Releases: yihui/knitr
Releases · yihui/knitr
CHANGES IN knitr VERSION 1.2
NEW FEATURES
- added a Pandoc wrapper function
pandoc()
to convert Markdown documents to other formats that Pandoc support such as LaTeX/PDF, OpenDocument, HTML5 slides and unfortunately also Word (#206) - in the past the chunk hooks were ignored when the chunk option
engine != 'R'
(i.e. code in the chunk is not R); now they are executed regardless of the language of the code chunk (#483) (thanks, @CDRV) - multiple WebGL objects from the rgl package can be generated in the same web page now; each object is uniquely identified by the corresponding chunk label; see https://dl.dropbox.com/u/15335397/misc/webgl-rmd.html for an example (#494) (thanks, Carson Sievert)
- if multiple graphical devices are used (the chunk option
dev
is a vector of length greater than 1), the chunk optiondev.args
can be a named list of lists of device arguments, with each element a list of arguments to be passed to the single device; see http://yihui.name/knitr/options - as announced in the last version, R 3.0.0 will support non-Sweave vignettes; now it is also possible to compile R HTML vignettes via knitr since
*.Rhtml
files are also registered by knitr as vignette files - a new chunk option
cache.vars
to manually specify which variables to save in the cache database; by default all newly created and modified variables are identified and saved, but in some cases, knitr may not be able to identify the modified variables, e.g.DT[, foo:=value]
in data.table (we can setcache.vars='DT'
to force knitr to save a copy ofDT
) - added a new engine
Rscript
to run the R code in a new R session; see http://stackoverflow.com/q/15271406/559676 for an example - the executable script
inst/bin/knit
can accept multiple input files now (e.g.knit foo.Rnw bar.Rmd zzz.Rhtml
) knit()
andknit2html()
gained aquiet
argument to suppress messages and the progress bar (thanks, Vince Buffalo)- added the
text
argument tospin()
andstitch()
respectively as an alternative way to provide the input likeknit()
(#509) (thanks, Craig Watson) - a new function
wrap_rmd()
to wrap long lines in Rmd files without affecting the code blocks (if there are any); this makes it easier for verson control purposes rst2pdf()
will pass a default output filename torst2pdf
(if the input isfoo.rst
, the output will befoo.pdf
)knit2wp()
gained a new argumentpublish = TRUE
(thanks, Eric Nantz) (#512)
BUG FIXES
- fixed the problem reported in http://stackoverflow.com/q/12448507/559676 now \usepackage{upquote} should appear after \usepackage{fontenc}, so single quotes in verbatim environments will no longer cause problems
- fixed #487:
stitch_rhtml()
andstitch_rmd()
should not use the chunk optionout.width = '.6\\linewidth'
(thanks, Tal Galili) - when the chunk option
engine
is notR
, the code is also executed under the directoryopts_knit$get('root.dir')
(if specified); thanks, Winawer http://stackoverflow.com/q/15512545/559676 :
is permitted infig.path
now (#513) (thanks, Sebastian)- fixed an encoding problem (
CP950
) for Hong Kong Windows users reported at http://bit.ly/16RQL5E
MAJOR CHANGES
- all child documents are inserted into the parent document as character strings of the (compiled) content, instead of being saved into files (e.g.
\input{foo-child.tex}
); no matter how many child documents there are, only one main output file will be generated; the package optionchild.command
was removed accordingly since it is no longer used - no longer generates concordance data for child documents; the past attempt did not really work well and the implementation was complicated, so now we only support concordance for the main document; the consequence of this change is the synchronization between PDF and Rnw for child documents no longer works at the line level (clicking in PDF will still bring the focus back to the child chunk)
- in previous versions, cached chunks were evaluated in separate (empty) environments in order to capture the newly created variables, but this brings confusion when we use functions depending on the current environment such as
ls()
(which will returncharacter(0)
); now all chunks, cached or not, are evaluated in the same environmentknit_global()
(finally fixed #456) knit2pdf()
andknit2html()
return the output filename when the input is a file (in previous versions,NULL
was returned in this case)- the package option
stop_on_error
is set to2
now when building package vignettes, which means R will stop on errors in vignettes; this make it easier to find out possible problems in vignettes duringR CMD build
- the document hook
hook_rjournal()
was removed; it was too hackish (see http://yihui.name/en/2013/02/contribute-to-the-r-journal-with-lyx-knitr/ for how to write an article for The R Journal in a less hackish way)
MINOR CHANGES
- the progress bar symbol was changed from
>
to.
so it looks less intrusive (#395) (thanks, Michael Friendly)
DOCUMENTATION
- the knitr book is forthcoming: http://www.crcpress.com/product/isbn/9781482203530 run
citation('knitr')
ortoBibtex(citation('knitr'))
in R to obtain the citation info - open
help(package = 'knitr', help_type = 'html')
to see the vignette examples (Rnw, R Markdown and R HTML)
CHANGES IN knitr VERSION 1.1
NEW FEATURES
- (experimental) R 3.0.0 will support non-Sweave vignettes, e.g. Rnw documents can be compiled by knitr instead of Sweave; in addition, R Markdown vignettes have also become first-class citizens as R package vignettes; see http://yihui.name/knitr/demo/vignette/ for details
- a new engine for coffeescript (i.e. the chunk option
engine='coffee'
); see https://github.com/yihui/knitr-examples/blob/master/080-engine-coffeescript.Rmd for an example (thanks, Nacho Caballero) - when the chunk option
eval=FALSE
,purl()
will comment out the code when extracting code chunks (thanks, Randall Pruim) - the global option
KNITR_PROGRESS
can be used to set the package optionprogress
inopts_knit
, e.g. afteroptions(KNITR_PROGRESS = FALSE)
, this option will be set toFALSE
when the package is loaded (#395) - the global option
KNITR_WIDTH
can be use to set the R optionwidth
before knitr is called; in the past this option was hard-coded to75
, and now it is set asoptions(width = getOption('KNITR_WIDTH', 75L))
- a new function
knit2wp()
which compiles R Markdown documents and publishes the results to WordPress; see http://yihui.name/knitr/demo/wordpress/ for details - a new hook
hook_webgl()
which writes the WebGL code of an rgl scene into the output usingrgl::writeWebGL()
so we can reproduce a 3D plot in the browser (thanks, Stephane Laurent http://stackoverflow.com/q/14879210/559676)
BUG FIXES
- fixed #465: when
eval=FALSE
andecho
is numeric, code was incorrectly filtered by the indices inecho
(thanks, @ateucher) >
was not allowed in HTML inline code expressions (http://stackoverflow.com/q/14360296/559676); now the regular expression works correctly to look for-->
instead of>
set_parent()
should not printNULL
in the child document: http://stackoverflow.com/q/14487718/559676 (thanks, Thomas Holz)- child documents now inherit the encoding parameter from their parent document, i.e. the
encoding
value inknit(..., encoding = ?)
is applied toknit_child()
; note this assumes the parent document and the child documents use the same encoding (thanks, Henrik Nyhus)
MAJOR CHANGES
- empty inline expressions are no longer recognized, e.g.
\Sexpr{}
will not be parsed; this allows one to write such markers in tutorials (e.g.<!--rinline -->
andr
); internallyall_patterns$foo$inline.code
was changed - the function
build_dep()
was removed (the warning has been there for a long time); please usedep_auto()
instead - the package option
filter.chunk.end
was removed; this means in Rnw documents, a single line@
has the meaning of terminating a chunk only if there is a chunk header<<>>=
before it; otherwise it does not have any special meanings - the function
run_chunk()
was removed; it is redundant because we already have the chunk optionref.label
as well as in-chunk reference<<label>>
MINOR CHANGES
- the function
imgur_upload()
uses Imgur API version 3 now; if you are using the key obtained from version 2, you need to register for your own client id: http://api.imgur.com (#439) - allow users to pass a custom environment to
Rcpp::sourceCpp()
in theRcpp
engine; fixes http://stackoverflow.com/q/14882486/559676 - slight improvement of encoding support in
knit()
CHANGES IN knitr VERSION 1.0
NEW FEATURES
- a new function
knit_expand()
which is similar to brew and mustache, e.g. it expandspi is {{pi}}
topi is 3.14
; it can also be used for building child documents (see https://github.com/yihui/knitr-examples/blob/master/075-knit-expand.Rnw for example) (#397) (thanks, Frank Harrell) knit()
gained a new argumentencoding
to specify the encoding of the input file (multilingual support is complete now), e.g.knit(..., encoding = 'GBK')
for Simplified Chinese- a new function
Sweave2knitr()
to convert Sweave documents to knitr; several automatic translations can be done, e.g.results=tex
toresults='asis'
,width=5
tofig.width=5
,echo=true
toecho=TRUE
,keep.source=TRUE
totidy=FALSE
,eps=TRUE
todev='postscript'
,\SweaveOpts{...}
toopts_chunk$set(...)
and so on; see the documentation in the package for details (#451) - if the Sweave syntax is detected in an Rnw document, a message box (tcltk) will pop up as a reminder on how to fix it
- inline R code also respects the option
opts_knti$get('stop_on_error')
now, e.g. if we set this option to2L
, R will completely stop when error occurs in inline R code - a new function
all_labels()
to get all chunk labels in a document; see one application at https://github.com/yihui/knitr-examples/blob/master/073-code-appendix.Rnw - chunk hooks will be run (if exist) even if the code chunk is empty
- added two wrapper functions
stitch_rhtml()
andstitch_rmd()
which use the R HTML and R Markdown templates respectively when callingstitch()
- the chunk label is used as the id of the div element in R HTML output, e.g.
<div id='chunk-label'>...</div>
MAJOR CHANGES
- (IMPORTANT) the internal compatibility with Sweave has been dropped as scheduled in the last version, and the knitr parser was greatly simplified accordingly; Sweave users can call the function
Sweave2knitr()
to convert old Rnw files to knitr files before runningknit()
- accordingly, the pattern elements
global.options
andinline.doc
were removed fromknit_patterns
(\SweaveOpts{}
and\SweaveInput{}
will no longer be supported; please callSweave2knitr()
to convert incompatible Sweave documents) - chunk labels can be arbitrary characters now; in the past they had to be valid R symbols, e.g.
2a
was an invalid label; this restriction has been removed, because chunk labels will be automatically quoted when necessary (<<2a>>=
will become<<'2a'>>=
, but<<'3-function'>>=
will remain untouched) - if the chunk option
include=FALSE
, the evaluation will stop if errors occur (i.e.stop_on_error=2L
for evaluate), because otherwise it will be very difficult for authors to notice errors in chunks which haveinclude=FALSE
(#453) (thanks, Joshua Pritikin) - the function
knit_env()
is no longer available (it is not exported any more), andknit_global()
has been exported now
MINOR CHANGES
- for inline R code, the value is returned only if the R code prints a visible value, e.g.
\Sexpr{x <- 1}
will be empty, and\Sexpr{pi}
will return the value of pi
BUG FIXES
- fixed #432: no longer uses
\\\\
in LaTeX output; only a single line break is converted to\\
(thanks, Kevin Wright) render_html()
guarantees that the R source code is highlighted when the chunk optionhighlight = TRUE
(#447) (thanks, Ramnath Vaidyanathan)dep_auto()
was unable to find the cache files if the input document is not under the current working directory (thanks, Hui Yao)
Documentation
- because Github has deprecated downloads, all downloads were moved to Bitbucket, and the links in the package website as well as all examples have been updated (#438)
CHANGES IN knitr VERSION 0.9
NEW FEATURES
- added a demo named
notebook
which is an R notebook based on the shiny package (https://github.com/rstudio/shiny); usedemo('notebook', package = 'knitr')
to see it, or visit http://glimmer.rstudio.com/yihui/knitr - for numeric inline output in LaTeX, the
I()
trick is no longer needed, e.g.$x=\Sexpr{1.2e10}$
is safe for LaTeX now due to\ensuremath{}
(#137) (thanks, Randall Pruim) - the chunk option
eval
can take numeric values now, specifying which expressions to evaluate in a chunk (#383) (thanks, Jared Lander) - a new package option
stop_on_error
which specifies the behavior of errors in code chunks; this option is passed to the evaluate package, e.g.opts_knit$set(stop_on_error = 2L)
will make knitr completely stop on errors (the default value is0L
which means to move on even if errors occurred); this makes it possible to see the call stacks viatraceback()
in an interactive R session when an error occurs (#344) (thanks, Hadley Wickham and Dzidorius Martinaitis) - added support to the Rcpp package through the chunk option
engine='Rcpp'
so that we can write C++ source code in the document; see https://github.com/yihui/knitr-examples/blob/master/029-engine-Rcpp.Rmd for an example (#415) (thanks, JJ Allaire) - knitr throws a warning when a cached chunk depends on an uncached chunk because this kind of dependency will be ignored (#431) (thanks, @ghostwheel)
- a list of arguments can be passed to
formatR::tidy.source()
as the chunk optiontidy.opts
now, e.g.tidy.opts=list(width.cutoff=60, keep.blank.line=FALSE)
(#429) - some chunk options are recycled for plots such as
fig.env
,out.width
andout.extra
, etc; this means if there are multiple plots per chunk, we can specify different output options for them individually (e.g.out.width=c('2in', '.4\\linewidth')
for two plots); see https://github.com/yihui/knitr-examples/blob/master/067-graphics-options.Rnw for an example (motivated by #430) (thanks, @autumnlin) - added a new chunk option
fig.subcap
for captions of subfigures in LaTeX; when there are multiple plots in a chunk, and neitherfig.subcap
norfig.cap
is NULL,\subfloat{}
will be used for individual plots (you need to add\usepackage{subfig}
in the preamble); also see https://github.com/yihui/knitr-examples/blob/master/067-graphics-options.Rnw for an example (#388) (thanks, @skipperhoyer) stitch()
accepts labeled R scripts now; if an R script contains chunk headers of the form## @knitr label, options
, they will be used in the template (#411) (thanks, @jamiefolson)- the function
read_chunk()
gained a few new arguments so that we can reference external code chunks in another way, which was an idea from the SweaveListingUtils package (thanks, Peter Ruckdeschel) - a new function
read_demo()
based onread_chunk()
to read demo scripts in R packages - a new convenience function
read_rforge()
to read code from R-Forge repositories; combined withread_chunk()
, it can insert R code from R-Forge into knitr dynamically; see https://github.com/yihui/knitr-examples/blob/master/046-read-rforge.Rmd for an example (thanks, Peter Ruckdeschel) - chunk options are also written after
## @knitr
along with chunk labels when tangling R scripts viapurl()
purl()
gained a new argumentdocumentation
to also write documentation lines into the R script (#391 and #401) (thanks, Noam Ross and Fernando Mayer)knit_rd()
generates a navigation frame on the left and builds links now; this is like the CHM help in old days (thanks, Michael Friendly)- a new function
knit_rd_all()
to build static html help pages for all the packages installed - we can also use
## @knitr
to write chunk options forspin()
now (#+
and#-
still work) - added new language support for Perl and Z Shell (
zsh
); see an example at https://github.com/yihui/knitr-examples/blob/master/028-engine-perl.Rmd (#406) (thanks, Jim Hester) render_jekyll()
gained an argumenthighlight
to specify which highlighting engine to use (Pygments or Prettify.js) (thanks, Yanping Chen)- two new chunk options for language engines:
engine.path
andengine.opts
; the former can be used to specify the path of the program (e.g.<<engine='ruby', engine.path='/usr/bin/ruby1.9.1'>>=
); the latter can be used to pass additional arguments to the engine program - added new engines for GraphViz (
engine='dot'
) and TikZ (engine='tikz'
); see https://github.com/yihui/knitr-examples/blob/master/057-engine-dot.Rmd and https://github.com/yihui/knitr-examples/blob/master/058-engine-tikz.Rmd for examples (#419) (thanks, Michel Kuhlmann) - added a preliminary engine for SAS which is basically a call like
system('sas chunk-code.sas')
(#354) - a new
document
hook to post-process the LaTeX output document to move code chunks out of figure/table environments so that code chunks will not float with the environments; see?hook_movecode
for details - chunk hooks are called in the reverse order after a chunk (and natural order before a chunk); this allows one to, e.g. write an opening environment before a chunk and close it properly after a chunk
- all language engines also respect the
comment
option when writing output just like R code chunks (by default the output is commented out by##
) - added a new function
set_alias()
as a wrapper toopts_knit$set(aliases = ...)
, e.g.set_alias(w = 'fig.width')
setsw
as an alias for the chunk optionfig.width
MAJOR CHANGES
- global options are strongly recommended to be set via real R code
opts_chunk$set(opt = value)
in a code chunk instead of the old syntax in text chunks like\SweaveOpts{opt = value}
, or<!--roptions opt=value-->
, etc, which will be deprecated in the next version; this will make it cleaner and safer to parse the source documents, e.g. we can write arbitrarily complicated expressions likeopts_chunk$set(fig.width = if (foo == 'beamer') { 5 } else { 7 })
which is impossible in the old syntax; if you still use the old syntax like\SweaveOpts{}
, you will see a warning with a pause of 10 seconds - based on the same reason, it is recommended to use the chunk option
child
to input child documents; old syntax like\SweaveInput{}
will be deprecated - for markdown output, results from inline R code will no longer be put in a pair of backticks (#379)
- the package option
opts_knit$get('cache.extra')
was removed because this option should really be a chunk option instead; see http://yihui.name/knitr/demo/cache/ for the updated documentation (#404 and #405) (thanks, Jim Hester) - the chunk option
highlight.opts
was deprecated and renamed toengine.opts
; this affects users who use Andre Simon's highlight through thehighlight
engine in knitr - the chunk option
file
for Awk was deprecated; we can also useengine.opts
to specify the file for Awk; see https://github.com/yihui/knitr-examples/blob/master/024-engine-awk.Rmd for example - the pattern
knit_pattern$get('ref.label')
was deprecated since it is unlikely to be customized; a fixed pattern'^#+\\s*@knitr(.*)$'
will be used instead
MINOR CHANGES
- when
opts_knit$get('verbose')
isTRUE
, atimestamp()
will be printed before each code chunk is evaluated (#377) (thanks, Carl Boettiger) stitch()
will no longer copy the template over to the current working directory (thanks, Michael Friendly)stitch()
will no longer open the PDF/HTML output automatically (#411) (thanks, Michel Kuhlmann)- the script
inst/bin/knit
can also convert R Markdown documents to HTML now; the argument--pdf
was removed and a new argument--no-convert
was added - dots in figure filenames will not be replaced with
_
when the output is not LaTeX (thanks, Stewart Macarthur)
BUG FIXES
- fixed #410: when the inline R code returns
NA_real_
, the scientific notation of numbers will run into errors (thanks, Rafik) - the syntax pattern for Rnw documents was not quite right:
all_patterns$rnw$chunk.end = '^\\s*@\\s*%*'
actually allows any characters after@
, but only LaTeX comments and white spaces are allowed; it has been fixed to^\\s*@\\s*(%+.*|)$
now
DOCUMENTATION
- an example of combining R, knitr and D3 to draw a contour plot: http://yihui.name/knitr/demo/javascript/
CHANGES IN knitr VERSION 0.8
NEW FEATURES
- output from other languages (e.g. python, awk, ...) can also be cached like R output when
cache=TRUE
; see 023-engine-python.Rmd for an example - added support for bash/shell scripts; use the chunk option
engine='bash'
orengine='sh'
to write shell scripts in code chunks (#361) - a new function
knit_rd()
to knit package documentation (run examples code and insert output in the HTML documentation) (#227) (thanks, Taiyun Wei) - added LuaTeX support for tikz graphics with the tikzDevice package (set
options(tikzDefaultEngine = 'luatex')
); this feature requires tikzDevice version > 0.6.2 (#358) (thanks, Alastair Andrew) - a new chunk option
fig.env
to set which environment to use for figures in LaTeX, e.g. we can setfig.env='marginfigure'
to use\begin{marginfigure}
(#364) (thanks, Bryan Hanson) - added a new package option
global.device
(defaultFALSE
) which specifies whether to use a global graphics device to capture plots; ifTRUE
, it is possible to writeplot(1:10)
in a previous chunk andabline(0, 1)
in a latter chunk because all code chunks share the same device, however, this may also bring unexpected consequences (in particular, usingpar()
can bring redundant plots)
BUG FIXES
- dots in figure paths are more safely replaced with
_
now, e.g.fig.path='../figure'
will no longer be replaced by__/figure
(#346) (thanks, @Ralfer) - the
c()
syntax for the chunk optiondependson
did not actually work, e.g.dependson=c('foo', 'bar')
(#350) (thanks, Cassio Pereira) - fixed a bug when
eval=FALSE
andprompt=TRUE
(the continuation character was used in some places where there should be the prompt character) (thanks, Derek Ogle) persp()
plots were not recognized in the last version (thanks, Jeffrey Racine)
MAJOR CHANGES
- leading spaces are allowed in chunk headers now, e.g. in the past
<<>>=
must appear in the beginning of a line, but now we can indent the chunk header by a number of white spaces; this amount of spaces will be stripped off the chunk if the whole chunk is indented (#236) (thanks, @jamiefolson and Vitalie Spinu) - markdown output will be indented if the original code chunk is indented; this allows chunk output to be nested within its parent environment, e.g. inside an ordered list (see 001-minimal.Rmd for example)
- when the global chunk option
eval=FALSE
, inline R code will not be evaluated, and??
is returned for inline R expressions (#367)
MINOR CHANGES
- if
getOption('OutDec')
is not.
, inline numeric output will be put inside\text{}
in LaTeX to avoid situations like #348 (the normal math mode may add a space after the comma in3,1415
) - if the chunk option
external==FALSE
(default isTRUE
), knitr will no longer automatically add\usepackage{tikz}
to the LaTeX preamble; you need to add it manually (but it is recommended to useexternal=TRUE
withcache=TRUE
for the sake of speed, because compilation of tikz graphics may be slow) *.brew
generates*.txt
by default (instead of*-out.brew
)knit(text = ...)
will no longer write output in the console (the output is only returned as a character string)
DOCUMENTATION
- added a simple reference card: https://bitbucket.org/stat/knitr/downloads/knitr-refcard.pdf
CHANGES IN knitr VERSION 0.7
NEW FEATURES
- added a new chunk option
out.extra
to write extra graphics output options, e.g.<<out.extra='angle=90'>>=
to rotate the figure by 90 degrees; see http://yihui.name/knitr/options (#301) (thanks, @knokknok) - when
opts_knit$get('verbose')
is TRUE, logs (messages, warnings and errors) along with the corresponding R code will be printed afterknit()
is done; this might help users figure out possible problems in R code quickly (#276) .Random.seed
is cached again for the sake of reproducibility; see http://yihui.name/knitr/demo/cache/ for how to maintain reproducibility when the computation involves with random number generation (#274) (thanks, Renaud)- the package option
opts_knit$get('cache.extra')
can be an unevaluated R expression now, e.g.opts_knit$set(cache.extra = quote(.Random.seed))
; see the cache page above for a concrete example - added a new package option
'root.dir'
(defaultNULL
) which can be used to set the root directory to evaluate code chunks in a document; by default, the root directory is the directory of the input document, and this option enables users to set other directories as the working directory for code chunks (#277) (thanks, Ken Williams) spin()
will add\documentclass{article}
for Rnw output if no document class is specified in the R script so that the LaTeX output will be a complete document (#295) (thanks, Christiaan Klijn)- added Ruby support in the
engine
option; see the example https://github.com/yihui/knitr/blob/master/inst/examples/knitr-lang.Rmd (#294) (thanks, Ramnath Vaidyanathan) - also added Haskell support in the option
engine='haskell'
through callingghc
(#336) (thanks, Michel Kuhlmann) - added support to Andre Simon's
highlight
through the optionengine='highlight'
; see https://gist.github.com/3114112 for an example of highlighting Matlab code in LaTeX (thanks, Dirk Eddelbuettel and Renaud Gaujoux) - the output hooks for LaTeX, HTML, Markdown and reST will respect the
engine
option now, so these hooks can be readily used for output when the language is not R, e.g.render_markdown(strict = TRUE)
also works for Python output (#251) (thanks, Chris Fonnesbeck) - the chunk options
eval
,echo
andresults
are also respected when the language is not R, e.g. for a Python code chunk witheval=FALSE
, the code will not be evaluated, or for a Ruby chunk withresults='hide'
, the output will be hidden (#293) (thanks, Ramnath Vaidyanathan) - chunk options
out.width
,out.height
andout.extra
also work for plots in HTML and Markdown output now, e.g.out.width='200px'
orout.extra='style="display:block;"'
(#297) (thanks, Taiyun Wei and Alan Severini) - the hook function to create animations in HTML output is exported now as
hook_ffmpeg_html()
- added a package option
opts_knit$get('animation.fun')
which defaults tohook_ffmpeg_html
; this option is used to create animations in HTML output so that we do not have to use FFmpeg - added two functions
hook_r2swf()
andhook_scianimator()
which can be set as the package optionopts_knit$get('animation.fun')
and create animations via the R2SWF package or the SciAnimator library (seeanimation::saveHTML
) (thanks, Taiyun Wei) - a new function
image_uri()
to create data URIs for image files; we can setopts_knit$set(upload.fun = image_uri)
so that images are embedded in the HTML output as data URIs (hence the HTML page does not depend on external images) (#298, #324) (thanks, Wush Wu) - added a new object
opts_template
which can be used to set a group of chunk options and they can be referenced later with the new chunk optionopts.label
; see?opts_template
for examples; this makes it easy to reuse groups of frequently used chunk options (#316, #320) (thanks, Cassio Pereira) - a new function
dep_prev()
to build chunk cache dependencies so that all later chunks will depend on previous chunks; if any of a previous chunk is updated, the cache of all chunks after it will be updated as well (#285) (thanks, @muelleki) - a new chunk hook function
hook_optipng()
to optimize PNG images usingoptipng
(#272) (thanks, Winston Chang) - added a new output hook named
document
inknit_hooks
(seeknit_hooks$get('document')
); this hook function is used to process the output of the whole document; it can be useful when we want to post-process the whote output before writing it to the output file - a new function
rst2pdf()
which uses the programrst2pdf
to convert reST documents to PDF; it is also supported byknit2pdf()
whencompiler='rst2pdf'
(#300) (thanks, Alex Zvoleff)
BUG FIXES
- fixed #286: messages (including warnings and errors) are guaranteed to be ended by
\n
, so even when chunk optioncomment=NA
, messages will also be rendered correctly (thanks, Carl Boettiger) - fixed #273: when knitting a file under another directory with cache turned on (e.g.
knit('foo/bar.Rnw')
),lazyLoad()
is unable to load the cache files under a relative path because the working directory has been changed to the directory of the input file during evaluation - fixed #292: layout() may cause the capture of unwanted plots (thanks, Austen Wallace Head)
- fixed #302: when there are multiple instances of
\documentclass
in the source document, knitr will be unable to insert the LaTeX preamble - fixed #308: if
options('OutDec')
was set to a character other than.
, the LaTeX code can be malformed (#308) (thanks, Cassio Pereira) opts_chunk$set()
in a child document was only working in that child document, but was expected to change chunk options globally; now it works everywhere, and will affect all chunks after this setting, no matter whereopts_chunk$set()
is (thanks, Guy Lebanon) (http://bit.ly/MexHXd)- fixed #332: calling
purl()
inside a source document whenknit()
the same document could cause clashes; now it is safe to putpurl()
inside a source document andknit()
it - fixed #342: when
eval=FALSE
, line breaks in the source code were missing
MAJOR CHANGES
- if the chunk label contains non-alphanumeric characters (except
-
and_
), these characters will be replaced by_
in the figure filenames (if there are any) and a warning will be issued; this is to guarantee the figure filenames are valid to LaTeX (#321) (thanks, (Roman Lustrik) - the highlight package is not enabled by default; use
opts_knit$set(use.highlight = TRUE)
to enable it - the default LaTeX output will put messages, warnings and errors in special LaTeX environments: errors are red, warnings are magenta, and messages are italic; in previous versions they were in the
verbatim
environment (#264) (thanks, @muelleki) - unnamed chunks are named sequentially in a single call of
knit()
according to the order of their appearance no matter where they are, e.g. if there are two unnamed chunks in two child documents respectively, they will be named asunnamed-chunk-1
andunnamed-chunk-2
; in previous versions, both will be named asunnamed-chunk-1
which can cause clashes of cache and figure files - the function
build_dep()
was renamed todep_auto()
which better reflects what this function really does; it is still available in this package but may be removed in future versions - the package tikzDevice was removed from the
Suggests
field, but this will not affect users who have already installed tikzDevice; for those who have not, this package has been archived on CRAN (hopefully only temporarily), so you have to install from the source
MINOR CHANGES
- the LaTeX environment
kframe
was updated so that it can be used in other environments such ascenter
ortabular
(#283) (thanks, @muelleki) - the OpenCPU demo is more robust to double quotes in the text (#271); see http://public.opencpu.org/userapps/opencpu/knitr/
- for Sweave output, the results will not be put inside the Schunk environment when
results='asis'
stitch()
templates use more sensible figure paths by default: the path for figures is'figure/input-script-name'
now, i.e. it will be different for different input R scripts to avoid possible clashesstitch()
templates no longer use default title and author names; if the user did not set them in the R script (as meta comments# title:
and# author:
), there will not be titles or authors in the output- knitr will no longer use scientific notations for integers in inline R code output; sci notation only applies to double-precision numbers (#296) (thanks, @knokknok)
options()
set in the main document will apply to its child documents (e.g.options('digits')
) (#306) (thanks, Cassio Pereira)- the
...
argument inknit2html()
is passed tomarkdownToHTML()
in the markdown package instead ofknit()
; this allows us to pass more arguments to control the rendering of HTML output, e.g.knit2html(input, fragment.only = TRUE)
(#333) (thanks, @bart6114)
DOCUMENTATION
- the example using other languages was updated to show how some chunk options (
eval
,echo
andresults
) also work for foreign languages: https://github.com/yihui/knitr/blob/master/inst/examples/knitr-lang.Rmd
CHANGES IN knitr VERSION 0.6.3 and 0.6
CHANGES IN knitr VERSION 0.6.3
MAJOR CHANGES
- this is a urgent patch version for CRAN: the dependencies on highlight and parser were removed because these two package were orphaned on CRAN; now knitr uses a naive syntax highlighter for LateX and HTML output if highlight is not available, which has a similar appearance with highlight; when the parser package is not available, users should be careful with the chunk option
tidy=TRUE
:replace.assign
may not work as expected; see the NEWS of formatR for details: https://github.com/yihui/formatR/blob/master/NEWS; you are welcome to improve the naive highlighter: https://github.com/yihui/knitr/tree/master/R/highlight.R
NEW FEATURES
spin()
gained a new argumentreport
for Rnw/Rtex/Rmd documents to be compiled to PDF/HTML respectively (#287) (thanks, kohske takahashi)
BUG FIXES
stitch()
andspin()
should useparent.frame()
to evaluate code by default; in 0.6, the default parent frame for the innerknit()
was a wrong environment to use (thanks, Michael Nelson)- use
unnamed-chunk-i
as the label when chunklabel == ''
(#280) (thanks, Josh Paulson) - fixed #279 and #281, both of which are about concordance
'\\maxwidth'
does not apply to LaTeX/PDF animations, so the default value ofout.width
for animations in LaTeX is stillNULL
; you will have to setout.width
manually for a reasonable width (#282) (thanks, Ramnath Vaidyanathan)
MISC
- knitr and RStudio had an invited talk at useR! 2012; slides at http://yihui.name/slides/2012-knitr-RStudio.html (source at https://github.com/yihui/knitr-talks)
CHANGES IN knitr VERSION 0.6
NEW FEATURES
- for LaTeX output, the chunk option
out.width
defaults to'\\maxwidth'
now; see http://yihui.name/knitr/demo/framed/ for its definition; this makes sure the figures do not overflow the page margins (#221) - the chunk option
size
now defines the font size of the whole chunk instead of only some special characters in it, so that the old trick of redefining theknitrout
environment for different font sizes is no longer necessary; see updates in the beamer examples: http://yihui.name/knitr/demo/beamer/ (thanks, Baptiste Auguie) - added a new chunk option
dev.args
which can be used to pass more arguments to the graphical device (#254) (thanks, knokknok) - warnings, messages and errors will be wrapped according to
options('width')
; this will make long messages stay within the page margin when the width option is appropriately small (#259) (thanks, @muelleki) - added a new function
spin()
to turn a specially formatted R script to a report; see http://yihui.name/knitr/demo/stitch/ (#223) (thanks, Rich FitzJohn) knit()
gained a new argumentenvir
to specify the environment in which to evaluate code chunks (by default in the parent frame); this will allow users to run code in a specified environment so that the global environment will not be cluttered by objects in chunks, which can hopefully make the documents more reproducible (#228)- added a new component
inline.comment
inknit_patterns
to strip off tokens of inline R code from inline comments, e.g. a comment line like% x is \Sexpr{x}
will become% x is x
(#110); this will only happen to LaTeX documents because HTML does not have inline comments (it only has block comments<!-- -->
) - concordance works for child documents as well now (try RStudio), although it is not very precise (#225); note when concordance is enabled, the results from child documents will be written into the parent output instead of individual tex files; also note you have to set
opts_knit$set(self.contained = FALSE)
for concordance to work better - added an OpenCPU app so that we can run knitr in the cloud now; see
system.file('opencpu', 'apps', 'index.html', package = 'knitr')
or http://public.opencpu.org/apps/knitr (thanks, Jeroen Ooms) - all messages, errors and warnings during evaluation are recorded in an internal object
knit_log
(useknitr:::knit_log$get()
to get all messages) and they are printed if the package optionverbose
isTRUE
(i.e.opts_knit$get('verbose')
) (#224) - child documents are also supported in other document formats besides LaTeX, e.g. Markdown and HTML, etc; please use the chunk option
child
to specify the child documents; seesystem.file('examples', 'child', 'knitr-main.Rmd', package = 'knitr')
for an example in markdown (#268) (thanks, @martinaryee)
BUG FIXES
- the templates for
stitch()
usedresults=hide
which should really beresults='hide'
(#219) (thanks, @r2d3) - format numbers with the reST syntax instead of HTML (#218) (thanks, Jeffrey Arnold)
hook_pdfcrop()
should work better under Windows now (#209) (thanks @DCCKC and @r2d3)- tikz compilation fails on Windows network drives
- FFmpeg does not really work for HTML/Markdown output because the dot in figure filenames was omitted (thanks, Ming Kuo)
- child documents can fail when they are in different sub directories (thanks, Christoph J)
set_parent()
failed to work in the last version due to a bug when inserting the parent preamble into the child document (#240)- better preserve plot sizes in interactive sessions (#258)
MAJOR CHANGES
.Random.seed
is not cached any more because of weird problems due to lazy loading (#248 and #253); users should useset.seed()
to make sure reproducibility of random simulations; the chunk output is cached in a.RData
database instead of a lazy load database to avoid problems in #253- the default graphics device is set to the null PDF device before evaluating code chunks, i.e.
pdf(file = NULL)
, so that neitherRplots.pdf
nor plot windows will be opened during knitting
MINOR CHANGES
- knitr will show a message when a chunk is empty; this helps users who do not actually want a chunk to be empty realize the problem like #229; in the past, knitr just silently returns an empty string from such chunks
- knitr will show a message when the cache is loaded and the option
opts_knit$get('verbose')
isTRUE
(#249) (thanks, Carl Boettiger) - the filename extensions
Snw
andStex
are also supported (foo.Snw
/foo.Stex
producesfoo.tex
) - the HTML output hooks are changed according to the suggestion of Barry Rowlingson (#250) and the default CSS is also slightly modified
knit()
will no longer try to remove the fileNA
generated bypdf(file = NULL)
before R 2.14.2 (which was a bug and fixed later); you should update R if you see this file
DOCUMENTATION
- added a minimal brew example under
system.file('examples', package = 'knitr')
CHANGES IN knitr VERSION 0.5
NEW FEATURES
- white spaces are allowed before
<<>>
when using chunk references, and this approach of references is supported in tex and html documents as well - added a new pattern list named
md
so that R code blocks can be written more naturally in extended markdown (e.g. GFM and pandoc): use ````{r label, opts}to begin a chunk and ````` (three or more backticks) to begin normal text, and write inline R code in ``r code.here``; it is the default syntax for markdown input, or you can call
pat_md()` before `knit()` so knitr can make use of this pattern list to process the input document - RStudio has added full support to knitr: we can knit HTML and Markdown documents easily now, and markdown output will be automatically converted to an HTML preview page just like TeX to PDF
- if the pattern list is not set in advance, knitr will try to detect the syntax automatically by matching all built-in pattern lists against the input document, e.g. if the input contains
<<>>=
, the Rnw syntax will be used, and if ````{r}` is detected, the markdown syntax will be used; this feature enables us to use different sets of syntax freely, e.g. we can use Sweave syntax in markdown files and knitr will be able to recognize it (#189) - new filename extensions with a prefix
R
orr
are introduced:*.Rhtml
,*.Rhtm
,*.Rtex
,*.Rmd
and*.Rmarkdown
will be recognized as source documents like*.Rnw
, and the output filename will be automatically determined by removing theR
prefix, e.g.foo.Rmd
producesfoo.md
by default; the old clumsy naming conventionfoo_knit_.md
is still preserved but not recommended any more (#187) - new function
knit2html()
to knit an Rmd file (R with markdown) and convert to HTML in one step using the markdown package - new functions
pat_rst()
andrender_rst()
to support reStructuredText; use.. {r label, options}
and.. ..
to write R code chunks; see https://github.com/yihui/knitr/tree/master/inst/examples/knitr-minimal.Rrst (thanks, Jeffrey Arnold and Ramnath Vaidyanathan) - new package option
self.contained
which decides whether to write style definitions (highlighting) in external files or put them in the output document; the highlighting definitions in LaTeX output is often too long, soopts_knit$set(self.contained = FALSE)
can help in this case (#176) (thanks, Ramnath Vaidyanathan) - new package option
filter.chunk.end
which decides if thechunk.end
pattern really meanschunk.end
; see http://yihui.name/knitr/options (thanks, Joe Cheng) - syntax highlighting themes are also available to HTML output now; the usage is the same as in LaTeX (#179) (thanks, Ramnath Vaidyanathan)
- the chunk option
fig.cap
is also used in markdown output now - the random seed
.Random.seed
is also cached for the sake of reprodubibility in random simulations - the function call
read_chunk()
will be evaluated when tangling R code viapurl()
(#175) (thanks, Carl Boettiger) - the default LaTeX output will use the upquote package if it exists so that single quotes are straight in the output (thanks, Mathematical Coffee http://bit.ly/IKjluw)
- the chunk option
engine
is back but it is used to run code from other languages instead of just ignoring the code in chunks which haveengine != 'R'
; currently this option is still in rough edges and only supports python and awk; other languages may be added in future versions, but users can also do it by themselves byknit_engines$set(language = function(options) {...})
; see an example atsystem.file('examples', 'knitr-lang.Rmd')
(#201) - new function
write_bib()
to write Bibtex citations for R packages; see the main manual for a sample usage (#13) hook_pdfcrop()
also supports cropping other image formats like PNG or JPEG through ImageMagick (convert -trim
) (#203) (thanks, @r2d3)
MAJOR CHANGES
- knitr will completely stop when duplicated labels are found and the corresponding chunks are non-empty; in previous version, only a warning is given and R code in later chunks will override previous chunks (#185) (thanks, Randall Pruim)
- the default graphical device for HTML and markdown output is
png()
now to avoid the possible unexpected consequence that PDF plots are included in an HTML page which will not work normally in browsers - markdown output will use the extended markdown hooks by default now:
render_markdown(strict = FALSE)
; in the past the default wasrender_jekyll()
; the major difference is that the code blocks are put inr and
; if you want the strict markdown syntax, you can allrender_markdown(strict = TRUE)
which will indent code blocks by 4 spaces render_gfm()
has been removed because the name can be misleading; the main purpose of this function was to put code blocks in `````, and now we can replace it byrender_markdown(FALSE)
; other markdown flavors also support such fenced code blocks (e.g. pandoc) -- it is not limited to Github only- the default value for the
fig.path
option is'figure/'
now so that plots will be put under this directory by default; the default was'./'
in the past which makes the current directory messy when there are many plots - knitr will fully stop when an error is encountered in
knit()
; in the past only a message was issued in this case in an interactive R session - the package option
all.patterns
has been dropped; please use the objectsall_patterns
orknit_patterns
directly if you want to tweak the syntax
BUG FIXES
- the compilation of tikz graphics can hang up when there are TeX errors in the tikz file; now we use
\nonstopmode
to avoid hiccup (#188) - multiple devices per chunk was buggy (#181)
- S4 objects will be printed by
show()
instead ofprint()
; this is a bug of the evaluate package, which has been fixed (please update it to be > 0.4.2)
MISC
- it is recommended to use
opts_chunk$set()
to set global chunk options now instead of\SweaveOpts{}
; all documentation has been updated (#216) - number of downloads (https://github.com/yihui/knitr/downloads) of knitr documentation before I removed and updated them on GitHub:
c(main = ?, graphics = 275+)
CHANGES IN knitr VERSION 0.4
NEW FEATURES
- Sweave concordance was finally implemented: when
opts_knit$get('concordance')
isTRUE
, knitr will write a file named'input-concordance.tex'
which contains the mapping between input Rnw and output tex line numbers; this feature is mainly for (but not limited to) RStudio to provide better error navigations: you can jump from the TeX error message to the Rnw source directly to know where the error comes from (the line number of the source of the error may not be accurate but should be in the ballpark) (#133) (thanks, JJ Allaire and Joe Cheng) - if output hooks have been set before calling
knit()
, they will be respected, i.e. knitr will no longer override them by default hooks; you need to make sure all output hooks are set appropriately, e.g. you can start byrender_latex()
and change some individual hooks later (#165) (thanks, Andrew Redd) - newly created objects in the global environment will also be cached if cache is turned on (
cache=TRUE
); in previous versions knitr is unaware of objects created inglobalenv()
, e.g.setGeneric()
creates S4 generic functions inglobalenv()
and knitr was unable to capture them (#138) (thanks, syoh) - chunk options
dev
,fig.ext
anddpi
can be vectors now; this allows one to save a plot to multiple formats, e.g.<<foo, dev=c('pdf', 'png')>>=
creates two files for the same plot:foo.pdf
andfoo.png
(#168) (thanks, MYaseen208) - an experimental feature for animations created by FFmpeg in HTML/markdown output when
fig.show='animate'
(#166) (thanks, gabysbrain) - the chunk option
fig.cap
supports multiple figure captions in LaTeX now, e.g. if a chunk produces two plots, we can usefig.cap = c('first caption', 'second caption')
to assign two different captions to them respectively whenfig.show = 'asis'
(#155) (thanks, Jonathan Kennel) - new package option
opts_knit$get('upload.fun')
which is a function that takes a plot file to upload to a certain host and returns the link to the image; by default it isimgur_upload()
, and you can use your own function to upload images to other hosts like Flickr (#159) (thanks, Carl Boettiger) - all packages loaded in the current session are also cached, so as long as a package has been loaded previously, it will be available to all following chunks (#160)
- new chunk option
autodep
and functionbuild_dep()
to build cache dependencies among cached chunks automatically by analyzing object names in all cached chunks; this is a loose alternative to thedependson
option (see main manual and?build_dep
for details) (#72) (thanks, Seth Falcon) - input and output in
knit()
are no longer restricted to files; they can bestdin()
/stdout()
or other types of connections (#162; see #162) (thanks, gabysbrain) - as-is output (
results='asis'
) and plots are no longer put in the framed environments because of incompatibilities (#163) (thanks, DCCKC, Murray Logan and Jennym Hutchison)
BUG FIXES
- for plots in LaTeX output, centering should be done with
{\centering }
instead of\centering{}
(#156) (thanks, Ramnath Vaidyanathan) - the recorded plot is a more precise representation of the expected plot now, because the recording device also takes the plot size into consideration (#157) (thanks, Christiaan Klijn and Frank Harrell)
format_sci()
now correctly formats 0; this function is used for inline R code to format numbers in scientific notation (#161) (thanks, Kihoro J. M.)- fixed a bug for the case in which the chunk option only contains the label like
<<label=foobar>>=
; knitr 0.3 was unable to parse the label correctly (<<foobar>>=
is OK) (thanks, Muhammad Yaseen)
MINOR CHANGES
imgur_upload()
returns the link to the image directly, with the XML list as its attribute (in v0.3 the list was returned)- more verbose messages in case of chunk errors: both line numbers of the source and chunk info will be printed
DOCUMENTATION
- website updated as usual: http://yihui.name/knitr
- added an example for subfloat environment: https://bitbucket.org/stat/knitr/downloads/knitr-subfloats.pdf
- most manuals (main or graphics manuals) have been updated
MISC
- number of downloads (https://github.com/yihui/knitr/downloads) of knitr documentation before I removed and updated them on GitHub: c(main = 400, graphics = 177)
CHANGES IN knitr VERSION 0.3
NEW FEATURES
- a fundamental and important new feature for writing chunk options: they can be written as valid R code now, just like we write function arguments (e.g.
echo=c(1, 3, 5)
,fig.cap="my figure caption"
); all options will be parsed and evaluated as R code by default; see http://yihui.name/knitr/options for details (#142) (thanks, Baptiste Auguie) - chunk references using
<<label>>
is supported now (#86); thanks to Kevin R. Coombe and Terry Therneau for the discussion - new function
run_chunk()
to run the code in a specified chunk, which is an alternative to the chunk reference in Sweave; see http://yihui.name/knitr/demo/reference/ - a executable script
knit
undersystem.files('bin', package = 'knitr')
which makes it easier to call knitr via command line under *nix (callknit input [output] [--pdf]
) - the inline hooks respect
getOption('digits')
andgetOption('scipen')
now (see?options
); numbers returned from inline R code will be formatted according to these two options (see a demo at http://yihui.name/knitr/demo/output/) - if you still use old Sweave syntax for chunk options, it is possible to write literal commas in chunk options now -- they have to be escaped by
\
, e.g.caption=hello\, world
; this will be parsed to'hello, world'
as a character string; of course this looks ugly and has limited power, so please please consider the new syntax! knit2pdf()
gained another argumentcompiler
which can be used to specify the program to compile the tex document to PDF, such as xelatex (#131) (thanks, Ramnath Vaidyanathan and Dennis Murphy)- a new function
imgur_upload()
to upload images to imgur.com; it can be used in HTML or Markdown hooks so the output is a self-contained document which does not need additional image files;opts_knit$get('upload.fun'
) can use this function (#66) (thanks, Ramnath Vaidyanathan) - a child document can be compiled individually with the LaTeX preamble borrowed automatically from a parent document using a new function
set_parent()
; see the help page for details (#136) (thanks, Helder Correia) - to avoid
$$
around numbers in the inline output, we can useI()
to protect the numeric inline output, e.g.$x = \Sexpr{I(10^7)}$
gives$x = 10^7$
whereas\Sexpr{10^7}
gives$10^7$
(thanks, Kevin Middleton) - the listings package is formally supported now (see
?render_listings
); the default style is borrowed fromSweavel.sty
written by Frank Harrell (#101) (thanks, Frank) - new package option
cache.extra
which allows more objects to affect cache; see http://yihui.name/knitr/demo/cache/ (#134) - new package option
child.path
to specify the search path of child documents relative to the parent document (#141) - new package option
aliases
to set aliases for chunk options; see http://yihui.name/knitr/options (#144) - new chunk options
fig.cap
,fig.scap
andfig.lp
to write captions, short captions, label prefix for the figure environment in LaTeX (#145) (thanks, Frank Harrell) - new package option
eval.after
to set a character vector of chunk options which should be evaluated after a chunk is executed (thanks, Frank Harrell) - a series of convenience functions
pat_rnw()
,pat_tex()
,pat_brew()
andpat_html()
to set built-in patterns (syntax) to read input
MINOR CHANGES
- package option
eval.opts
has been dropped: all options of classessymbol
orlanguage
will be evaluated, so there is no need to specify which options to evaluate manually; remember, the chunk options are similar to function arguments, so you can use any valid R code there - the default value for the
output
argument inknit()
is NULL now, so we can also provide output filenames tostitch()
andknit2pdf()
(#119) - standard LaTeX messages are suppressed when a tikz plot is compiled to PDF so that we can see the knitr process more clearly
%\SweaveInput{}
will be ignored now (#150)results=asis
will no longer affect thechunk
hook (in the past, the chunk output was not wrapped in thekframe
environment whenresults=asis
); it only affects theoutput
hook now- the package website allows comments now
MAJOR CHANGES
- the starting pattern of normal texts in an Rnw document is
^@\\s*%*
instead of^@\\s*$
now, meaning you can write@ % a comment
to end a code chunk (this is consistent with Sweave) - the default value of the argument
output
ofknit()
will be a filename under the current working directory; in previous versions, the output file will be under the same directory as the input file; this change makes it possible to completely separate the input files and output files into different places, and hopefully will give users better experience in managing a whole collection of files (including child documents): put all source files in one place and output files in another place - the package homepage is http://yihui.name/knitr now (the previous URL yihui.github.com/knitr will be automatically redirected to the new address)
BUG FIXES
- the object
opts_current
does not give the evaluated version of the current chunk options because it was created before the options are evaluated; this has been fixed andopts_current$get()
will give the expected values of options (thanks, Frank Harrell)
MISC
- number of downloads (https://github.com/yihui/knitr/downloads) of knitr documentation before I removed and updated them on GitHub: c(main = 1300, graphics = 549, themes = 130, beamer = 565, listings = 240, minimal = 160)