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‎AEET_2025/reproducible_science.qmd‎

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To view both the user and the associated email:
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`git config --global --list`
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⚡What is the shell? The shell (or terminal) is a program on your computer whose job is to run other programs (see https://happygitwithr.com/shell.html#shell). RStudio includes a terminal that you can use to interact with Git; however, it also has a tab called "Git" that provides basic Git functionalities and makes its use much easier.
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![Terminal](images/terminal.png)
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```
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👀 It’s a good idea to describe the purpose of the token in the *Note* field, since you can have several PATs. You won’t be able to view this token again, so don’t close or leave the browser window until you’ve stored the PAT locally. Treat this PAT like a password!
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## Git repositories and projects
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1. Create a repository on GitHub and connect it to a new RStudio project (this will generate a repository (folder) on your computer in the location you specified). Include a "*.gitignore*" file. Create a new R script in the working directory (that is, create an R script and save it inside the repository you just created)
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2. In RStudio, go to the Git tab to see all the documents that have been identified by Git
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![Git en RStudio](images/clipboard-1722222267.png)
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1. Add your project’s `.Rproj` file to the `*.gitignore*` file.
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2. Create a folder named `datos` (data) in your working directory. Add it to the `*.gitignore*` file and save. What happened in the **Git** tab?
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## Structure of a GitHub repository
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#### Text Formatting
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+---------------------------------+---------------------------------+
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| Markdown Syntax | Output |
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+=================================+=================================+
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| ``` | *italics* and **bold** |
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| *italics* and **bold** | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | superscript^2^ / subscript~2~ |
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| superscript^2^ / subscript~2~ | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | ~~strikethrough~~ |
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| ~~strikethrough~~ | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | `verbatim code` |
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| `verbatim code` | |
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| ``` | |
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+---------------------------------+---------------------------------+
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+--------------------------------+--------------------------------+
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| Markdown Syntax | Output |
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+================================+================================+
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| ``` | *italics* and **bold** |
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| *italics* and **bold** | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | superscript^2^ / subscript~2~ |
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| superscript^2^ / subscript~2~ | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | ~~strikethrough~~ |
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| ~~strikethrough~~ | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | `verbatim code` |
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| `verbatim code` | |
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| ``` | |
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+--------------------------------+--------------------------------+
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: {tbl-colwidths="\[50,50\]"}
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#### Headings {.smaller}
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| Markdown Syntax | Output |
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+=================================+=================================+
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| ``` | # Header 1 |
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| # Header 1 | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | ## Header 2 |
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| ## Header 2 | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | ### Header 3 |
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| ### Header 3 | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | #### Header 4 |
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| #### Header 4 | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | ##### Header 5 |
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| ##### Header 5 | |
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| ``` | |
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+---------------------------------+---------------------------------+
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| ``` | ###### Header 6 |
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| ###### Header 6 | |
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| ``` | |
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+---------------------------------+---------------------------------+
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+--------------------------------+--------------------------------+
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| Markdown Syntax | Output |
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+================================+================================+
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| ``` | # Header 1 |
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| # Header 1 | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | ## Header 2 |
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| ## Header 2 | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | ### Header 3 |
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| ### Header 3 | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | #### Header 4 |
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| #### Header 4 | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | ##### Header 5 |
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| ##### Header 5 | |
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| ``` | |
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+--------------------------------+--------------------------------+
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| ``` | ###### Header 6 |
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| ###### Header 6 | |
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| ``` | |
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+--------------------------------+--------------------------------+
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: {tbl-colwidths="\[50,50\]"}
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Unordered list:
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**Markdown:**
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- sub-item 1
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- sub-sub-item 1
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Ordered list:
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**Markdown:**
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i. sub-item 1
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A. sub-sub-item 1
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#### Quotes
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**Single class**: Two equivalent syntaxes
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No `{`, and no `.`:
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```
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**Multiple classes**: use `{` and `.`, separate with spaces
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- Add a caption to the second callout box.
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- Make the third callout box collapsible. Then, switch over to the source editor to inspect the markdown code.
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##### Footnotes
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#### Anatomy of a code chunk
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```{r}
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- Engine (`r`) is indicated between curly braces `{r}`
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- Options stated with the `#|` (hashpipe): `#| option1: value`
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Available code cell options: <https://quarto.org/docs/reference/cells/cells-knitr.html>
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- If you want to both execute the code and return the full code including backticks (like in a teaching scenario) `echo: fenced` is your friend!
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Source:
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In addition to rendering the complete document to view the results of code chunks you can also run each code chunk interactively in the `RStudio` editor by clicking the icon or keyboard shortcut (`Cmd/Ctrl + Shift + Enter`).
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##### Markdown figures with options
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![Penguins playing with a Quarto ball](images/penguins-quarto-ball.png){fig-align="left"}
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### Quarto Projects
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💡[Here](https://github.com/DatSciR/intro_git-github/blob/main/centra/dia3_comandos.md) (in the "Otros comandos útiles" section - in Spanish) you can see how to delete branches and other useful commands.
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# Useful Links

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