Extra tasks

In the following are some extra tasks concerning the more advanced R Markdown techniques and tips that we looked at in the end. Choose the task that you are interested in most. Start with that one and then move on the next.

3.1 Source an R script in R Markdown

Step 1: Create new files

Create the following files:

Step 2: Move R code to the R script

Think of the R code from the .Rmd file that you want to move to the R script. Some example might be:

Move the respective code from the .Rmd file into the R script. Make sure that you store every result you want to reuse in R Markdown in a variable.

Step 3: Source R script in R Markdown

Go back to the .Rmd file. Source the .R file in the setup chunk using the source() function.

One tip when constructing the path to the R file in the source function: Start making the quotes (source("")) and then in between then hit the tab key of your keyboard. Then you can construct the path to your R file using auto-completion. This is much less error prone than typing out the path.

Step 4: Knit the document

Knit the document and fix potential error messages.

3.2 Split larger documents into multiple .Rmd files

In this exercise, split the penguin paper from the last task into multiple R Markdown files.

Step 1: create the .Rmd files

Create separate R markdown files for the sections and one control file:

Remove all template text from the files.

Step 2: Fill the control document

Start with the control document Main.Rmd. This file will hold the following information:

Insert these elements into Main.Rmd and knit the document. There should be no error messages and you should have an almost empty document as a result with only headings.

Step 3: Source the child documents

Below the section headings in Main.Rmd add a code chunk. Include the child documents using the child chunk option.

Knit the document again. The result should be the same as in the step before, as the child documents are empty still. But there should be no error messages.

Step 4: Fill the child documents

Go back to the penguin paper from the last task. Copy the content for the main sections into the child documents.

Save the child documents. Then knit Main.Rmd again.

Now the result should look like the the penguin paper from the previous task.

3.3 Render your document from an R script

Create a new R file. To use the render function, load the rmarkdown package on top:

library(rmarkdown)

Write a render function that takes the .Rmd file of the penguin paper as input and specify which output format you want to render. Run the R function and see if the document is rendered correctly.

One tip when constructing the path to the R file in the source function: Start making the quotes (render(input = "")) and then in between then hit the tab key of your keyboard. Then you can construct the path to your Rmd file using auto-completion. This is much less error prone than typing out the path.

If that worked well, you can try some other arguments to the render function that you saw on the slides. You can also check ?render to see all options.

3.4 Parameterized reports (most tricky one)

Before you do this task, make sure you do task 3.3 first.

Now like in the slides, parameterize the report, so you can flexibly choose which penguin species you want to generate a report for.

To do this, first create a copy of the penguin paper to work on for this task.

Step 1: Introduce parameters

Add a field for the parameters to the YAML header. Add one parameter for the species you want to select and give this parameter a default value. Have a look at the slides to see how.

Step 2: Adapt your document to use the parameter

Go through the document and use the parameter list params that you now have available to change the R code in the document.

Identify the positions where you want to filter the data before continuing with the analysis. Have a look at the example in the slides for inspiration.

Knit the document often to see if everything works correctly.

Step 3: Render document from render function

Adapt the render function from task 3.3 and add the params argument to the function. Run the function for different values for the species param and check if the rendered document is correct.

Step 4: Render documents in a for loop

Write a for loop similar to the one on the slides that renders the documents for all three penguin species at once into files with different output names.