NEWS.md

CHANGES IN knitr VERSION 1.2

NEW FEATURES

• 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)

MAJOR CHANGES

• 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)

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 option progress in opts_knit, e.g. after options(KNITR_PROGRESS = FALSE), this option will be set to FALSE when the package is loaded (#395)

• the global option KNITR_WIDTH can be use to set the R option width before knitr is called; in the past this option was hard-coded to 75, and now it is set as options(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 using rgl::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 and echo is numeric, code was incorrectly filtered by the indices in echo (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 print NULL 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 in knit(..., encoding = ?) is applied to knit_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 --> and `r `); internally all_patterns$foo$inline.code was changed

• the function build_dep() was removed (the warning has been there for a long time); please use dep_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 option ref.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 the Rcpp 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 expands pi is {{pi}} to pi 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 argument encoding 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 to results='asis', width=5 to fig.width=5, echo=true to echo=TRUE, keep.source=TRUE to tidy=FALSE, eps=TRUE to dev='postscript', \SweaveOpts{...} to opts_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 to 2L, 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() and stitch_rmd() which use the R HTML and R Markdown templates respectively when calling stitch()

• 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 running knit()

• accordingly, the pattern elements global.options and inline.doc were removed from knit_patterns (\SweaveOpts{} and \SweaveInput{} will no longer be supported; please call Sweave2knitr() 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 have include=FALSE (#453) (thanks, Joshua Pritikin)

• the function knit_env() is no longer available (it is not exported any more), and knit_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 option highlight = 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); use demo('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 is 0L which means to move on even if errors occurred); this makes it possible to see the call stacks via traceback() 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 option tidy.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 and out.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 neither fig.subcap nor fig.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 on read_chunk() to read demo scripts in R packages

• a new convenience function read_rforge() to read code from R-Forge repositories; combined with read_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 via purl()

• purl() gained a new argument documentation 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 for spin() 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 argument highlight to specify which highlighting engine to use (Pygments or Prettify.js) (thanks, Yanping Chen)

• two new chunk options for language engines: engine.path and engine.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 to opts_knit$set(aliases = ...), e.g. set_alias(w = 'fig.width') sets w as an alias for the chunk option fig.width

MAJOR CHANGES

• global options are strongly recommended to be set via real R code opts_chunk$set(opt = value) in a code chunk instead of the old syntax in text chunks like \SweaveOpts{opt = value}, or <!--roptions opt=value-->, etc, which will be deprecated in the next version; this will make it cleaner and safer to parse the source documents, e.g. we can write arbitrarily complicated expressions like opts_chunk$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 to engine.opts; this affects users who use Andre Simon's highlight through the highlight engine in knitr

• the chunk option file for Awk was deprecated; we can also use engine.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') is TRUE, a timestamp() 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' or engine='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 set fig.env='marginfigure' to use \begin{marginfigure} (#364) (thanks, Bryan Hanson)

• added a new package option global.device (default FALSE) which specifies whether to use a global graphics device to capture plots; if TRUE, it is possible to write plot(1:10) in a previous chunk and abline(0, 1) in a latter chunk because all code chunks share the same device, however, this may also bring unexpected consequences (in particular, using par() 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 option dependson did not actually work, e.g. dependson=c('foo', 'bar') (#350) (thanks, Cassio Pereira)

• fixed a bug when eval=FALSE and prompt=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 in 3,1415)

• if the chunk option external==FALSE (default is TRUE), knitr will no longer automatically add \usepackage{tikz} to the LaTeX preamble; you need to add it manually (but it is recommended to use external=TRUE with cache=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 after knit() 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' (default NULL) 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 calling ghc (#336) (thanks, Michel Kuhlmann)

• added support to Andre Simon's highlight through the option engine='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 and results are also respected when the language is not R, e.g. for a Python code chunk with eval=FALSE, the code will not be evaluated, or for a Ruby chunk with results='hide', the output will be hidden (#293) (thanks, Ramnath Vaidyanathan)

• chunk options out.width, out.height and out.extra also work for plots in HTML and Markdown output now, e.g. out.width='200px' or out.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 to hook_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() and hook_scianimator() which can be set as the package option opts_knit$get('animation.fun') and create animations via the R2SWF package or the SciAnimator library (see animation::saveHTML) (thanks, Taiyun Wei)

• a new function image_uri() to create data URIs for image files; we can set opts_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 option opts.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 using optipng (#272) (thanks, Winston Chang)

• added a new output hook named document in knit_hooks (see knit_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 program rst2pdf to convert reST documents to PDF; it is also supported by knit2pdf() when compiler='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 option comment=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$set() in a child document was only working in that child document, but was expected to change chunk options globally; now it works everywhere, and will affect all chunks after this setting, no matter where opts_chunk$set() is (thanks, Guy Lebanon) (http://bit.ly/MexHXd)

• fixed #332: calling purl() inside a source document when knit() the same document could cause clashes; now it is safe to put purl() inside a source document and knit() 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 as unnamed-chunk-1 and unnamed-chunk-2; in previous versions, both will be named as unnamed-chunk-1 which can cause clashes of cache and figure files

• the function build_dep() was renamed to dep_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 as center or tabular (#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 clashes

• stitch() 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 in knit2html() is passed to markdownToHTML() in the markdown package instead of knit(); 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 and results) also work for foreign languages: https://github.com/yihui/knitr/blob/master/inst/examples/knitr-lang.Rmd

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 argument report for Rnw/Rtex/Rmd documents to be compiled to PDF/HTML respectively (#287) (thanks, kohske takahashi)

BUG FIXES

• stitch() and spin() should use parent.frame() to evaluate code by default; in 0.6, the default parent frame for the inner knit() was a wrong environment to use (thanks, Michael Nelson)

• use unnamed-chunk-i as the label when chunk label == '' (#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 of out.width for animations in LaTeX is still NULL; you will have to set out.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 the knitrout 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 argument envir 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 in knit_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 (use knitr:::knit_log$get() to get all messages) and they are printed if the package option verbose is TRUE (i.e. opts_knit$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; see system.file('examples', 'child', 'knitr-main.Rmd', package = 'knitr') for an example in markdown (#268) (thanks, @martinaryee)

BUG FIXES

• the templates for stitch() used results=hide which should really be results='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 use set.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 neither Rplots.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') is TRUE (#249) (thanks, Carl Boettiger)

• the filename extensions Snw and Stex are also supported (foo.Snw/foo.Stex produces foo.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 file NA generated by pdf(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 or r 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 the R prefix, e.g. foo.Rmd produces foo.md by default; the old clumsy naming convention foo_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() and render_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, so opts_knit$set(self.contained = FALSE) can help in this case (#176) (thanks, Ramnath Vaidyanathan)

• new package option filter.chunk.end which decides if the chunk.end pattern really means chunk.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 via purl() (#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 have engine != '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 by knit_engines$set(language = function(options) {...}); see an example at system.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 was render_jekyll(); the major difference is that the code blocks are put in ```r and ```; if you want the strict markdown syntax, you can all render_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 by render_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 objects all_patterns or knit_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 of print(); 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') is TRUE, 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 by render_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 in globalenv(), e.g. setGeneric() creates S4 generic functions in globalenv() and knitr was unable to capture them (#138) (thanks, syoh)

• chunk options dev, fig.ext and dpi 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 and foo.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 use fig.cap = c('first caption', 'second caption') to assign two different captions to them respectively when fig.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 is imgur_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 function build_dep() to build cache dependencies among cached chunks automatically by analyzing object names in all cached chunks; this is a loose alternative to the dependson 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 be stdin()/stdout() or other types of connections (#162; see yihui#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 under system.files('bin', package = 'knitr') which makes it easier to call knitr via command line under *nix (call knit input [output] [--pdf])

• the inline hooks respect getOption('digits') and getOption('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 argument compiler 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 use I() 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 from Sweavel.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 and fig.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() and pat_html() to set built-in patterns (syntax) to read input

MINOR CHANGES

• package option eval.opts has been dropped: all options of classes symbol or language 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 in knit() is NULL now, so we can also provide output filenames to stitch() and knit2pdf() (#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 the chunk hook (in the past, the chunk output was not wrapped in the kframe environment when results=asis); it only affects the output 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 of knit() 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 and opts_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)

CHANGES IN knitr VERSION 0.2

NEW FEATURES

• added support for including child documents in a main document (like \SweaveInput{} but with different implementations); see http://yihui.name/knitr/demo/child/ (#92)

• for inline R code, character results are returned as-is now (without \texttt{})

• new function purl() as a wrapper to knit(..., tangle = TRUE) which extracts R code from the input document (thanks to Dieter Menne's wife who suggested the function name)

• the error hook applies to inline R code when an error occurs in the inline R code, in which case knitr will not stop by default; instead, it writes the error message into the output (#85)

• chunk option split also works for HTML output now using <iframe></iframe> (#82)

• knit() gained an argument text as an alternative to input (#88)

• new chunk option child to include child documents into the main document (#92)

• chunk option external defaults to TRUE now (was FALSE by default in the last version)

• added a new demo to show how to build package vignettes with knitr: http://yihui.name/knitr/demo/vignette/

• added support to the quartz() device under Mac (#103); now the dev option has more choices (see http://yihui.name/knitr/options)

• chunk option echo can take a numeric vector to select which R expressions to echo into the output now (#108); see http://yihui.name/knitr/options

• a new function stitch() which is a convenience function to insert an R script into a template and compile (to quickly create a report based on an R script)

• for a chunk hook to run, the corresponding chunk option no longer has to be TRUE; it can be any non-null values; this enables us to make use of the option value directly instead of only knowing it is TRUE (see http://yihui.name/knitr/demo/cache/ for an example)

• knit() will no longer writes figure or cache files in the same directory as the input document; instead, these files are written in the current working directory (see ?knit)

• a new function knit_env() that makes the environment of the current chunk accessible to the user

BUG FIXES

• the code used to merge global chunk options and local options was buggy for cache; it has been fixed now, so cache is more stable (#105), but users may see previously cached chunks being re-evaluated with this version, which should be regarded as a normal phenomenon, and on the second run, the cached chunks will not be evaluated again

• fixed a buglet when using both options out.width and out.height in Rnw (#113)

CHANGES IN knitr VERSION 0.1

NEW FEATURES

• first version of knitr: it covers most features in Sweave, cacheSweave and pgfSweave; see package homepage for documentation and examples: http://yihui.name/knitr/

MISC

• knitr won an Honorable Mention prize (before it was formally released to CRAN) in the Applications of R in Business Contest hosted by Revolution Analytics: http://bit.ly/wP1Dii http://bit.ly/wDRCPV

• in this NEWS file, #n means the issue number on GitHub, e.g. #142 is yihui#142