Knit a document
Description
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).
Usage
knit(
input,
output = NULL,
tangle = FALSE,
text = NULL,
quiet = FALSE,
envir = parent.frame(),
encoding = "UTF-8"
)
purl(..., documentation = 1L)
Arguments
input |
Path to the input file.
|
output |
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.
|
tangle |
Boolean; whether to tangle the R code from the input file (like
utils::Stangle).
|
text |
A character vector. This is an alternative way to provide the
input file.
|
quiet |
Boolean; suppress the progress bar and messages?
|
envir |
Environment in which code chunks are to be evaluated, for
example, parent.frame(), new.env(), or
globalenv()).
|
encoding |
Encoding of the input file; always assumed to be UTF-8 (i.e.,
this argument is effectively ignored).
|
... |
arguments passed to knit() from purl()
|
documentation |
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.
|
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 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$get('out.format')), a set of
output hooks will be set to mark up results from R (see
render_latex). The output format can be LaTeX, Sweave and HTML,
etc. The output hooks decide how to mark up the results (you can customize
the hooks).
The name knit comes from its counterpart ‘weave’ (as in Sweave),
and the name purl (as ‘tangle’ in Stangle) comes from a knitting
method ‘knit one, purl one’.
If the input document has child documents, they will also be compiled
recursively. See knit_child.
See the package website and manuals in the references to know more about
knitr, including the full documentation of chunk options and demos,
etc.
Value
The compiled document is written into the output file, and the path
of the output file is returned. If the text argument is not
NULL, the compiled output is returned as a character vector. In
other words, if you provide a file input, you get an output filename; if
you provide a character vector input, you get a character vector output.
Note
The working directory when evaluating R code chunks is the directory of
the input document by default, so if the R code involves external files
(like read.table()), it is better to put these files under the same
directory of the input document so that we can use relative paths. However,
it is possible to change this directory with the package option
opts_knit$set(root.dir = ...) so all paths in code chunks are
relative to this root.dir. It is not recommended to change the
working directory via setwd() in a code chunk, because it may
lead to terrible consequences (e.g. figure and cache files may be written
to wrong places). If you do use setwd(), please note that
knitr will always restore the working directory to the original one.
Whenever you feel confused, print getwd() in a code chunk to see
what the working directory really is.
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, it is 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
write 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
do not
get it.
References
Package homepage: https://yihui.org/knitr/. The knitr
main manual: and
graphics manual.
See citation('knitr') for the citation information.
Examples
library(knitr)
(f = system.file("examples", "knitr-minimal.Rnw", package = "knitr"))
knit(f)
purl(f)
purl(f, documentation = 0)
purl(f, documentation = 2)
unlink(c("knitr-minimal.tex", "knitr-minimal.R", "figure"), recursive = TRUE)
