knit

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, quiet = FALSE, 
    envir = parent.frame(), encoding = getOption("encoding"))
purl(..., documentation = 1L)

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, 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.txt if ext is not txt, otherwise the output is foo-out.txt. 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.

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 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.

If the output argument is a file path, it is strongly recommended to be in the current working directory (e.g. foo.tex instead of somewhere/foo.tex), especially when the output has external dependencies such as figure files. If you want to write the output to a different directory, you are recommended to set the working directory to that directory before you knit a document. For example, if the source document is foo.Rmd, and the expected output is out/foo.md, you can do setwd('out/'); knit('../foo.Rmd'), instead of knit('foo.Rmd', 'out/foo.md').

N.B. There is no guarantee that the R script generated by purl() can reproduce the computation done in knit(). The knit() process can be fairly complicated (special values for chunk options, custom chunk hooks, computing engines besides R, and the envir argument, etc). If you want to reproduce the computation in a report generated by knit(), be sure to use knit(), instead of merely executing the R script generated by purl(). This seems to be obvious, but some people http://bit.ly/SnLi6h{just do not get it}.

References

Package homepage: http://yihui.name/knitr/. The knitr http://bit.ly/117OLVl{main manual}: and http://bit.ly/114GNdP{graphics manual}.

See citation('knitr') for the citation information.

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