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