Adapt content to outbreak context and R packages

[avallecam]

• Please check if the PR fulfils these requirements

• I have read the CONTRIBUTING guidelines

• What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

  • Adapt episodes 1-14 from git-novice to use the terminal and the console, in an outbreak scenario to create a sitrep. This fixes create a outbreak related scenario #12

• What breaking change does this PR introduce?

  • The approach now is to adapt our topic/approach to the git-novice with minimum replacements, instead of adapting the git-training slides to a workbench format.
  • Benefits from this: use as much as possible plain-text commands, either in the console or in the terminal. This keeps the material accessible, given that it reduces the need for screenshots with actions in graphical window interfaces.

• For Reviewers:

  • Please, read the CONTRIBUTING.md reviewer role steps.

[avallecam]

Thank you for the review!

I covered your edit suggestions in the recent commits.

I created new issues covering comments in this PR:

• add an installation step to the reviewer guidelines #17
• replace "Word's" inside the figure with "Google Docs's" #21
• add EN translation to reproducibility gradient figure in ES #22
• change all instances of Rstudio to RStudio. #23
• clear the Summary and Setup Page #24

Given the scope of this PR, I think I can solve them in separate PRs, prioritizing #24 and #17. Let me know if you agree with this.

[joshwlambert]

@avallecam Really nice work on the tutorial!

I've added all of my comments within the PR to specific lines.

The only other comment I had was I think that more information on branching and merging using Git is required for a beginner. The collaboration workflow is heavily dependent on Git users being able to branch and make changes in parallel to collaborators. A lot of this information is already included in 14-supplemental-rstudio.html#create-a-branch but I think this should be moved into a standalone chapter with some more information. If you decide to do this it can be done in a separate PR like the issues you raised in the comment above.

[avallecam]

The only other comment I had was I think that more information on branching and merging using Git is required for a beginner. The collaboration workflow is heavily dependent on Git users being able to branch and make changes in parallel to collaborators. A lot of this information is already included in 14-supplemental-rstudio.html#create-a-branch but I think this should be moved into a standalone chapter with some more information. If you decide to do this it can be done in a separate PR like the issues you raised in the comment above.

I agree with your comment. I'll cite this in a new issue for a standalone chapter