Plain vs. enhanced text

Simple text. No editing, no hyperlinks, no enhanced fields.

Enhanced text integrates r-code.

This is an example of how automatization can be implemented in the work flow. 
My list of movies include `r nrow(dfmv)` entries. 
The title of those movies are `r dfmv$Movie`. 
Is there a movie that I actually dont like on that list, well, the answer is that I dislike exactly 
`r dfmv %>% filter(Like %in% c("No","no","NO")) %>% nrow()`
movies on that list.

Knit with parameters

# specify parameter in yaml header
title: "example"
output: html_document
date: "2024-05-09"
params:
  actor:
    label: "Actor"
    value: "Keanu Reeves"
    input: select
    choices: ["Keanu Reeves", "Alec Baldwin","Arnold Schwarzenegger"]
    multiple: yes

# assign parameter to object
actor<-params$actor

# use parameter in code
tmptbl<-dfmv %>% 
  filter(Actor %in% actor)

Quarto

Retains all the functions of a RMarkdown document while it enhances and simplifies the work flow further.

Integrates more programming languages and makes it easier to use css, latex formatting directly in the source document .qmd.

Basically, Quarto makes it much much much easier for everyone to create presentations, live documents, websites, books and so on.

It can integrate shiny features too.

What we need to focus on is the .qmd.

flowchart LR
  A(Plain text) --> Z{.qmd}
  B(Code) --> Z{.qmd}
  C(Images) --> Z{.qmd}
  D(External source file) --> Z{.qmd}
  E(Formatting source file) --> Z{.qmd}
  F(...) --> Z{.qmd}

Similar to the RMarkdown set up.

1 - r

2 - RStudio

3 - Quarto, which can be downloaded https://quarto.org/docs/get-started/

After you’ve successfully installed r, RStudio, and quarto on your computer, we can start with creating websites and books.

Default quarto website

.qmd, .yml, .css as well as a folder “_site”.

Live preview by typing in the Terminal:

quarto preview

Render by typing in the Terminal:

quarto render

.qmd file

Virtually identical to .Rmd.

.yml file

.yml file is for the entire website.

yaml header inside .qmd is for that .qmd only!

.css file

Called inside the .yaml file.

The default .css file is empty.

.css stands for Cascade Style Sheets and is a language used most typically for styling HTML files.

Website content

Use the knowledge from previous sessions and create content for your website. Or, a basic structure that you could edit at a later stage.

Deploy website via quartopub.com

First, quarto preview the website locally and make sure all is good.

We can deploy directly from Terminal to quartopub.com using

quarto render

then

quarto publish quarto-pub

The website will open in your default browser once successfully deployed. Rendering may take some time.

Deploy website via GitHub

Let’s assume this is our preferred strategy.

Before we begin creating content, we create a new repository on GitHub that we’re planning to use for the website. We can call this repository personal website, or any other name.

Once created, we will clone this empty repository on our local machine which become the working directory (project folder) for the website. This solves the link between local machine and online server GitHub.

Open the <> Code panel, make sure the SSH tab is selected, and copy the repository address starting with git@github...

In your terminal (gitbash), decide where you’d like to deposit this repository – this must remain fixed otherwise the link to GitHub is lost.

You can use these commands to navigate until the desired folder

ls = lists everything in the folder cd = enters a folder

Then clone the website repository on your local machine.

We can now use this folder to create our default website as shown previously.

We then create content for the website as shown previously.

When we’re ready, we render the website,

quarto render

then we push to the online repository.

git add .
git commit -m "Push website"
git push

We finally setup GitHub to “read” the website from the sub-folder docs.

You can publish your website (or book, as we will see in the next section) on a custom domain. For this you’d need to pay a monthly or yearly fee.

See for details this ultra-brief guide https://adrianstanciu.eu/sitedummy.html I wrote some time ago but still remains valid.

quarto.com vs. GitHub

The choice depends on the domain.

On quarto.com, a custom domain is not possible. The website domain will contain the root to your quarto account followed by the website name.

Via GitHub, a custom domain is possible against costs. The standard domain will contain the root to your GitHub account followed by the website name.

Why an online book

It can be shared online.

It can be easily structured into sections and chapters.

It can integrate r (as well as other languages) code.

You maintain full control over content and formatting.

It can be downloaded as PDF or EPUB (for e-readers, not covered in this class).

From it, one can download material…

Default quarto book

.qmd, .yml, .bib as well as a folder “_book”.

Live preview by typing in the Terminal:

quarto preview

Render by typing in the Terminal:

quarto render

.qmd file

Identical with the .qmd for websites.

.yml file

Identical with the one for creating websites but contains different attributes.

.yml - tips

.bib file

Citation file format that gets integrated in the output document through pandoc.

.bib - tips

Book content

Use the knowledge from previous sessions and create content for your book. Or, a basic structure that you could edit at a later stage.

Deploy book

First, quarto preview the book locally and make sure all is good.

We can deploy directly from Terminal to quartopub.com using

quarto render

then

quarto publish quarto-pub

The book will open in your default browser once successfully deployed. Rendering may take some time.