knitr: elegant, flexible, and fast dynamic report generation with R

# Objects to manipulate options, patterns and hooks

### 2017-02-03

The knitr package uses a special object to control options and settings (denoted as obj below); it has the following methods:

• obj$get(name): returns an option named name or a list of several options if name is a character vector of length greater than 1, and it returns all the options if name not provided • obj$set(...): permanently changes options; the argument ... can be of the form tag = value or a list of options list(opt1 = value1, opt2 = value2)
• obj$merge(values): temporarily merges a list of new options into the current list and returns the merged list (original list not changed) • obj$restore(): restores the object

These objects are visible to users in knitr:

• opts_chunk and opts_current: manages options for code chunks
• opts_knit: manages options for the knitr package
• knit_hooks: manages hook functions
• knit_patterns: manages regular expressions to extract R code from the input document
• knit_engines: functions to deal with other languages

Except knit_patterns, all other objects are initialized with default values, and knit_patterns will be automatically determined according to the type of input document if not provided. The knit_hooks object is supposed to be used most frequently, and the other three are usually not to be used directly. For example, opts_chunk is usually set in the input document rather than using the command line directly.

Knitr’s settings must be set in a chunk before any chunks which rely on those settings to be active. It is recommended to create a knit configuration chunk as the first chunk in a script with cache = FALSE and include = FALSE options set. This chunk must not contain any commands which expect the settings in the configuration chunk to be in effect at the time of execution. The configuration chunk could look something like this:

<<setup, cache=FALSE, include=FALSE>>=
library(knitr)