knit

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Knit a document

This function takes an input file, extracts the R code in it according to a list of patterns, evaluates the code and writes the output in another file. It can also tangle R source code from the input document (purl() is a wrapper to knit(..., tangle = TRUE)).

Usage
knit(input, output = NULL, tangle = FALSE, text = NULL, envir = parent.frame(), ...)

purl(..., documentation = 1L)

Arguments
input
path of the input file
output
path of the output file; if NULL, this function will try to guess and it will be under the current working directory
tangle
whether to tangle the R code from the input file (like Stangle)
text
a character vector as an alternative way to provide the input file
envir
the environment in which the code chunks are to be evaluated (can use new.env() to guarantee an empty new environment)
documentation
an integer specifying the level of documentation to go the tangled script: 0 means pure code (discard all text chunks); 1 (default) means add the chunk headers to code; 2 means add all text chunks to code as
...
arguments passed to knit() from purl(); ignored if the arguments do not match with any arguments in knit()
Details

For most of the time, it is not necessary to set any options outside the input document; in other words, a single call like knit('my_input.Rnw') is usually enough. This function will try to determine many internal settings automatically. For the sake of reproducibility, it is a better practice to include the options inside the input document (to be self-contained), instead of setting them before knitting the document.

First the filename of the output document is determined in this way: foo.Rnw generates foo.tex, and other filename extensions like .Rtex, .Rhtml (.Rhtm) and .Rmd (.Rmarkdown) will generate .tex, .html and .md respectively. For other types of files, the file extension is reserved; if the filename contains _knit_, this part will be removed in the output file, e.g., foo_knit_.html creates the output foo.html; if _knit_ is not found in the filename, foo.ext will produce foo-out.ext. If tangle = TRUE, foo.ext generates an R script foo.R.

We need a set of syntax to identify special markups for R code chunks and R options, etc. The syntax is defined in a pattern list. All built-in pattern lists can be found in all_patterns (call it apat). First knitr will try to decide the pattern list based on the filename extension of the input document, e.g. Rnw files use the list apat$rnw, tex uses the list apat$tex, brew uses apat$brew and HTML files use apat$html; for unkown extensions, the content of the input document is matched against all pattern lists to automatically which pattern list is being used. You can also manually set the pattern list using the knit_patterns object or the pat_rnw series functions in advance and knitr will respect the setting.

According to the output format (opts_knit$get('out.format')), a set of output hooks will be set to mark up results from R (see render_latex). The output format can be LaTeX, Sweave and HTML, etc. The output hooks decide how to mark up the results (you can customize the hooks).

See the package website and manuals in the references to know more about knitr, including the full documentation of chunk options and demos, etc.

Value

  • The compiled document is written into the output file, and the path of the output file is returned, but if the output path is NULL, the output is returned as a character vector.

Note

The name knit comes from its counterpart weave (as in Sweave), and the name purl (as tangle in Stangle) comes from a knitting method `knit one, purl one'.

If the input document has child documents, they will also be compiled recursively. See knit_child.

The working directory when evaluating R code chunks is the directory of the input document by default, so if the R code involves with external files (like read.table()), it is better to put these files under the same directory of the input document so that we can use relative paths. However, it is possible to change this directory with the package option opts_knit$set(root.dir = ...) so all paths in code chunks are relative to this root.dir.

The arguments input and output do not have to be restricted to files; they can be stdin()/stdout() or other types of connections, but the pattern list to read the input has to be set in advance (see pat_rnw), and the output hooks should also be set (see render_latex), otherwise knitr will try to guess the patterns and output format.

References

Package homepage: http://yihui.name/knitr/

The knitr main manual: https://github.com/downloads/yihui/knitr/knitr-manual.pdf

The knitr graphics manual: https://github.com/downloads/yihui/knitr/knitr-graphics.pdf

Aliases
  • knit
  • purl
Examples
library(knitr)
(f = system.file("examples", "knitr-minimal.Rnw", package = "knitr"))
knit(f)  # compile to tex

purl(f)  # tangle R code
purl(f, documentation = 0)  # extract R code only
purl(f, documentation = 2)  # also include documentation
Documentation reproduced from package knitr, version 0.9, License: GPL

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