# Logbook of the reproducible research MOOC

This logbook will contain the main points I learnt and found useful in this MOOC, 
as well as some usefull references and resources.

## Module 1: note books and lab books

### 20.03.20 - 24.03.20

This module was mostly about taking notes. What I keep from it:

* Markdown is cool to take random notes, and keep information. This could replace the current Latex files I am using to keep some info on bibliography.
* The use of tags in my files could greatly improve my ability to find back some informations ! They suggest to use DocFetcher, which makes reaserches into text files. There is a tutorial in the MOOC I should check later. Here is the [web page of DocFectcher](http://docfetcher.sourceforge.net/en/index.html).
* Git is awsome! I am starting to be more efficient with git. I will keep on feeding my GitHub for R packages development, but I am thinking of creating a private project on GitLab to store and share data analysis scripts and files with colleagues.
* [ ] Cool! This is a task list!

I am not sure about what we should record as: 
> des données quotidiennes qui vous intéressent (temps, etc.). Vous les utiliserez par la suite dans le module 2.

But just in case, today is sunny, and I would like to eat a lemon icecream. Ah yeah, btw... COVID-19

Things I would like to figure out:
* On GitLab:
    * Can the changes made in this file be saved without being commited? *Doesn't look so*
    * what is the maximum storage?
    * can I give access to a private project to someone with a link, or does the person need to own a GitLab account?
    * what is this "No wrap"/"Soft wrap" button? *It just does automatic cut of the lines si everything can fit on the screen*

**There is an obvious lack of structure in this section!**

## Module 2: computational documents

### 25.03.20

What is needed for a study to be reproducible?

* The data should and the way they were collected should be available
* Each choice made in the methodology should be explained justified : all this should be ketp in the lab book

Le clique boutton, les tableurs et les logiciels propriétaires c'est pas top!

**Be organized, and store your data, randomize your experimental design, use text format, use free software!**

It sunny and I just realised that I can ear the church bell from my garden. Ah yeah, btw... COVID-19

#### Rstudio tutorial
I choose to follow the Rstudio tutorial even if I already know how to produce Rmarkdown files, but it would be cool to try later OrgMode, so that I could use Emacs to do eveything (while fore now I am only using it to produce Latex documents).

Something I didn't know: when you use another langage than R (for example when I use some pieces of bash/python for OBITOOLS pipelines), the variables generated in a chunck are not kept in memory and cannot be used from one chunk to another (which is the case for R code).