knitr
The R package knitr is a general-purpose literate programming engine,
with lightweight API's designed to give users full control of the output
without heavy coding work. It combines many features into one package with
slight tweaks motivated from my everyday use of Sweave. See the package
homepage for details and examples. See
FAQ's for a list of
frequently asked questions (including where to ask questions).
Installation
You can install the stable version on
CRAN:
install.packages('knitr')
You can also install the development version from
XRAN, which provides daily build of knitr:
# update all existing packages first
update.packages(ask = FALSE, repos = 'https://cran.r-project.org')
install.packages('knitr', repos = c('https://xran.yihui.org', 'https://cran.r-project.org'))
Note that if you want to build the source package via R CMD INSTALL without a previously installed version of knitr, you must either pre-install knitr from CRAN, or run R CMD INSTALL on this source repo, otherwise R CMD build will fail (which is probably a bug of base R).
Motivation
While Sweave and related add-on packages like
cacheSweave and
pgfSweave are fairly good
engines for literate programming in R, I often feel my hands are tied.
For example:
- I stared at the source code of Sweave and wished for hundreds of times,
if only I could easily insert[width=.8\textwidth]between
\includegraphicsand{my-plot.pdf}. (The official way in Sweave is
\setkeys{Gin}but it is setting a global width, which is unrealistic
since we often have to set widths individually; yes, you can use
\setkeys{Gin}for many times, but why not just provide an option for
each chunk?) - I wished for many times, if only I could use graphics devices other
than PDF and postscript; now the dream has come true in the official R,
but what I was hoping for was an option as simple asdev = 'png'ordev = 'CairoJPEG'. - I wished multiple plots in a code chunk could be recorded instead of only
the last one. - I wished there was a way to round the numbers in
\Sexpr{}other than
writing expressions like\Sexpr{round(x, 3)}for each single\Sexpr{} - I wished I did not have to
print()plots from.
ggplot2 and a simple
qplot(x, y)would just give me a plot in Sweave. - I wished users would never need instructions on
Sweave.styor run into
troubles due to the fact that LaTeX cannot findSweave.sty. - I wished cacheSweave could print the results of a code chunk even if
it was cached. - I wished brew could support
graphics. - I wished R2HTML could
support R code syntax highlighting. - ...
The package knitr was designed to give the user access to every part of
the process of dealing with a literate programming document, so there is no
need to hack at any core components if you want more freedom. I have gone
through the source code of pgfSweave and cacheSweave for a couple of
times and I often feel uncomfortable with the large amount of code copied
from official R, especially when R has a new version released (I will begin
to worry if the add-on packages are still up-to-date with the official
Sweave).
Usage
library(knitr)
?knit
knit(input)
If options are not explicitly specified, knitr will try to guess
reasonable default settings. A few manuals are available such as the main
manual, and the
graphics
manual. For a
more organized reference, see the knitr book.
License
This package is free and open source software, licensed under GPL.