You don’t necessary need to author an R Markdown document to create a dynamic report. In fact, you can take any R script and compile it into a report that includes commentary, source code, and script output. Reports can be compiled to any output format including HTML, PDF, MS Word, and Markdown.
To compile a report from an R script you simply pass the script to render. For example:
rmarkdown::render("analysis.R")
rmarkdown::render("analysis.R", "pdf_document")
The first call to render creates an HTML document, whereas the second creates a PDF document.
If you are using RStudio then you can also create a report using the Compile Report command (Ctrl+Shift+K).
By default the name of the script, username, and current date and time are included in the header of the report You can override this default behavior by including metadata in a specially formatted R comment:
#' ---
#' title: "Crop Analysis Q3 2013"
#' author: "John Smith"
#' date: "May 3rd, 2014"
#' ---
You can also specify the output format within the metadata, for example:
#' ---
#' title: "Crop Analysis Q3 2013"
#' output: pdf_document
#' ---
Note that the R comment used above to add a title, author, and date includes a single-quote as a special prefix character. This is a roxygen2 style comment, and it’s actually possible to include many such comments in an R script, all of which will be converted to markdown content within the compiled report For example:
#' A script comment that includes **markdown** formatting.
Rather than displaying as an R comment in the compiled report any roxygen2 style comment will be treated as markdown and rendered accordingly.
Including markdown within R comments is possible because rmarkdown::render
calls the knitr::spin
function to convert the R script to an Rmd file. The spin function also enables you to add knitr chunk options with another special comment prefix (#+
). For example:
#+ fig.width=5, fig.height=5
plot(cars)
For more information on using spin see:
Spin documentation: http://yihui.name/knitr/demo/stitch/
Spin example: https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.R
Note that when using rmarkdown::render
the spin function is called automatically under the hood as part of rendering.