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Options
Chunk options and package options

The knitr package shares most options with Sweave, but some were dropped/changed and some new options were added. The default values are in the parentheses below. Note that the chunk label for each chunk is assumed to be unique, i.e., no two chunks share the same label. This is especially important for cache and plot filenames. Chunks without labels will be assigned labels like unnamed-chunk-i where i is the chunk number.

Chunk Options

Take Rnw files as an example: usually we write chunk options in the form tag=value like this:

{% highlight r %} <<mychunk, cache=TRUE, eval=FALSE, dpi=100>>= @ {% endhighlight %}

And \SweaveOpts{} can change the default global options in a document (e.g. \SweaveOpts{comment=NA, fig.width=6, fig.height=6}), but it is recommended to use real R code opts_chunk$set(opt = value) to change global options instead. A few special notes on the options:

  1. Chunk options must be written in one line, and you should not break them into multiple lines; no spaces are allowed before << or @ (see #236);
  2. Avoid spaces and periods . in chunk labels and directory names; if your output is a TeX document, these characters can cause troubles (in general it is recommended to use alphabetic characters with words separated by - or _ and avoid other characters), e.g. setup-options is a good label, whereas setup.options and chunk 1 are bad; fig.path='figures/mcmc-' is a good prefix for figure output if this project is about MCMC, and fig.path='markov chain/monte carlo' is bad;
  3. All option values, except the chunk label, must be valid R expressions just like how we write function arguments. For example, options that take character values must be quoted as you do in R (e.g. should write fig.path="abc" instead of fig.path=abc, and out.width='\\textwidth' instead of out.width=\textwidth), and for logical options, TRUE and FALSE are OK, and true/false will not work as you might have expected; you can write arbitrarily complicated expressions as you want; if you come from the Sweave land, please read the transition page carefully because the syntax is different;

All built-in options in knitr are:

Code Evaluation

  • eval: (TRUE; logical) whether to evaluate the code chunk

Text Results

  • echo: (TRUE; logical or numeric) whether to include R source code in the output file; besides TRUE/FALSE which completely turns on/off the source code, we can also use a numeric vector to select which R expression(s) to echo in a chunk, e.g. echo=2:3 means only echo the 2nd and 3rd expressions, and echo=-4 means to exclude the 4th expression
  • results: ('markup'; character) takes three possible values
    • markup: mark up the results using the output hook, e.g. put results in a special LaTeX environment
    • asis: output as-is, i.e., write raw results from R into the output document
    • hide hide results; this option only applies to normal R output (not warnings, messages or errors)
    • note markup and asis are equivalent to verbatim and tex in Sweave respectively (you can still use the latter two, but they can be misleading, e.g., verbatim does not really mean verbatim in R, and tex seems to be restricted to LaTeX)
  • warning: (TRUE; logical) whether to preserve warnings (produced by warning()) in the output like we run R code in a terminal (if FALSE, all warnings will be discarded)
  • error: (TRUE; logical) whether to preserve errors (from stop()) (by default, the evaluation will not stop even in case of errors!!)
  • message: (TRUE; logical) whether to preserve messages emitted by message()
  • split: (FALSE; logical) whether to split the output from R into separate files and include them into LaTeX by \input{} or HTML by <iframe></iframe>
  • include: (TRUE; logical) whether to include the chunk output in the final output document; if include=FALSE, nothing will be written into the output document, but the code is still evaluated and plot files are generated if there are any plots in the chunk, so you can manually insert figures; note this is the only chunk option that is not cached, i.e., changing it will not invalidate the cache

Code Decoration

  • tidy: (TRUE; logical) whether R code should be tidied up using the function tidy.source() in the formatR package; if it failed to tidy up, original R code will not be changed; tidy=TRUE is like keep.source=FALSE in Sweave, but it also tries not to discard R comments (N.B. this option does not work in certain cases; see https://github.com/yihui/formatR/wiki for more information)
  • prompt: (FALSE; logical) whether to add the prompt characters in the R code (see prompt and continue in ?base::options; note that adding prompts can make it difficult for readers to copy R code from the output, so prompt=FALSE may be a better choice
  • comment: ('##'; character) the prefix to be put before source code output; default is to comment out the output by ##, which is good for readers to copy R source code since output is masked in comments (set comment=NA to disable this feature)
  • highlight: (TRUE; character) whether to highlight the source code (it is FALSE by default the output is markdown or Sweave or listings)
  • size: ('normalsize'; character) font size for the default LaTeX output (see ?highlight in the highlight package for a list of possible values)
  • background: ('#F7F7F7'; character or numeric) background color of chunks in LaTeX output (passed to the LaTeX package framed); the color model is rgb; it can be either a numeric vector of length 3, with each element between 0 and 1 to denote red, green and blue, or any built-in color in R like red or springgreen3 (see colors() for a full list), or a hex string like #FFFF00, or an integer (all these colors will be converted to the RGB model; see ?col2rgb for details)

Cache

  • cache: (FALSE; logical) whether to cache a code chunk; when evaluating code chunks, the cached chunks are skipped, but the objects created in these chunks are (lazy-) loaded from previously saved databases (.rdb and .rdx) files, and these files are saved when a chunk is evaluated for the first time, or when cached files are not found (e.g. you may have removed them by hand); note the filename consists of the chunk label with an MD5 digest of the R code in the chunk (the MD5 string is a summary of the chunk text, and any changes in the chunk will produce a different MD5 digest); unlike the cacheSweave package which uses stashR, this package directly uses internal functions in base R for cache, and another difference is that results of the code will still be included in the output even when cache is used (whereas cacheSweave has no output when a chunk is cached), because knitr also caches the printed output of a code chunk as a character string
  • cache.path: ('cache/'; character) a prefix to be used for the names of cache files (by default they are saved to a directory named cache relative to the current working directory; you can also use an absolute dir here, e.g. /home/foo/bar- or D:\\abc\\mycache, but it is not recommended since such absolute directories may not exist in other people's systems, therefore it is recommended to use relative directories)
  • dependson: (NULL; character) a character vector of chunk labels to specify which other chunks this chunk depends on; this option applies to cached chunks only -- sometimes the objects in a cached chunk may depend on other cached chunks, so when other chunks are changed, this chunk must be updated accordingly
  • autodep: (FALSE; logical) whether to figure out the dependencies among chunks automatically by analyzing the global variables in the code (may not be reliable) so that dependson does not need to be set explicitly

Plots

  • fig.path: ('figure/'; character) prefix to be used for figure filenames (fig.path and chunk labels are concatenated to make filenames); it may contain a directory like figure/prefix- (will be created if it does not exist); this path is relative to the current working directory
  • fig.keep: ('high'; character) how plots in chunks should be kept; it takes five possible values (see the end of this section for an example)
    • high: only keep high-level plots (merge low-level changes into high-level plots);
    • none: discard all plots;
    • all: keep all plots (low-level plot changes may produce new plots)
    • first: only keep the first plot
    • last: only keep the last plot
  • fig.show: ('asis'; character) how to show/arrange the plots; three possible values are
    • asis: show plots exactly in places where they were generated (as if the code were run in an R terminal);
    • hold: hold all plots and output them in the very end of a code chunk;
    • animate: wrap all plots into an animation if there are mutiple plots in a chunk;
  • dev: ('pdf' for LaTeX output and 'png' for HTML/markdown; character) the function name which will be used as a graphical device to record plots; for the convenience of usage, this package has included all the graphics devices in base R as well as those in Cairo, cairoDevice and tikzDevice, e.g. if we set dev='CairoPDF', the function with the same name in the Cairo package will be used for graphics output; if none of the 20 built-in devices is appropriate, we can still provide yet another name as long as it is a legal function name which can record plots (it must be of the form function(filename, width, height)); note the units for images are always inches (even for bitmap devices, in which DPI is used to convert between pixels and inches); currently available devices are bmp, postscript, pdf, png, svg, jpeg, pictex, tiff, win.metafile, cairo_pdf, cairo_ps, CairoJPEG, CairoPNG, CairoPS, CairoPDF, CairoSVG, CairoTIFF, Cairo_pdf, Cairo_png, Cairo_ps, Cairo_svg, tikz and a series of quartz devices including quartz_pdf, quartz_png, quartz_jpeg, quartz_tiff, quartz_gif, quartz_psd, quartz_bmp which are just wrappers to the function quartz() with different file types
    • the three options dev, fig.ext and dpi can be vectors (shorter ones will be recycled), e.g. <<foo, dev=c('pdf', 'png')>>= creates two files for the same plot: foo.pdf and foo.png
  • dev.args: (NULL) more arguments to be passed to the device, e.g. dev.args=list(bg='yellow', pointsize=10); note this depends on the specific device (see the device documentation)
  • fig.ext: (NULL; character) file extension of the figure output (if NULL, it will be derived from the graphical device; see knitr:::auto_exts for details)
  • dpi: (72; numeric) the DPI (dots per inch) for bitmap devices (dpi * inches = pixels)
  • fig.width, fig.height: (both are 7; numeric) width and height of the plot, to be used in the graphics device (in inches) and have to be numeric
  • out.width, out.height: (NULL; character) width and height of the plot in the final output file (can be different with its real fig.width and fig.height, i.e. plots can be scaled in the output document); depending on the output format, these two options can take flexible values, e.g. for LaTeX output, they can be .8\\linewidth, 3in or 8cm and for HTML, they may be 300px (do not have to be in inches like fig.width and fig.height; backslashes must be escaped as \\); for LaTeX output, the default value for out.width will be changed to \\maxwidth which is defined here
  • resize.width, resize.height: (NULL; character) the width and height to be used in \resizebox{}{} in LaTeX; these two options are not needed unless you want to resize tikz graphics because there is no natural way to do it; however, according to tikzDevice authors, tikz graphics is not meant to be resized to maintain consistency in style with other texts in LaTeX; if only one of them is NULL, ! will be used (read the documentation of graphicx if you do not understand this)
  • fig.align: ('default'; character) alignment of figures in the output document (possible values are left, right and center; default is not to make any alignment adjustments)
  • fig.cap: (NULL; character) figure caption to be used in a figure environment in LaTeX (in \caption{}); if NULL or NA, it will be ignored, otherwise a figure environment will be used for the plots in the chunk (output in \begin{figure} and \end{figure})
  • fig.scap: (NULL; character) short caption; if NULL, all the words before . or ; or : will be used as a short caption; if NA, it will be ignored
  • fig.lp: ('fig:'; character) label prefix for the figure label to be used in \label{}; the actual label is made by concatenating this prefix and the chunk label, e.g. the figure label for <<foo-plot>>= will be fig:foo-plot by default
  • fig.pos: (''; character) a character string for the figure position arrangement to be used in \begin{figure}[fig.pos]
  • external: (TRUE; logical) whether to externalize tikz graphics (pre-compile tikz graphics to PDF); it is only used for the tikz() device in the tikzDevice package (i.e., when dev='tikz') and it can save time for LaTeX compilation
  • sanitize: (FALSE; character) whether to sanitize tikz graphics (escape special LaTeX characters); see documentation in the tikzDevice package

Note any number of plots can be recorded in a single code chunk, and this package does not need to know how many plots are in a chunk in advance -- it can figure out automatically, and name these images as fig.path-label-i where i is incremental from 1; if a code chunk does not actually produce any plots, knitr will not record anything either (the graphics device is open only when plots are really produced); in other words, it does not matter if fig.keep='high' but no plots were produced.

Low-level plotting commands include lines() and points(), etc. To better understand fig.keep, consider the following chunk:

{% highlight r %} <>= plot(1) # high-level plot abline(0, 1) # low-level change plot(rnorm(10)) # high-level plot

many low-level changes in a loop (a single R expression)

for(i in 1:10) { abline(v = i, lty = 2) } @ {% endhighlight %}

Normally this produces 2 plots in the output (i.e. when fig.keep='high'); for fig.keep='none', no plots will be saved; for fig.keep='all', 4 plots are saved; for fig.keep='first', the plot produced by plot(1) is saved, and for fig.keep='last', the last plot with 10 vertical lines is saved.

There are two hidden options which are not designed to be set by the users: fig.cur (the current figure number or index when there are multiple figures) and fig.num (the total number of figures in a chunk). The purpose of these two options is to help knitr deal with the filenames of multiple figures as well as animations. In some cases, we can make use of them to write animations into the output using plot files which are saved manually (see the graphics manual for examples).

Animation

  • interval: (1; numeric) number of seconds to pause between animation frames
  • aniopts: ('controls,loop') extra options for animations; see the documentation of the animate package

Chunk Reference

  • ref.label: (NULL; character) a character vector of labels of the chunks from which R code is borrowed (see the demo for chunk reference)

Child Documents

  • child: (NULL; character) a character vector of filenames of child documents to be run and input into the main document

Language Engines

  • engine: ('R'; character) the language name of the code chunk; currently other possible values are 'python' and 'awk'/'gawk'; the object knit_engines in this package can be used to set up engines for other languages

Package Options

The package options can be changed using the object opts_knit; for example,

{% highlight r %} opts_knit$set(progress = TRUE, verbose = TRUE) {% endhighlight %}

All package options are:

  • aliases: (NULL) a named character vector to specify the aliases of chunk options, e.g. c(h = 'fig.height', w = 'fig.width') tells knitr that the chunk option h really means fig.height, and w is an alias for fig.width; this option can be used to save some typing efforts for long option names
  • base.dir: (NULL) an absolute directory under which the plots are generated
  • base.url: (NULL) the base url for HTML pages
  • cache.extra: (NULL) extra content that should affect cache
  • child.command: ('input') the LaTeX command to be used to insert child documents into the main document (usually input or include)
  • child.path: ('') the search path for child documents; by default child documents are searched for relative to the directory of the parent document
  • concordance: (FALSE) whether to write a concordance file to map the output line numbers to the input line numbers; this enables one to navigate from the output to the input and can be helpful especially when TeX error occurs (this feature is mainly for RStudio)
  • eval.after: (NULL) a character vector of option names; these options will be evaluated after a chunk is evaluated, and all other options will be evaluated before a chunk (e.g. for chunk option fig.cap=paste('p-value is', t.test(x)$p.value), it will be evaluated after the chunk according to the value of x if eval.after='fig.cap')
  • filter.chunk.end: (TRUE) whether to match the chunk.end pattern with chunk.begin; if TRUE, chunk.end without chunk.begin will not be treated as real chunk.end, which is not the original meaning of literate programming (chunk.end always means the beginning of normal text); if FALSE, chunk.end will not be tested against chunk.begin
  • header: the text to be inserted into the output document before the document begins (e.g. after \documentclass{article} in LaTeX, or <head> in HTML); this is useful for defining commands and styles in the LaTeX preamble or HTML header; the beginning of document is found using the pattern defined in knit_patternss$get('document.begin')
  • out.format: (NULL) possible values are latex, sweave, html, markdown and jekyll; it will be automatically determined based on the input file, and this option will affect which set of hooks to use (see ?render_latex for example); note this option has to be set before knit() runs (i.e. it does not work if you set it in the document), or alternatively, you can use the render_* series inside the document to set up the hooks
  • progress: (TRUE) whether to display a progress bar when running knitr
  • root.dir: (NULL) the root directory when evaluating code chunks; if NULL, the directory of the input document will be used
  • self.contained: (TRUE) whether the output document should be self-contained (TeX styles written in the tex document, and CSS styles in HTML document)
  • upload.fun: (identity) a function that takes a filename as its input, processes it and returns a character string when the output format is HTML or Markdown; typically it is a function to upload a image and return the link to the image, e.g. opts_knit$set(upload.fun = imgur_upload) can upload a file to http://imgur.com (see ?imgur_upload)
  • verbose: (FALSE) whether to show verbose information (e.g., R code in each chunk and message logs) or just show chunk labels and options