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)). The knitr.purl.inline
option can be used to also tangle the code of inline expressions (disabled by
default).
knit(
input,
output = NULL,
tangle = FALSE,
text = NULL,
quiet = FALSE,
envir = parent.frame(),
encoding = "UTF-8"
)purl(..., documentation = 1L)
The compiled document is written into the output file, and the path
of the output file is returned. If the text argument is not
NULL, the compiled output is returned as a character vector. In
other words, if you provide a file input, you get an output filename; if
you provide a character vector input, you get a character vector output.
Path to the input file.
Path to the output file for knit(). If NULL, this
function will try to guess a default, which will be under the current
working directory.
Boolean; whether to tangle the R code from the input file (like
utils::Stangle).
A character vector. This is an alternative way to provide the input file.
Boolean; suppress the progress bar and messages?
Environment in which code chunks are to be evaluated, for
example, parent.frame(), new.env(), or
globalenv()).
Encoding of the input file; always assumed to be UTF-8 (i.e., this argument is effectively ignored).
arguments passed to knit() from purl()
An integer specifying the level of documentation to add to
the tangled script. 0 means to output pure code, discarding all text chunks);
1 (the default) means to add the chunk headers to the code; 2 means to
add all text chunks to code as roxygen comments.
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 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 determine 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).
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.
See the package website and manuals in the references to know more about knitr, including the full documentation of chunk options and demos, etc.
Package homepage: https://yihui.org/knitr/. The knitr main manual: and graphics manual.
See citation('knitr') for the citation information.
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
unlink(c("knitr-minimal.tex", "knitr-minimal.R", "figure"), recursive = TRUE)
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