nhs-r-community / intro-quarto

Introduction to Quarto based on the Introduction to RMarkdown materials

Introduction to Quarto

This is a first edition of the Introduction to Quarto material based on the course content for Introduction to RMarkdown

The links to the published materials is in a suggested order.

Course preparation

Data for the course is held in a separate repository and details on how to get set up for the course can be found in the NHS-R Way book.

Part 1

Introduction

• Setting up
• What's Inside
• Source and Visual views
• Text
• Code chunks

Part 2

• Images
• Inline code
• Tabs
• Output formats
• Rendering
• Parameters

Break

Break

Spotted a mistake?

Please let us know if there are mistakes or improvements by creating an issue.

intro-quarto's Issues

Move the chunks slides before images

Images refers to {knitr} which uses chunk options so better to have chunk options explained first.

Change image from purrr.png to bakers_3.png

So this can be copied and tried about by attendees as purrr.png is stored with the html slides.
Also remove from the repository.

Markdown resizing of images

Chunks before images
If click on image in Visual can resize, either in pixels or %, gives in Source: {fig-alt="the bakers_3 image" fig-align="center" width="73%"}

Add fuzzy creatures on a roundabout image

https://nhs-r-community.github.io/intro-quarto/session-parameters.html#/rendering-multiple-reports

Helps to explain "loop"?

Incorrect file name

https://nhs-r-community.github.io/intro-quarto/session-images.html#/your-turn---add-an-image-in-visual-view-in-rstudio

bakers_1.png not bakers1.png

Also highlight the word image

Errors on slide

https://nhs-r-community.github.io/intro-quarto/session-images.html#/your-turn---add-an-image-in-visual-view-in-rstudio

Errors in name bakers_1.png
Highlight the / and image to be clearer that these are text to type

Create separate data repository

In order to make getting the files for the course easier and not have to download all the slides.

Improve function parameters?

Is it confusing to have country = country and month_start = month_start? Better to rename the arguments to be clear how they are distinct from the reports params.

https://nhs-r-community.github.io/intro-quarto/session-parameters.html#/a-function

Revise the images slides

In Source first, looking at code for ()
In same folder: bakers_1.png
In subfolder bakers_2.opng
In root then subfolder bakers_3.png

Then in Visual for adding another image (need to add a new picture – possibly purr), particularly to show that code is self generated in this view.

Note that Visual doesn't offer Alt text option with dots in top right unless something is added at the very start - this may be an enhancement/bug but for RStudio not Quarto.

https://nhs-r-community.github.io/intro-quarto/session-images.html#/your-turn---add-an-image-in-visual-view-in-rstudio

Your turn - add an image in Visual view in RStudio

Suggestion: a button to return to the GitHub repo page from quarto slides

Hello,

Just a thought/suggestion... it would be great if there was a button on the quarto slides which returned you straight back to the GitHub repo page. At the moment if you go back a page (using the back page arrow button - top-left of browser), it will take you back to the previous slide. It can then take a few back clicks to get back to the start of the slides and then GitHub repo page.

This is really a minor detail and mainly just me being lazy 😴 , but could be a useful addition, especially in the workshops :)
I do love the slides 🎓

Give example of `pull()`

Have code available from a tibble to show how pull can return a single cell as a vector:

https://nhs-r-community.github.io/intro-quarto/session-inline-code.html#/avoid-long-inline-code

Render on save button not available as default on Cloud

https://nhs-r-community.github.io/intro-quarto/session-rendering.html#/rendering-as-you-save

The option in Global Options.../Code/Saving/Automatically save when editor loses focus.

On local RStudio this is not ticked.

Add GitHub Action to render slides

Incorrect . on a slide

https://nhs-r-community.github.io/intro-quarto/session-rendering.html#/excluding-files

I think you decided the . in "!.files/" was incorrect?

This is my first GitHub "issue"!

Add numbers to options in slide

https://nhs-r-community.github.io/intro-quarto/session-intro.html#/what-is-quarto-is-it - put numbers in slides as that helps people refer to them. Make the question clearer, perhaps with Your Turn?

Incorrect slide as markdown does support resizing

https://nhs-r-community.github.io/intro-quarto/session-images.html#/resizing-images

By using the visual view and wizard, the markdown code is generated for sizes.

Remove ``` code from the slides

Because the course goes between visual and source, the chunks are better without the ```{r} code in them for copying and sharing:

https://nhs-r-community.github.io/intro-quarto/session-code-chunks.html#/default-code-chunk-settings

Rename report name

https://nhs-r-community.github.io/intro-quarto/session-code-chunks.html#/your-turn

to covid-analysis.qmd

Remove time for break slide

https://nhs-r-community.github.io/intro-quarto/session-whats-inside.html#/time-for-a-break

Use the specific break slide instead to help with more flexible timings

Chunk options for knitr - requires `output = asis`

https://nhs-r-community.github.io/intro-quarto/session-images.html#/your-turn---add-an-image-in-visual-view-in-rstudio

knitr needs output = asis also known as results = asis from RMarkdown

https://quarto.org/docs/computations/execution-options.html

Clarity needed on the particular view is through source, not visual

https://nhs-r-community.github.io/intro-quarto/session-images.html#/seeing-the-image-in-the-script

This is only available in the source view, not visual.

Update the highlight colour

To match the introduction to R and R Studio which uses a purple rather than bright green.

Code for importing the development {NHSRdatasets} needed sooner

https://nhs-r-community.github.io/intro-quarto/session-code-chunks.html#/eval uses code from {NHSRdatasets} but this may not be installed yet for those using their own computers.

Also make it clearer that the covid-analysis.qmd file has been opened for this code (because they relate in content rather than rely on it).

Remove `self-contained` line

intro-quarto/_quarto.yml

Line 13 in e14f409

self-contained: true

is not necessary as embed-resources does the same thing. Self-contained is the RMarkdown terminology which has changed for Quarto.

{tidyverse} warning or message?

This is usually only for one chunk but ](https://nhs-r-community.github.io/intro-quarto/session-code-chunks.html#/warning)

Is the information generated from {tidyverse} a warning or message? Double check which parameter suppresses it.

Update css colours

Consistency in slide about folder name

https://nhs-r-community.github.io/intro-quarto/session-rendering.html#/excluding-files

Refers in the code to folder-example but the text beneath hasn't been updated and still says files.

Add CNAME to GitHub

Chunk reference comes before chunk chapter

https://nhs-r-community.github.io/intro-quarto/session-images.html#/adding-images-using-knitr-and-code-chunks

and

https://nhs-r-community.github.io/intro-quarto/session-images.html#/alt-text-using-knitr

Chunks haven't been explained before this and perhaps needs to be reconsidered on the order? The image should be updated to one that's available in the data repository or include purrr_cat.png to be able to replicate.

Update quarto message box

https://nhs-r-community.github.io/intro-quarto/session-text.html#/headers

Still says optional caption (warning).

Code chunk slide needs to be clearer

New slide requires more clear instructions (and says to remove label but should be content) https://nhs-r-community.github.io/intro-quarto/session-code-chunks.html#/your-turn

Add this code to covid-analysis.qmd?

#| label: peek
glimpse(NHSRdatasets::covid19)

#| label: peek

Recycling chunks

#| eval: false
#| echo: true
#| label: another-peek
glimpse(NHSRdatasets::covid19)

This is the output alone

#| eval: true
#| echo: false
#| label: another-peek

Tabset headers need to be updated

The code no longer works with:

::: {.panel-tabset}
# Country analysis
## Overview
## Covid cases
:::

and needs to be:

# Country analysis
::: {.panel-tabset}
## Overview
## Covid cases
:::

Slide: https://nhs-r-community.github.io/intro-quarto/session-tabs.html#/tabsets-rely-upon-on-few-features