This package is forked from yihui's knitr and I implemented a function named formatBash to tidy the code chunks of BASH, so that I can use it for my bash pipe line. Feel free to use it.
The original readme of knit is listed as following:
###################################################################### 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).
You can install the stable version on CRAN:
install.packages('knitr', dependencies = TRUE)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.name', '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).
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 as
dev = '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 simpleqplot(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).
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.
This package is free and open source software, licensed under GPL.