Examples

Data

Load the gapminder data:

library(gapminder)

Examples

This section includes code for the examples shown. These may differ slightly from the examples shown in the live demonstration.

Example 1: Parameterized plots with ggplot2

See example

Let’s make a plot of how the life expectancy has changed in Asia over time. We start by filtering the data:

library(dplyr)
gapminder_asia <- gapminder |>
  filter(continent == "Asia")

We then make a plot:

library(ggplot2)
ggplot(data = gapminder_asia) +
  geom_boxplot(
    mapping = aes(x = factor(year), y = lifeExp)
  ) +
  labs(
    x = NULL, y = "Life Expectancy (years)",
    title = "Life Expectancy in Asia"
  )

If we wanted to create the same plot but for Europe, what would we need to change?

• The value that the data is filtered on
• The text in the title

Let’s create a variable for the continent:

choose_continent <- "Asia"

and then use that value in our code:

# Filter data
gapminder_continent <- gapminder |>
  filter(continent == choose_continent)

# Plot
library(glue)
ggplot(data = gapminder_continent) +
  geom_boxplot(
    mapping = aes(x = factor(year), y = lifeExp)
  ) +
  labs(
    x = NULL, y = "Life Expectancy (years)",
    title = glue("Life Expectancy in {choose_continent}")
  )

This makes it easier to turn it into a function:

continent_plot <- function(choose_continent, data = gapminder) {
  # Filter data
  gapminder_continent <- data |>
    filter(continent == choose_continent)
  # Plot
  g <- ggplot(data = gapminder_continent) +
    geom_boxplot(
      mapping = aes(x = factor(year), y = lifeExp)
    ) +
    labs(
      x = NULL, y = "Life Expectancy (years)",
      title = glue("Life Expectancy in {choose_continent}")
    )
  return(g)
}

Check it works:

continent_plot("Europe")

Example 2: Parameterized reports with Quarto

See example

Here’s a file, example.qmd, we’ll use as a template for our report:

example.qmd

---
title: "Gapminder Report on Life Expectancy in Asia"
execute: 
  echo: false
---

```{r}
#| label: load-pkgs
#| message: false
library(gapminder)
library(dplyr)
library(ggplot2)
library(glue)
```

This is a report using the [Gapminder](https://www.gapminder.org/data/) data. @fig-life-exp shows a box plot of how the life expectancy in Asia has changed over time.

```{r}
#| label: fig-life-exp
#| fig-cap: "Life expectancy in Asia"
# Edit the code below with your plot function!
plot(1:10, 1:10)
```

Let’s start by editing the example.qmd file to add a document parameter for the continent.

---
title: "Gapminder Report on Life Expectancy in Asia"
execute: 
  echo: false
params:
  choose_continent: "Europe"
---

```{r}
#| label: load-pkgs
#| message: false
library(gapminder)
library(dplyr)
library(ggplot2)
library(glue)
```

This is a report using the [Gapminder](https://www.gapminder.org/data/) data. @fig-life-exp shows a box plot of how the life expectancy in Asia has changed over time.

```{r}
#| label: fig-life-exp
#| fig-cap: "Life expectancy in Asia"
# Edit the code below with your plot function!
plot(1:10, 1:10)
```

Then, we add our plotting function, and pass in the parameter:

---
title: "Gapminder Report on Life Expectancy in Asia"
execute: 
  echo: false
params:
  choose_continent: "Europe"
---

```{r}
#| label: load-pkgs
#| message: false
library(gapminder)
library(dplyr)
library(ggplot2)
library(glue)
```

This is a report using the [Gapminder](https://www.gapminder.org/data/) data. @fig-life-exp shows a box plot of how the life expectancy in Asia has changed over time.

```{r}
#| label: fig-life-exp
#| fig-cap: "Life expectancy in Asia"
continent_plot <- function(choose_continent, data = gapminder) {
  # Filter data
  gapminder_continent <- data |>
    filter(continent == choose_continent)
  # Plot
  g <- ggplot(data = gapminder_continent) +
    geom_boxplot(
      mapping = aes(x = factor(year), y = lifeExp)
    ) +
    labs(
      x = NULL, y = "Life Expectancy (years)",
      title = glue("Life Expectancy in {params$choose_continent}")
    )
  return(g)
}
continent_plot(params$choose_continent)
```

We can use the parameter multiple times e.g. to add a table

---
title: "Gapminder Report on Life Expectancy in Asia"
execute: 
  echo: false
params:
  choose_continent: "Europe"
---

```{r}
#| label: load-pkgs
#| message: false
library(gapminder)
library(dplyr)
library(ggplot2)
library(glue)
```

This is a report using the [Gapminder](https://www.gapminder.org/data/) data. @fig-life-exp shows a box plot of how the life expectancy in Asia has changed over time.

```{r}
#| label: fig-life-exp
#| fig-cap: "Life expectancy in Asia"
continent_plot <- function(choose_continent, data = gapminder) {
  # Filter data
  gapminder_continent <- data |>
    filter(continent == choose_continent)
  # Plot
  g <- ggplot(data = gapminder_continent) +
    geom_boxplot(
      mapping = aes(x = factor(year), y = lifeExp)
    ) +
    labs(
      x = NULL, y = "Life Expectancy (years)",
      title = glue("Life Expectancy in {params$choose_continent}")
    )
  return(g)
}
continent_plot(params$choose_continent)
```

Adding a table of data:


```{r}
#| label: tbl-stats
#| tbl-cap: "Statistics in Asia"
library(tinytable)
gapminder |> 
  filter(continent == params$choose_continent) |> 
  group_by(year) |> 
  summarise(across(c(lifeExp, pop, gdpPercap), mean)) |> 
  tt()
```

Example 3: Parameterized text with Quarto

See example

Add inline code:

The number of rows is `r nrow(gapminder)`.

which displays as:

The number of rows is 1704.

We can apply this to our document and use the parameters inline:

---
title: "Gapminder Report on Life Expectancy in Asia"
execute: 
  echo: false
params:
  choose_continent: "Europe"
---

```{r}
#| label: load-pkgs
#| message: false
library(gapminder)
library(dplyr)
library(ggplot2)
library(glue)
```

This is a report using the [Gapminder](https://www.gapminder.org/data/) data. @fig-life-exp shows a box plot of how the life expectancy in `r params$choose_continent` has changed over time.

```{r}
#| label: fig-life-exp
#| fig-cap: "Life expectancy in Asia"
continent_plot <- function(choose_continent, data = gapminder) {
  # Filter data
  gapminder_continent <- data |>
    filter(continent == choose_continent)
  # Plot
  g <- ggplot(data = gapminder_continent) +
    geom_boxplot(
      mapping = aes(x = factor(year), y = lifeExp)
    ) +
    labs(
      x = NULL, y = "Life Expectancy (years)",
      title = glue("Life Expectancy in {params$choose_continent}")
    )
  return(g)
}
continent_plot(params$choose_continent)
```

Including in the title:

---
title: "Gapminder Report on Life Expectancy in `r params$choose_continent`"
execute: 
  echo: false
params:
  choose_continent: "Europe"
---

```{r}
#| label: load-pkgs
#| message: false
library(gapminder)
library(dplyr)
library(ggplot2)
library(glue)
```

This is a report using the [Gapminder](https://www.gapminder.org/data/) data. @fig-life-exp shows a box plot of how the life expectancy in `r params$choose_continent` has changed over time.

```{r}
#| label: fig-life-exp
#| fig-cap: "Life expectancy in Asia"
continent_plot <- function(choose_continent, data = gapminder) {
  # Filter data
  gapminder_continent <- data |>
    filter(continent == choose_continent)
  # Plot
  g <- ggplot(data = gapminder_continent) +
    geom_boxplot(
      mapping = aes(x = factor(year), y = lifeExp)
    ) +
    labs(
      x = NULL, y = "Life Expectancy (years)",
      title = glue("Life Expectancy in {params$choose_continent}")
    )
  return(g)
}
continent_plot(params$choose_continent)
```

We edit the figure caption slightly differently:

---
title: "Gapminder Report on Life Expectancy in `r params$choose_continent`"
execute: 
  echo: false
params:
  choose_continent: "Europe"
---

```{r}
#| label: load-pkgs
#| message: false
library(gapminder)
library(dplyr)
library(ggplot2)
library(glue)
```

This is a report using the [Gapminder](https://www.gapminder.org/data/) data. @fig-life-exp shows a box plot of how the life expectancy in `r params$choose_continent` has changed over time.

```{r}
#| label: fig-life-exp
#| fig-cap: !expr 'paste("Life expectancy in ", params$choose_continent)'
continent_plot <- function(choose_continent, data = gapminder) {
  # Filter data
  gapminder_continent <- data |>
    filter(continent == choose_continent)
  # Plot
  g <- ggplot(data = gapminder_continent) +
    geom_boxplot(
      mapping = aes(x = factor(year), y = lifeExp)
    ) +
    labs(
      x = NULL, y = "Life Expectancy (years)",
      title = glue("Life Expectancy in {params$choose_continent}")
    )
  return(g)
}
continent_plot(params$choose_continent)
```

Example 4: Rendering multiple reports

See example

Render one report using the quarto R package:

library(quarto)
quarto_render(
  input = "example.qmd",
  execute_params = list(
    continent = "Europe"
  )
)

Use the purrr package to create multiple reports at the same time:

library(purrr)
walk(
  .x = unique(gapminder$continent),
  .f = ~quarto_render(
    input = "example.qmd",
    execute_params = list(
      choose_continent = .x
    )
  )
)

Why is there only one report? We need to give each report a different name, to stop it being overwritten. Let’s use glue() again, this time for the file names.

walk(
  .x = unique(gapminder$continent),
  .f = ~quarto_render(
    input = "example.qmd",
    output_file = glue("report_{.x}.html"),
    execute_params = list(
      choose_continent = .x
    )
  )
)

To ensure the images aren’t overwritten as well, you may need to add embed-resources: true to your Quarto document YAML:

---
format:
  html:
    embed-resources: true
---

This keeps any plots created embedded within the HTML document, instead of in a separate folder.