Introduction to Quarto

RStudio

Warning

If you’re new to R, follow the online ModernDrive chapter https://moderndive.netlify.app/1-getting-started.html

Using Project

GIF for creating an RStudio Project

RStudio Layout

Locate the following panes:

Console
Source
History
Help

Recommended Options

Tools –> Global Options –>
Set “Save workspace to .RData on exit” to “No”.

Recommended option for RStudio

R Basics

Install R Packages

See https://twitter.com/visnut/status/1248087845589274624

# Install the tidyverse "meta" package
# install.packages("tidyverse")
# Install the here package
# install.packages("psych")

!!! Don’t you dare include any install.packages() statements in your homework !!!

Load a Package

# Uncomment the code below to load the tidyverse package
# library(tidyverse)

Built-In Data

data(bfi, package = "psych")  # make the "bfi" data set available for use
head(bfi, 10)  # show the first 10 rows of data

Quarto

https://quarto.org/

Open-source scientific and technical publishing system
Next-generation version of R Markdown

Elements of Quarto

See https://quarto.org/docs/get-started/hello/rstudio.html

YAML header
Code chunks
Markdown text

YAML

Exercise 1

Update your name in the author field
Change the option from toc: false to toc: true
Insert today’s date using the date field

Markdown Text

See https://quarto.org/docs/authoring/markdown-basics.html

Bold **Bold**
italic *italic*
code `code`
Link to USC [Link to USC](https://www.usc.edu)
Header

# Level 1

## Level 2

### Level 3

Unordered list

item 1
item 2
- item 2a

Ordered list

item 1
item 2
1. item 2a

Equations (LaTeX)

Inline: $Y_i = \beta_0 + \beta_1 X_i + e_i$

Display:

\[\rho = \frac{\tau^2}{\tau^2 + \sigma^2}\]

Inline Code

The value of $\pi$ is `r pi`

The value of $\pi$ is 3.1415927

Code Chunks

Content to be interpreted by R engine

1 + 1

[1] 2

v1 <- c(1, 2, 6, 8)  # create a vector `v1`
v1[3]  # extract 3rd element of v1

[1] 6

# extract the `A2` column, and compute the median
median(bfi$A2)

[1] NA

Chunk Options

echo: false: Do not show the input command
fig-width, fig-height: Size of figure

library(ggplot2)
ggplot(bfi, aes(x = A2)) +
    geom_bar()

Warning: Removed 27 rows containing non-finite values (`stat_count()`).

Exercise 2

Change the aspect ratio of the graph above to 1:1

Rendering

format: html, pdf, docx, etc
- If running into problems for PDF, enter the following to the Terminal:
```
Terminal
```
```
quarto install tool tinytex
```
Try also revealjs!

Note: Different R sessions are used for the console and for knitting

Exercise

Download the Rmd file, then do the following

Complete Ex1 above.
Complete Ex2 above.
Type this equation in LaTeX: https://www.gstatic.com/education/formulas2/472522532/en/cronbach_s_alpha.svg. Make sure you get all the subscripts right.
Install and load the modelsummary package, run the following, and write down what the chunk does. You’ll need to set eval: true (or remove the line) so the chunk runs.

# Install and load the modelsummary package first; otherwise, it won't run
library(dplyr)
library(modelsummary)
datasummary(O1 + O2 + O3 + O4 + O5 ~ 
                Factor(gender, levelnames = c("Males", "Females")) * 
                (Mean + SD),
            data = bfi)

Run the following and find out what the code chunk does.

bfi %>%
    select(A1:C5) %>%
    datasummary_correlation()

Run the following and find out what the code chunk does.

bfi %>%
    select(E1:E5) %>%
    psych::alpha()

Run the following and find out what this code chunk does.

library(tidyr)
bfi %>%
    select(N1:N5) %>%
    pivot_longer(cols = N1:N5, names_to = "item", values_to = "score") %>%
    ggplot(aes(x = score)) +
    geom_bar() +
    facet_wrap(~ item)

Render the document to a PDF output.
Submit the knitted PDF to Blackboard.

--- title: "Introduction to Quarto" format: html --- # RStudio ```{r} #| include: false # Define a function that shows gif with HTML, and only a link if PDF include_gif <- function(path) { if (knitr:::is_latex_output()) { knitr::asis_output(sprintf("\\url{%s}", path)) } else { knitr::include_graphics(path) } } ``` ::: {.callout-warning icon=false} If you're new to R, follow the online ModernDrive chapter <https://moderndive.netlify.app/1-getting-started.html> ::: ## Using Project ```{r} #| fig-alt: "GIF for creating an RStudio Project" #| echo: false include_gif("https://github.com/marklhc/teaching_assets/raw/main/rstudio_project.gif") ``` ## RStudio Layout Locate the following panes: - Console - Source - History - Help ## Recommended Options - Tools --> Global Options --> - Set "Save workspace to .RData on exit" to "No". ```{r} #| fig-alt: "Recommended option for RStudio" #| echo: FALSE include_gif("https://github.com/marklhc/teaching_assets/raw/main/rstudio_not_save_workspace.gif") ``` # R Basics ## Install R Packages See <https://twitter.com/visnut/status/1248087845589274624> ```{r} # Install the tidyverse "meta" package # install.packages("tidyverse") # Install the here package # install.packages("psych") ``` !!! Don't you dare include any `install.packages()` statements in your homework !!! ## Load a Package ```{r} # Uncomment the code below to load the tidyverse package # library(tidyverse) ``` ## Built-In Data ```{r} data(bfi, package = "psych") # make the "bfi" data set available for use head(bfi, 10) # show the first 10 rows of data ``` # Quarto <https://quarto.org/> - Open-source scientific and technical publishing system - Next-generation version of R Markdown ## Elements of Quarto See <https://quarto.org/docs/get-started/hello/rstudio.html> - YAML header - Code chunks - Markdown text ## YAML ::: {.callout-note} ## Exercise 1 - Update your name in the `author` field - Change the option from `toc: false` to `toc: true` - Insert today's date using the `date` field ::: ## Markdown Text See <https://quarto.org/docs/authoring/markdown-basics.html> - **Bold** `**Bold**` - *italic* `*italic*` - `code` `` `code` `` - [Link to USC](https://www.usc.edu) `[Link to USC](https://www.usc.edu)` - Header ````markdown # Level 1 ## Level 2 ### Level 3 ```` --- Unordered list - item 1 - item 2 - item 2a Ordered list 1. item 1 2. item 2 a. item 2a --- ### Equations (LaTeX) Inline: $Y_i = \beta_0 + \beta_1 X_i + e_i$ Display: $$\rho = \frac{\tau^2}{\tau^2 + \sigma^2}$$ ## Inline Code ````markdown The value of $\pi$ is `r '\x60r pi\x60'` ```` The value of $\pi$ is `r pi` ## Code Chunks Content to be interpreted by R engine ```{r} 1 + 1 v1 <- c(1, 2, 6, 8) # create a vector `v1` v1[3] # extract 3rd element of v1 # extract the `A2` column, and compute the median median(bfi$A2) ``` --- ### Chunk Options - `echo: false`: Do not show the input command - `fig-width`, `fig-height`: Size of figure ```{r} #| fig-width: 4 #| fig-height: 2 library(ggplot2) ggplot(bfi, aes(x = A2)) + geom_bar() ``` ::: {.callout-note} ## Exercise 2 Change the aspect ratio of the graph above to 1:1 ::: ## Rendering - `format`: `html`, `pdf`, `docx`, etc * If running into problems for PDF, enter the following to the **Terminal**: ```{.bash filename="Terminal"} quarto install tool tinytex ``` - Try also `revealjs`! Note: Different R sessions are used for the console and for knitting # Exercise Download the Rmd file, then do the following 1. Complete Ex1 above. 2. Complete Ex2 above. 3. Type this equation in LaTeX: <https://www.gstatic.com/education/formulas2/472522532/en/cronbach_s_alpha.svg>. Make sure you get all the subscripts right. 4. Install and load the `modelsummary` package, run the following, and write down what the chunk does. You'll need to set `eval: true` (or remove the line) so the chunk runs. ```{r} #| message: false #| eval: false # Install and load the modelsummary package first; otherwise, it won't run library(dplyr) library(modelsummary) datasummary(O1 + O2 + O3 + O4 + O5 ~ Factor(gender, levelnames = c("Males", "Females")) * (Mean + SD), data = bfi) ``` --- 5. Run the following and find out what the code chunk does. ```{r} #| eval: false bfi %>% select(A1:C5) %>% datasummary_correlation() ``` 6. Run the following and find out what the code chunk does. ```{r} #| eval: false bfi %>% select(E1:E5) %>% psych::alpha() ``` --- 7. Run the following and find out what this code chunk does. ```{r} #| eval: false library(tidyr) bfi %>% select(N1:N5) %>% pivot_longer(cols = N1:N5, names_to = "item", values_to = "score") %>% ggplot(aes(x = score)) + geom_bar() + facet_wrap(~ item) ``` --- 8. Render the document to a PDF output. 9. Submit the knitted PDF to Blackboard.