# knitr v1.23

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## A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

# 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.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).

## 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 \includegraphics and {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' or dev = '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.sty or run into troubles due to the fact that LaTeX cannot find Sweave.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.

This package is free and open source software, licensed under GPL.

## Functions in knitr

 Name Description current_input Query the current input filename engine_output An output wrapper for language engine output knit_child Knit a child document knit_code The code manager to manage code in all chunks knit_expand A simple macro preprocessor for templating purposes knit_filter Spell check filter for source documents knit_theme Syntax highlighting themes clean_cache Clean cache files that are probably no longer needed combine_words Combine multiple words into a single string knit2html Convert markdown to HTML using knit() and markdownToHTML() knit_watch Watch an input file continuously and knit it when it is updated set_alias Set aliases for chunk options knit2pandoc Convert various input files to various output files using knit() and Pandoc set_header Set the header information knit_params_yaml Extract knit parameters from YAML text knit_patterns Patterns to match and extract R code in a document raw_block Mark character strings as raw blocks in R Markdown extract_raw_output Mark character strings as raw output that should not be converted all_patterns All built-in patterns asis_output Mark an R object with a special class hook_plot_html Default plot hooks for different output formats rocco Knit R Markdown using the classic Docco style image_uri Encode an image file to a data URI rst2pdf A wrapper for rst2pdf kable Create tables in LaTeX, HTML, Markdown and reStructuredText Sweave2knitr Convert Sweave to knitr documents all_labels Get all chunk labels in a document hook_ffmpeg_html Hooks to create animations in HTML output cache_engines Cache engines of other languages hook_movecode Some potentially useful document hooks knit Knit a document include_url Embed a URL as an HTML iframe or a screenshot in knitr documents hook_pdfcrop Built-in chunk hooks to extend knitr inline_expr Wrap code using the inline R expression syntax knitr-package A general-purpose tool for dynamic report generation in R imgur_upload Upload an image to imgur.com knit_meta Metadata about objects to be printed knit_params Extract knit parameters from a document include_graphics Embed external images in knitr documents load_cache Load the cache database of a code chunk plot_crop Crop a plot (remove the edges) using PDFCrop or ImageMagick opts_chunk Default and current chunk options knit_global The global environment in which code chunks are evaluated opts_hooks Hooks for code chunk options pandoc A Pandoc wrapper to convert documents to other formats fig_chunk Obtain the figure filenames for a chunk knit2pdf Convert Rnw or Rrst files to PDF fig_path Path for figure files knit_hooks Hooks for R code chunks, inline R code and output knit2wp Knit an R Markdown document and post it to WordPress knit_engines Engines of other languages opts_knit Options for the knitr package opts_template Template for creating reusable chunk options read_chunk Read chunks from an external script rand_seed An unevaluated expression to return .Random.seed if exists knit_exit Exit knitting early knit_print A custom printing function read_rforge Read source code from R-Forge set_parent Specify the parent document of child documents spin Spin goat's hair into wool pat_rnw Set regular expressions to read input documents vignette_engines Package vignette engines wrap_rmd Wrap long lines in Rmd files knit_rd Knit package documentation render_html Set output hooks for different output formats is_latex_output Check if the current output type is LaTeX or HTML write_bib Generate BibTeX bibliography databases for R packages spin_child Spin a child R script stitch Automatically create a report based on an R script and a template dep_auto Build automatic dependencies among chunks dep_prev Make later chunks depend on previous chunks No Results!

## Vignettes of knitr

 Name assets/template-refcard.tex datatables.Rmd docco-classic.Rmd docco-linear.Rmd knit_expand.Rmd knit_print.Rmd knitr-html.Rhtml knitr-intro.Rmd knitr-markdown.Rmd knitr-refcard.Rmd knitr-refcard.lyx No Results!