02-Code chunks

Author

Ottavia M. Epifania

Code chunk

Open a new chunk code: shift + ctrl + i or

. . .

Chunk options

`echo`: Control the code display

Code executed & Shown

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

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

Code executed & Not Shown

```{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

. . .

Code executed & entire chunk shown

```{r}
#| echo: fenced
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

`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)

. . .

The code is executed, neither the code nor the results are show

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

include: false

Super convient as first code chunk to load all the packages, data, preprocessing

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

. . .

Overruled by specific code-chunk options:

```{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

Images & Graphs

@fig-peacock1 illustrates a peacock

```{r}
#| out-width: 50%
#| fig-align: center
#| fig-cap: A peacock living the life
#| fig-cap-location: bottom
#| label: fig-peacock1
knitr::include_graphics("img/peacock.png")
```

1: The width of the picture
2: The alignment
3: The caption
4: The caption location
5: The label to use for cross-referencing

Figure 1 illustrates a peacock

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

Graphics

Code
Output

@fig-mtcars1 illustrates a plot

```{r}
#| out-width: 50%                                
#| fig-align: center                             
#| fig-cap: A graph from `mtcars`
#| fig-cap-location: margin
#| label: fig-mtcars1
ggplot(mtcars, aes(hp, mpg, color = factor(am))) +
  geom_point() +
  geom_smooth(formula = y ~ x, method = "loess") +
  theme(legend.position = 'bottom')
```

Figure 2 illustrates a plot

```{r}
#| out-width: 50%
#| fig-align: center
#| fig-cap: A graph from `mtcars`
#| fig-cap-location: margin
#| label: fig-mtcars
#| code-line-numbers: "|2|3|4|5|6"
ggplot(mtcars,                                   
       aes(hp, mpg, color = factor(am))) +       
  geom_point() +
  geom_smooth(formula = y ~ x, method = "loess") +
  theme(legend.position = 'bottom')
```

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

Tables

`kable`

# knitr default
kable(head(mtcars))

1: Basic table, the kable() function is in the knitr package

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
Mazda RX4	21.0	6	160	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108	93	3.85	2.320	18.61	1	1	4	1
Hornet 4 Drive	21.4	6	258	110	3.08	3.215	19.44	1	0	3	1
Hornet Sportabout	18.7	8	360	175	3.15	3.440	17.02	0	0	3	2
Valiant	18.1	6	225	105	2.76	3.460	20.22	1	0	3	1

# kableExtra

# install.packages("kableExtra")
library(kableExtra)
kable(mtcars) %>%
  scroll_box(height = "450px", width = "100%")

1: Install package (Uncomment if you need to install the package)
2: Upload package
3: Produce the table
4: Add fancy stuff (height and with of the scroll box)

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
Mazda RX4	21.0	6	160.0	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160.0	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108.0	93	3.85	2.320	18.61	1	1	4	1
Hornet 4 Drive	21.4	6	258.0	110	3.08	3.215	19.44	1	0	3	1
Hornet Sportabout	18.7	8	360.0	175	3.15	3.440	17.02	0	0	3	2
Valiant	18.1	6	225.0	105	2.76	3.460	20.22	1	0	3	1
Duster 360	14.3	8	360.0	245	3.21	3.570	15.84	0	0	3	4
Merc 240D	24.4	4	146.7	62	3.69	3.190	20.00	1	0	4	2
Merc 230	22.8	4	140.8	95	3.92	3.150	22.90	1	0	4	2
Merc 280	19.2	6	167.6	123	3.92	3.440	18.30	1	0	4	4
Merc 280C	17.8	6	167.6	123	3.92	3.440	18.90	1	0	4	4
Merc 450SE	16.4	8	275.8	180	3.07	4.070	17.40	0	0	3	3
Merc 450SL	17.3	8	275.8	180	3.07	3.730	17.60	0	0	3	3
Merc 450SLC	15.2	8	275.8	180	3.07	3.780	18.00	0	0	3	3
Cadillac Fleetwood	10.4	8	472.0	205	2.93	5.250	17.98	0	0	3	4
Lincoln Continental	10.4	8	460.0	215	3.00	5.424	17.82	0	0	3	4
Chrysler Imperial	14.7	8	440.0	230	3.23	5.345	17.42	0	0	3	4
Fiat 128	32.4	4	78.7	66	4.08	2.200	19.47	1	1	4	1
Honda Civic	30.4	4	75.7	52	4.93	1.615	18.52	1	1	4	2
Toyota Corolla	33.9	4	71.1	65	4.22	1.835	19.90	1	1	4	1
Toyota Corona	21.5	4	120.1	97	3.70	2.465	20.01	1	0	3	1
Dodge Challenger	15.5	8	318.0	150	2.76	3.520	16.87	0	0	3	2
AMC Javelin	15.2	8	304.0	150	3.15	3.435	17.30	0	0	3	2
Camaro Z28	13.3	8	350.0	245	3.73	3.840	15.41	0	0	3	4
Pontiac Firebird	19.2	8	400.0	175	3.08	3.845	17.05	0	0	3	2
Fiat X1-9	27.3	4	79.0	66	4.08	1.935	18.90	1	1	4	1
Porsche 914-2	26.0	4	120.3	91	4.43	2.140	16.70	0	1	5	2
Lotus Europa	30.4	4	95.1	113	3.77	1.513	16.90	1	1	5	2
Ford Pantera L	15.8	8	351.0	264	4.22	3.170	14.50	0	1	5	4
Ferrari Dino	19.7	6	145.0	175	3.62	2.770	15.50	0	1	5	6
Maserati Bora	15.0	8	301.0	335	3.54	3.570	14.60	0	1	5	8
Volvo 142E	21.4	4	121.0	109	4.11	2.780	18.60	1	1	4	2

Another option: DT

# DT
# install.packages("DT")
library(DT)
datatable(mtcars)

1: Install package (Uncomment if you need to install the package)
2: Upload package
3: Print the table

Cross referencing

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

. . .

YAML:

[...]
lang: en

Language	Code
English	`en`
Chinese	`zh`
Spanish	`es`
French	`fr`
Japanese	`ja`
German	`de`

Language	Code
Portuguese	`pt`
Russian	`ru`
Czech	`cs`
Finnish	`fi`
Dutch	`nl`
Italian	`it`
Polish	`pl`
Korean	`ko`

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

Code
Output

@tbl-iris illustrates a table

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

kable(head(iris))
```

Table 1 illustrates a table

Table 1: Iris Data

Sepal.Length	Sepal.Width	Petal.Length	Petal.Width	Species
5.1	3.5	1.4	0.2	setosa
4.9	3.0	1.4	0.2	setosa
4.7	3.2	1.3	0.2	setosa
4.6	3.1	1.5	0.2	setosa
5.0	3.6	1.4	0.2	setosa
5.4	3.9	1.7	0.4	setosa

Code

Code lst
Output

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

plot(cars)
```

@lst-basicPlot illustrates a basic use of the function plot()

Listing 1: Basic use of the plot() function

plot(cars)

Listing 1 illustrates a basic use of the function plot()

Equations

Code
Output

@eq-standardize illustrates how to standardize a value

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

Equation 1 illustrates how to standardize a value

\[ z = \frac{x_i - \bar{x}}{s} \tag{1}\]

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

Margins

Content

Code
Output

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


![](img/peacock.png)

:::

Code

Code
Ouput

```{r}
#| column: margin

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

1: Fit a Linear Model with an interaction effect

Graphs

Code
Ouput

```{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

Code
Ouput

```{r}
#| column: margin

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

Multiple mixed outputs

Code: fig-margin
Ouput: fig-margin

```{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))
```

Multiple plots

Code
Output

@fig-plotsModels illustrates different things. @fig-plotsModels-1 illustrates this, @fig-plotsModels-2 illustrates that and so on

```{r}
#| label: fig-plotsModels
#| column: screen-inset-shaded
#| layout-nrow: 2
#| layout-ncol: 2
#| fig-cap: "One dataset, different models" 
#| fig-subcap:
#|   - "The data"
#|   - "Polynomial"
#|   - "Linear Model"
#|   - "GLM with Poisson" 


ggplot(mtcars,
       aes(mpg, hp, size = gear)) +
  geom_point()

ggplot(mtcars,
       aes(mpg, hp, size = gear)) +
  geom_point() + 
  geom_smooth()

ggplot(mtcars,
       aes(mpg, hp, size = gear)) +
  geom_point() + 
  geom_smooth(method = "lm")
ggplot(mtcars,
       aes(mpg, hp, size = gear)) +
  geom_point() + 
  geom_smooth(method = "glm", method.args = list(family = "poisson"))


```

Figure 4 illustrates different things. Figure 4 (a) illustrates this, Figure 4 (b) illustrates that and so on

Multiple Tables

Code
Output

@tbl-tables presents two datasets: @tbl-tables-1 is cars and @tbl-tables-2 is pressure

```{r}
#| label: tbl-tables
#| tbl-cap: "Datasets"
#| tbl-subcap: 
#|   - "Cars"
#|   - "Pressure"
#| layout-ncol: 2

kable(head(cars))

kable(head(pressure))
```

Table 2 presents two datasets: Table 2 (a) is cars and Table 2 (b) is pressure

Table 2: Datasets

(a) Cars

speed	dist
4	2
4	10
7	4
7	22
8	16
9	10

(b) Pressure

temperature	pressure
0	0.0002
20	0.0012
40	0.0060
60	0.0300
80	0.0900
100	0.2700

Your turn

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

Code annotation

In general

YAML:

[...]
code-annotations: hover

. . .

Options:

below: The annotation appears below the code
hover: The annotation appears when the mouse hovers over the annotation marker
select: The annotation appears when the annotation marker is clicked

An example

Remove the dot between this symbol # and this symbol <

Code
Output

## GGplot

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

1. This does that

2. This other thing is this

3. And look at this!

4. Please have mercy

## GGplot

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

1: This does that
2: This other thing is this
3: And look at this!
4: Please have mercy

Inline executable code

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)`

. . .

The mean of the gear variable in mtcars is 3.6875

. . .

If you want the display of the code but not its execution:

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

. . .

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

Code chunk

Chunk options

echo: Control the code display

eval & include: Control the execution of the code

Other options

YAML: Overall chunk options

YAML: Show all code

YAML: Code Fold

Images & Graphs

External images: .png and .jpg

Graphics

Your turn

Tables

kable

Another option: DT

Cross referencing

In general

Images

Tables

Code

Equations

Your turn

Margins

Content

Code

Graphs

Tables

Multiple mixed outputs

Multiple plots

Multiple Tables

Your turn

Code annotation

In general

An example

Inline executable code

In general

`echo`: Control the code display

`eval` & `include`: Control the execution of the code

External images: `.png` and `.jpg`

`kable`