#Knitr# Knitr-Options

公良弘毅

2023-12-01

转载自：http://yihui.name/knitr/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:

<<mychunk, cache=TRUE, eval=FALSE, dpi=100>>=
@

And opts_chunk$set() can change the default global options in a document (e.g. put this in a code chunk: opts_chunk$set(comment=NA, fig.width=6, fig.height=6)), and \SweaveOpts{} will no longer be supported (it is good if you do not know what this means). A few special notes on the options:

Chunk options must be written in one line; no line breaks are allowed inside chunk options;
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; non-alphanumeric characters except - and _ in figure filenames will be replaced with _ automatically;
All option values 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)
- in theory, the chunk label should be quoted as well but the sake of convenience it will be automatically quoted if you did not quote it (e.g. <<2a>>= will become <<'2a'>>=)
- for logical options, TRUE and FALSE are OK, and true/false will not work as you might have expected because true is not TRUE
- you can write arbitrarily complicated expressions as you want as long as they are legitimate R code
- 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; it can also be a numeric vector to select which R expression(s) to evaluate, e.g. eval=c(1, 3, 4) or eval=-(4:5)

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)
- tidy.opts: (NULL; list) a list of options to be passed to tidy.source(), e.g. tidy.opts=list(keep.blank.line=FALSE, width.cutoff=60); these formatR options can also be set globally via options()
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)

There is a hidden option indent which stores the possible leading white spaces of the chunk, e.g. for the chunk below, indent is a character string of two spaces:

  ```{r}
  rnorm(10)
  ```

Currently this option is only used to indent markdown output, because leading white spaces have special meanings in markdown.

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)
cache.vars: (NULL) a character vector of variable names to be saved in the cache database; by default all variables created in the current chunks are identified and saved, but we can manually set the variables to be saved
dependson: (NULL; character or numeric) 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
- if dependson is a numeric vector, it means the indices of chunk labels, e.g. dependson=1 means this chunk depends on the first chunk in the document, and dependson=c(-1, -2) means it depends on the previous two chunks (negative indices stand for numbers of chunks before this chunk, and note they are always relative to the current chunk)
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); when dev has multiple elements, dev.args can be a list of lists of arguments with each list of arguments to be passed to each single device, e.g. <<dev=c('pdf', 'tiff'), dev.args=list(pdf = list(colormodel = 'cmyk', useDingats = TRUE), tiff = list(compression = 'lzw'))>>=
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
out.extra: (NULL; character) extra options for figures, e.g. out.extra='angle=90' in LaTeX output will rotate the figure by 90 degrees; it can be an arbitrary string, e.g. you can write multiple figure options in this option; it also applies to HTML images (extra options will be written into the <img /> tag, e.g. out.extra='style="display:block;"')
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.env: ('figure') the LaTeX environment for figures, e.g. set fig.env='marginfigure' to get \begin{marginfigure}
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]
fig.subcap: (NULL) captions for subfigures; when there are multiple plots in a chunk, and neither fig.subcap nor fig.cap is NULL, \subfloat{} will be used for individual plots (you need to add \usepackage{subfig} in the preamble); see 067-graphics-options.Rnw for an example
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:

<<test-plot>>=
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)
}
@

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

Option templates

opts.label: (NULL; character) the label of options set in opts_template (see ?opts_template); this option can save some typing efforts for sets of frequently used chunk options

Package Options

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

opts_knit$set(progress = TRUE, verbose = TRUE)

All package options are:

animation.fun: (hook_ffmpeg_html) a hook function to create animations in HTML output; the default hook uses FFmpeg to convert images to an MP4 video
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
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)$p.value), it will be evaluated after the chunk according to the value of x if eval.after='fig.cap')
header: the text to be inserted into the output document before the document begins (e.g. after \documentclass{article} in LaTeX, or <head> in HTML); this is useful for defining commands and styles in the LaTeX preamble or HTML header; the beginning of document is found using the pattern defined in knit_patternss$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; note it also depends on the R option KNITR_PROGRESS (it this variable is set to FALSE via options(KNITR_PROGRESS = FALSE), the progress option will be set to FALSE when knitr is loaded)
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)
stop_on_error: (0L) an integer (0L, 1L or 2L) to be passed to the evaluate package to decide the behavior of errors in code chunks; see ?evaluate::evaluate for details
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)
use.highlight: (FALSE) whether to use the highlight package
verbose: (FALSE) whether to show verbose information (e.g., R code in each chunk and message logs) or just show chunk labels and options

If you have any questions, please consider asking them on StackOverflow, where you may get more attention and fast answers.