NEWS

		 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](https://github.com/yihui/knitr-examples/blob/master/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](https://github.com/yihui/knitr-examples/blob/master/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://github.com/downloads/yihui/knitr/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**](http://cran.r-project.org/package=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
  https://github.com/yihui/knitr/issues/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://github.com/downloads/yihui/knitr/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
  https://github.com/yihui/knitr/issues/142