Using spreadsheets
* [Correct]c. Code review and continuous integratio
* [Correct]d. Using version control systems and several backup mechanisms

3. What are the most legitimate/valid fears associated with the systematic disclosure of data (open data) ?
    *Answer*
* [False]a. Be seen as a fool because others may then find your mistakes.: 
* [False]b. Someone could benefit from my work.
* [Correct]c. Some information may be sensitive and its disclosure may hurt people.: 
* [Correct]d. My resources are limited. If I systematically host all this data on the web page provided by my employer, I am likely to quickly exceed my quota.: 

## Quiz 09 (1/2 points)

1. What is commonly found in a computational document?
     *Answer*
* a. Commentaries
* b. Code
* c. An overview of data
* e. Computational results
* f. Hypertext links
* g. Images

2. What does a computational document allow?
     *Answer*
* a. Inspect the computations
* b. Easily re-run the computations if the original environment is available
* c. Document the code
* d. Explain why a particular computation is made based on the data analysis so far

    ***correction***

* a. Inspect the computations
* b. Easily re-run the computations if the original environment is available
* c. Document the code
* d. Explain why a particular computation is made based on the data analysis so far
* e. Perform non-regression tests in a systematic way

## 2.4. Familiarization with the tools
### 2.4A Get started with Jupyter tool

## QuizP 01 (3/3 points)
1. What does an environment like Jupyter provide in comparison to working in the Python console or running R scripts directly?
   *Answer*
* a. It provides a well-structured history of the analyses performed.
* b. It allows you to inspect data, keep a history of this inspection, and explain the transformations you perform as you go along.
* c. It saves intermediate results, whether textual or graphical. 
* e. It allows you to generate documents in HTML or PDF .
* f. It allows you to ensure that a figure is the result of the computation described in the document.

2. In Jupyter, what features are provided for the Python language but not available for the R language?
   *Answer*
* f. There are the same features for both languages

3. What allows you to be effective in an environment like Jupyter?
   *Answer*
* a. The export functions and the ability to easily re-run the code from the beginning 
* c. Autocompletion
* e. Learning keyboard shortcuts
* f. Reading the documentation and cheat sheets

Jupyter installation and configuration

# Module 3
## Quiz 12 (2/2)
1. What distinguishes a replicable data analysis from a traditional analysis?
   *Answer*
*    b. The code for all computations is included 


2. What are the advantages of a replicable analysis? What are the advantages of a replicable analysis? 
   *Answer*
* a. It is easier to prepare b. It is easier to modify
* d. It is easier to verify

## Quiz 13 (4/4)
1. Where do the data on the incidence of influenza-like illness come from?.
   *Answer*
* a. From the “réseau Sentinelles”, a network of general practitioners 

2. In which format are the data avialable?
   *Answer*
* b. CSV format 

3. Which is the sampling frequency of the incidence data?
   *Answer*
*  c. One value per week 

4. Why do we advise against removing the missing data line from the downloaded data file?
   *Answer*
*  b. It would leave no visible trace of the manipulation 

Data import-Jupyter