eval & include: Control the execution of the code

The code is not executed (but it is shown)

```{r}
#| echo: true
#| eval: false
head(rock)
```

head(rock)

```{r}
#| include: false
head(rock)
```

Other options

• warning: true

  (default) the warnings obtained from the code executed in the chunk are displayed

• message: true

  (default) the messages associated to the code (e.g., when you upload a package with library(package))

• error

  • error: false

    (default) If there is an error in the code, knitting stops and the document will not be generated until the error is fixed

  • error: true

    If there is an error in the code, the error message is shown in the document and the knitting goes on

YAML: Overall chunk options

Defined in the YAML, they are applied to all code chunks unless otherwise specified:

[...]
execute: 
  echo: fenced
  message: true
  error: true

```{r}
#| echo: false
head(rock)
```

  area    peri     shape perm
1 4990 2791.90 0.0903296  6.3
2 7002 3892.60 0.1486220  6.3
3 7558 3930.66 0.1833120  6.3
4 7352 3869.32 0.1170630  6.3
5 7943 3948.54 0.1224170 17.1
6 7979 4010.15 0.1670450 17.1

YAML: Show all code

[...]
format: 
  html:
    code-tools: 
     source: true
     toggle: false
     caption: This is my code

YAML: Code Fold

[...]
execute: 
  echo: fenced
  message: true
  error: true
code-fold: true
code-summary: See this specific code

Your turn

From the previous document

• Add an external image with knitr::include_graphics(), with a caption and a cross reference

• From the dataset of the course, the following plot, with a cross-reference and a caption:

ggplot(dataset, 
       aes(x = flexibility, y = anxiety, color = mindfulness)) +
  geom_point()

• The code used for the plot should be visible only if the person click on “Show code”. All other code-chunk should not be visible

kable

# knitr default
1kable(head(mtcars))

Another option: DT

# DT
1# install.packages("DT")
2library(DT)
3datatable(mtcars)

In general

At this page https://quarto.org/docs/authoring/cross-references.html you can find all the details and help for a correct use of cross-referencing.

@obj-label

[...]
lang: en

Images

• Code
• Output

@fig-pea illustrates a peacock

```{r}
#| out-width: 50%
#| fig-align: center
#| fig-cap: A peacock living the life
#| fig-cap-location: bottom
#| label: fig-pea
#| code-line-numbers: "|4-6|"
knitr::include_graphics("img/peacock.png")
```

Figure 3 illustrates a peacock

Tables

```{r}
#| echo: fenced
#| label: tbl-iris
#| tbl-cap: "Iris Data"
#| code-line-numbers: "|2|3|"

kable(head(iris))
```

Code

```{r}
#| lst-label: lst-basicPlot
#| lst-cap: Basic use of the plot() function

plot(cars)
```

plot(cars)

Equations

$$
  z = \frac{x_i - \bar{x}}{s}
$$ {#eq-standardize}

Your turn

• Add a table based on the dataset, with a caption and a cross-reference
• The code used for the previous ggplot graph:
  • Cross reference to the obtained graph
  • Cross reference to the code used to obtain it
• Add a collapsing callout block

Content

::: {.column-margin}
I want this picture displayed in the margin 


![](img/peacock.png)

:::

Code

```{r}
#| column: margin

1lm(hp ~ mpg*am, data = mtcars)
```

Graphs

```{r}
#| column: margin

ggplot(mtcars, 
       aes(hp, mpg, color = factor(am))) +
  geom_point() +
  geom_smooth(formula = y ~ x, method = "loess") +
  theme(legend.position = 'bottom')

```

Tables

```{r}
#| column: margin

datatable(mtcars,
  options = list(pageLength = 5))
```

Multiple mixed outputs

```{r}
#| eval: false
#| fig-column: margin

ggplot(mtcars, 
       aes(hp, mpg, color = factor(am))) +
  geom_point() +
  geom_smooth(formula = y ~ x, method = "loess") +
  theme(legend.position = 'bottom')

datatable(mtcars,
  options = list(pageLength = 5))
```

Your turn

• Side by side:
  • graph & table
  • graph & graph (add + geom_smooth() to the previous code)
  • Table & table

In general

YAML:

[...]
code-annotations: hover

An example

## GGplot

mtcars %>%                               # .<1>
  ggplot( aes(mpg, hp, size = gear)) +   # .<2>
  geom_point() +                         # .<3>    
  geom_smooth(method = "lm")             # .<4>

## GGplot

1mtcars %>%
2  ggplot( aes(mpg, hp, size = gear)) +
3  geom_point() +
4  geom_smooth(method = "lm")

In general

This allows for showing and executing code chunks directly in the text:

The mean of the gear variable in mtcars is `r mean(mtcars$gear)`

This is the code to compute the mean `mean(mtcars$gear)`