Rendering

You can render (sometimes called "knitting") reports in several different ways:

• Pressing the Knit button in RStudio (as we have done this far)
• Running the R command render: to Knit the file my_file.Rmd run rmarkdown::render("my_file.Rmd") in the R console.
• Running from the command line: R -e 'rmarkdown::render("my_file.Rmd")'

Using the render command, we can also set YAML header options and change defaults (i.e. override those specified in the R Markdown document itself). Here are a few useful arguments (see ?rmarkdown::render for a full list):

• output_format: change output format, e.g. html_document or pdf_document
• output_file and output_dir: change directory and file name of the generated report file (defaults to the same name and directory as the .Rmd file)
• params: change parameter defaults. Note that only parameters already listed in the YAML header can be set, no new parameters can be defined

Try to use the render command to knit your template R Markdown document and set the two parameters data and color. Hint: the params argument should be a list, e.g.:

rmarkdown::render("my_file.Rmd", params = list(data = "cars", color = "green"))

You might already have noticed the various ways in which you can run code chunks directly in RStudio:

• Place the cursor on an R command and press CTRL + Enter (Windows) or Cmd + Enter (Mac) to run that line in R.
• Select several R command lines and use the same keyboard shortcut as above to run those lines.
• To the right in each chunk there are two buttons; one for running the code in all chunks above the current chunk and one for running the code in the current chunk (depending on your layout, otherwise you can find the options in the Run drop-down).
• You can easily insert an empty chunk in your Rmd document in RStudio by pressing Code --> Insert Chunk in the menu.

Depending on your settings, the output of the chunk code will be displayed inline in the Rmd document, or in RStudio's Console and Plot panels. To customize this setting, press the cog-wheel next to the Knit button and select either "Chunk Output Inline" or "Chunk Output in Console". Additionally, in the top right in the editor panel in RStudio there is a button to toggle the document outline. By making that visible you can click and jump between sections (headers and named code chunks) in your R Markdown document.