Add R Code

2.1 Load the palmerpenguins in your document

We will now include some analysis of the penguins data in the document.

As with “normal” R code, you need to load the palmerpenguins package in your document in the beginning.

A convenient location to load packages is the setup code chunk.

Just add library(palmerpenguins) as a line in this chunk.

You can always come back to the setup chunk and add all the packages that you need in your analysis. Then you have all the library() calls in one place.

2.2 Add R code chunks

Now add some R code that produces different types of output in the document.

The output types we will include using the penguin data set are:

• A figure
• A summary table

For each output type, go through the following steps:

1. Select a location in your document, where the output should be (probably the result section).
2. Insert a new code chunk at the location
   • Use the RStudio interface Code -> Insert Chunk or
   • Use the keyboard shortcut Ctrl/Cmd + Alt/Option + I
3. Write the code that produces the output (you can copy it from my examples below)
4. Run the code inside the document:
   • Click on the little green arrow button next to the code chunk
   • Careful: if you get an error message, make sure that you run all chunks that your code depends on before. E.g. you probably have to run the setup chunk to load all the packages first.
5. Knit the document and see how the output looks like

Below, you find example code for a figure and a table. For now, just copy my code to your R chunk. If you still have time in the end, change the code or write new code chunks yourself for different types of output.

Don’t forget to knit your document often to detect errors early on.

Figure

I use ggplot2 to produce the figures, so don’t forget to load the package in the setup chunk.

Choose one of the two figure ideas from below:

1. Create a histogram of the body mass for the 3 penguin species

ggplot(penguins, aes(x = body_mass_g, fill = species)) +
  geom_histogram(alpha = 0.6) +
   scale_fill_manual(values = c("darkorange", "purple", "cyan4")) +
  theme_minimal()

2. Create a scatter plot of the relationship between bill length and bill depth

ggplot(
  data = penguins,
  aes(
    x = bill_length_mm,
    y = bill_depth_mm,
    color = species,
    shape = species
  )
) +
  geom_point(size = 3, alpha = 0.8) +
  geom_smooth(method = "lm", se = FALSE) +
  scale_color_manual(values = c("darkorange", "purple", "cyan4")) +
  theme_minimal()

Summary table

I use the dplyr package here, so don’t forget to load it in the setup chunk.

Create a summary table of the mean variable values grouped by penguin species and sex.

penguins %>% 
  filter(!(is.na(sex))) %>% 
  group_by(species, sex) %>% 
  summarize(
    bill_length = mean(bill_length_mm, na.rm = TRUE),
    bill_depth = mean(bill_depth_mm, na.rm = TRUE),
    flipper_length = mean(flipper_length_mm, na.rm = TRUE),
    body_mass = mean(body_mass_g, na.rm = TRUE)
  )

2.3 Add inline code

Add some sentences to the document that use R code to report numbers.

You can start with the example below. If you still have time in the end, you can add more sentences:

• Report the mean body mass of all penguins, e.g. like this:
  • The mean body mass of all penguins is 4202 g.

2.4 Chunk options

Now modify some of the code chunk behaviour using chunk options.

Start with the chunk that produces the figure:

• Add a figure caption.
• If you want, change the figure size using either fig.width and fig.height or out.width
• Align the figure where you like to have it

Knit the document and look at the output.

Now think of some global chunk options that might make sense for your document. Add these options to the knitr options in the setup chunk.

You can for example think of things like:

• Should the R code be shown in the document?
• Should warnings and messages be printed into the document as well?

Extras

Get creative. Add new code chunks that produced different types of output. Find some ideas below:

More inline code

Can you report the number of penguins and their body mass separately for the three penguin species?

Hint: Calculate the mean weight of the penguin species in a separate code chunk and save them in 3 variables. Then you can use these variables in the inline code.

knitr::include_graphics()

Include the penguin illustration from within a code chunk instead of with ![](). This will allow you to make it a smaller so the document looks nicer. To do so

• Download the image from [here]((https://raw.githubusercontent.com/allisonhorst/palmerpenguins/main/man/figures/lter_penguins.png) (depends on browser but something like Right Click -> Save image as). Save it in the same location as your .Rmd document.
• Include the downloaded image in a code chunk in a similar way as on the slides.
• Make the image smaller until it looks good in your document

Add an interactive plot

Careful because this only works with HTML output and will give you an error for pdf and word output. You can use the plotly package to include an interactive plot in your document. To turn a “normal” plot into an interactive plot you just need the following steps:

• Install the plotly package with install.packages("plotly")
• Save the plot you want to turn interactive in a variable
• Call the ggplotly() function

Below you find an example. You can do the same now for one of the plots that you already have in your document.

# Make the plot and save it in a variable
my_boxplot <- ggplot(
  data = penguins,
  aes(
    y = bill_depth_mm,
    fill = species,
    x = species
  )
) +
  geom_boxplot()+
  scale_fill_manual(values = c("darkorange", "purple", "cyan4")) +
  theme_minimal()

# Turn the plot interactive
plotly::ggplotly(my_boxplot)