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CHANGES IN knitr VERSION 0.9
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@yihui yihui released this 25 May 21:30
· 4283 commits to master since this release
v0.9
29442ea

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

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