In this chapter, we treat three different ways to produce reports that automatically include the results of an analysis.
A very important feature of reproducible science is generating reports. The main idea of automatic report generation is that the results of analyses are not manually copied to the report. Instead, both the R code and the report's text are combined in one or more plain text files. The report is generated by a tool that executes the chunks of code, captures the results (including figures), and generates the report by weaving the report's text and results together. To achieve this, you need to learn a few special commands, called markup specifiers, that tell the report generator which part of your text is R code, and which parts you want in special typesetting such as boldface or italic. There are several markup languages to do this, but the following is a minimal example using the Markdown language:
A simple example with Markdown
The left panel...