LeaRning - “Markdown & Quarto”

Author

PJ | LeaRning

1. Discussion Questions 1

Let’s talk about the following hot-takes from our textbook (Winter 2019, 48). Are these truth-bombs or gate-keeping?

  • “The scientific community, including the linguistic community, needs to rethink what it means to ‘publish’ a result.”

  • “The minimal requirement for reproducible research is that the data and scripts are shared (‘open data, open code’).”

  • “The scientific process hasn’t finished unless the data and code are provided as well.”

  • “The choice of software influences reproducibility.”

  • For storing data, “Use publicly accessible platforms such as OSF and GitHub.”

2. Some Key Terms

Term Definition
Replicate Same study with new data
Reproduce Same study with same data
Open science A movement to make scientific research and findings transparent and freely available to all.

3. Problem > Solution

Problem > Causes > Solution

  • Due to issues of transparency, it can be difficult, and sometimes impossible, to reproduce the research of others.

  • This has contributed to a “replication crisis” in some fields.

  • Lack of transparency

  • Use of proprietary software

  • Sharing of findings without sharing of process

  • Use R Markdown or Quarto to share findings

  • Clear documentation of the process

  • Replicable

  • Reproducible

  • Able to be proven wrong or right

4. Walkthrough

Headings:

# Heading 1
## Heading 2

Adding emphasis:

**bold text**
*italic text*

Bullet points:

-bullet point 1
-bullet point 2

Adding code:

```{r}
# code goes here
```

Options in Quarto (R Markdown has the same options but different syntax):

  • {r message = FALSE} disables the printing of messages.

  • {r output = FALSE} disables the printing of output, only the code is displayed.

  • {r echo = FALSE} disables the printing of code, only the output is displayed).

Use single back ticks to create an inline code span. It will be read exactly as typed, like this palmerpenguins.

`palmerpenguins`

5. Task

  • Reproduce in Quarto the document Dominate Your Next Social Gathering through Charisma!

6. Discussion Questions 2

More quotes from our textbook to talk about. These are about objections to this type of transparency (Winter 2019, 48–49).

  • “I don’t want my results or ideas stolen.”

  • “I fear retaliation or loss of reputation if somebody finds an error, or provides an alternative analysis with different conclusions.”

  • “I cannot actually share the data for ethical reasons.”

  • “I fear that companies may use my data for wrongdoing.”

  • “I feel embarrassed about my code.”

  • “Sharing data and code is not a common practice in my field.”

5. Additional resources

Bonus! To render your quarto document as a pdf:

  • Open a new terminal: tools>terminal>new terminal
  • Type: install tinytex and wait for it to install.
  • Scroll up to the top of your Quarto document.
  • Change the format from html to pdf
  • Render

Downloads

Use this link to download this .qmd file.

Notebook Download

References

Winter, Bodo. 2019. Statistics for Linguists: An Introduction Using R. 1st ed. New York: Routledge. https://doi.org/10.4324/9781315165547.