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NEWS
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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](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://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**](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.)