Releases | Open Source Science

rmarkdown - rmarkdown 2.29

find_external_resources() now correctly detects knitr child document provided with option like child = c("child.Rmd") (thanks, @rempsyc, #2574).
knit_params_ask() uses a select input for parameters which allow multiple selected values (#2576). Previously, a radio input was incorrectly used when the parameter had a small number of choices.

yaml params: primaries: choices: ["red", "yellow", "blue"] multiple: true

When multiple is not enabled, parameter configuration still uses radio when there are fewer than five choices.

The input parameter field can still be used to force the configuration control.

yaml params: grade: input: radio choices: ["A", "B", "C", "D", "F"]

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Published by yihui over 1 year ago

rmarkdown - rmarkdown 2.28

Add classes odd, even, and header back to table rows for Pandoc >= 3.2.1, so tables can be styled properly (thanks, @therealgenna, #2567).
beamer_presentation support handling latex dependencies via the new extra_dependencies argument and declarations within chunks (e.g., knitr::asis_output("", meta = list(rmarkdown::latex_dependency("longtable")))) (thanks, @cderv, @atusy, #2478).

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Published by yihui over 1 year ago

rmarkdown - rmarkdown 2.27

Provide a global option rmarkdown.files.suffix to configure the suffix of the directory for auxiliary files (thanks, @certara-tzweers, #2550). By default, this suffix is _files, which can cause HTML output files to be deleted automatically on Microsoft OneDrive or Google Drive. If that is the case for you, you may set a different suffix in your .Rprofile, e.g., options(rmarkdown.files.suffix = "_rmdfiles").
Fix a regression in 2.26 regarding image paths post-processing in html_document_base(). Now absolute paths to image in the output directory (output_dir) are correctly made relative to the output directory again.

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Published by yihui almost 2 years ago

rmarkdown - rmarkdown 2.26

rmarkdown now requires knitr >= 1.43.
Get rid of the superfluous warning in find_pandoc() (thanks, @jszhao, #2527).
Removed the stringr dependency since it is used only once in the package and the equivalent base R code is simple enough (thanks, @etiennebacher, #2530).
For the output format option fig_crop: auto, it will now use the same logic as in knitr to decide if cropping is possible (yihui/knitr#2246).
Avoid corrupting input files by accident (thanks, @J-Moravec, #2534).

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Published by yihui almost 2 years ago

rmarkdown - rmarkdown 2.25

Fixed a bug that filenames beginning with - cause incorrect invocation of Pandoc (thanks, @mbaynton, #2503).
Documented how to merge output_format_dependency() to the output format (thanks, @atusy, #2508).
ioslides_presentation() now correctly works with new shiny 1.7.5 (thanks, @nicolasgaraycoa, #2514, @gadenbuie, #2516).
Added a new argument metadata to the pre_knit function in output_format() so that users will have access to the YAML metadata of the input document before knitting it (#2485). Please note that if you define pre_knit for a custom output format, you are strongly recommended to leave a ... argument in pre_knit, so we (rmarkdown package authors) are free to add more arguments to pre_knit without breaking your code. If your pre_knit function does not have the ... argument, you will get a warning.

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Published by yihui over 2 years ago

rmarkdown - rmarkdown 2.24

Fixed file_scope being lost when extending output formats that considers the file_scope using output_format(). Merge behavior is to apply overlay file_scope function onto the result of base_format's file_scope function. This implies that file_scope gains second argument which receives the returned values of the base file_scope (thanks, @atusy, #2488).
Added output_format_dependency() which allows extending output format from within chunks (thanks, @atusy, #2462)
Fix an issue with shiny prerendered document where dependencies context were written twice leasing to parsing error (thanks, @gadenbuie, rstudio/learn#597, #2500).

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Published by yihui over 2 years ago

rmarkdown - rmarkdown 2.23

find_external_resources() works with formats defining there own theme argument, like cleanrmd::html_document_clean(), not related to bslib supports (thanks, @gadenbuie, #2493, r-lib/pkgdown#2319).
Fixed version number comparison problems as requested by CRAN.

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Published by yihui over 2 years ago

rmarkdown - rmarkdown 2.22

Using css with .scss and .sass file, or with a bslib theme, now works as expected with a shiny runtime (thanks, @cpsievert, #2443, #2447).
Add a pandoc_metadata_file_arg() function to match Pandoc's CLI flag --metadata-file.
Mentions that webshot or webshot2 is required to take screenshot of HTML widget. When not installed, an error message mentionning always_allow_html: true solution will be shown, but setting this is not the solution (quarto-dev/quarto-cli#4225).
html_dependency_jqueryui() updated to 1.13.2 from version bundled in shiny (thanks, @daschnerm, #2477).
Fix an issue with YAML header ending with a commented line containing incomplete yaml (thanks, @keithnewman, #2483).
When code folding is enabled in html_document(), the text on the button to show the content has been changed from "Code" to "Show", because the content to show is not necessarily code, e.g., yihui/knitr#2227.

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Published by yihui over 2 years ago

rmarkdown - rmarkdown 2.21

Now HTML output formats use the Font Awesome HTML dependency from the fontawesome package instead of shipping an outdated version of Font Awesome in rmarkdown (thanks, @rich-iannone, #2451).
Fixed a bug caused by a change in the is_blank() function in xfun 0.38 (thanks, @andreahgsin, #2469).

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Published by yihui almost 3 years ago

rmarkdown - rmarkdown 2.20

The defunct tufte_handout() has been removed from rmarkdown. Please use tufte::tufte_handout() instead.
If an input path to rmarkdown::render() is a symbolic link, it is no longer resolved to its real path (thanks, @SamDM @jmw86069, #1508).
Make sure to avoid creating invalid paths when copying resources (thanks, @mnazarov, #2429).
Make sure logo is properly embedded in ioslides_presentation() when self_contained = TRUE (thanks, @mnazarov, #2428).

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Published by yihui about 3 years ago

rmarkdown - rmarkdown 2.19

No longer use xfun::isFALSE() internally.

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Published by yihui about 3 years ago

rmarkdown - rmarkdown 2.18

rmarkdown::render() argument output_file is now used for all output formats, if there is only one name for multiple output formats (thanks, @MaelAstruc, #2421).
Custom output formats can provide a custom function to convert Markdown input to the desired output format now. To do so, define the output format via output_format(pandoc = pandoc_options(convert_fun = function(...) {})). The default converting function is pandoc_convert() in this package. See the help page ?pandoc_options for more details.

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Published by yihui over 3 years ago

rmarkdown - rmarkdown 2.17

rmarkdown::render_site() will now also look for index.rmd in addition to index.Rmd for custom site generator in YAML with site: (thanks, @kamalsacranie, #2409).
Icons in tabset dropdown are now correctly shown, including when self_contained: false (thanks, @cpsievert, #1697).

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Published by yihui over 3 years ago

rmarkdown - rmarkdown 2.16

Pandoc 2.19 has deprecated the argument --self-contained. If you have installed Pandoc 2.19+, rmarkdown will use --embed-resources --standalone as recommended by Pandoc for output formats that use the option self_contained = TRUE (#2382).
pandoc_version() returns a version number of the form X.Y.Z.YYYY.MM.DD for the nightly build of Pandoc now, where YYYY.MM.DD is its build date. Previously it would return X.Y.Z.9999 to indicate the nightly version.

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Published by yihui over 3 years ago

rmarkdown - rmarkdown 2.15

Fix navbar issue with website when using Boostrap 5 with bslib (thanks, @guasi, #2379, @cpsievert, #2384).
The tufte_handout() function inside rmarkdown is defunct now. Its codebase was moved to the tufte package in 2016, and this function was marked as deprecated in 2021. Please use tufte::tufte_handout() instead of rmarkdown::tufte_handout(). The latter will be removed eventually from this package.
github_document() gains math_method = "default" and defaults to it. No special processing will be done to inline maths in $ and block maths in $$ as now Github supports it and will render using Mathjax (thanks, @kylebutts, #2361).

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Published by yihui over 3 years ago

rmarkdown - rmarkdown 2.14

Improved highlighting theme arrow regarding accessibility.
Fixed an issue with site_generator() detection of a site project (thanks, @bhattmaulik, #2344).
Fixed an issue with Shiny prerendered documents and Pandoc not correctly rendering last Markdown paragraph in HTML (thanks, @gadenbuie, #2336).
Fixed a bug that site_generator() fails to detect the root dir of the site and causes infinite recursion (thanks, @fisher-j, #2339).
html_vignette() gains code_folding argument (thanks, @atusy, #2340).
html_document() can opt-out code_folding = "show" or "hide" for individual code blocks by adding the fold-none class to the code blocks (thanks, @atusy, #2348).
When using a development version of Pandoc, a .9999 suffix is appended to version number so that pandoc_available() can correctly compared version with last release.

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Published by yihui almost 4 years ago

rmarkdown - rmarkdown 2.13

Fix an issue with older R version and vignette building (#2324).
Fix an issue with older R version and preserve_yaml = TRUE in md_document() (#2325).
Long title in ioslides_presentation failed to work with Pandoc 2.17.x (thanks, @Am386DX-40, #2327).

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Published by yihui almost 4 years ago

rmarkdown - rmarkdown 2.12

html_document() and html_document_base() gains the math_method argument to support all the math rendering engines from Pandoc: "mathjax", "katex", "mathml", "webtex", and "gladtex". For backward compatibility, the mathjax argument still works and will take precedence over math_method, but we recommend using the new math_method argument instead of the mathjax argument, and the latter could be deprecated in the future.

You can specify a math engine via math_method as an engine name, e.g.,

yaml output: html_document: math_method: katex

or provide both a name and a URL (for mathjax, katex and webtex):

yaml output: html_document: math_method: engine: mathjax url: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml-full.js

For math_method = "katex", KaTeX CDN will be inserted in version 0.15.2 by default (from jsdelivr). A custom URL toward another CDN can be passed as url.

For math_method = "webtex", it will default to inset SVG using https://latex.codecogs.com/svg.image?. Use https://latex.codecogs.com/png.image? for PNG. See https://latex.codecogs.com for supported options (dpi, background, ...).

Most HTML output format using html_document() or html_document_base() as based format should benefit from this new feature. See ?rmarkdown::html_document() for details (thanks, @atusy, #1940).

github_document() also gains the math_method argument set to "webtex" by default so that LaTeX equations can be rendered in the Github Markdown document as images. Previously, LaTeX equations were not rendered. Set math_method = NULL to deactivate.
Added support for katex R package as a math engine with math_method = "r-katex" in HTML documents. This method offers server-side rendering of all the equations, which means no JS processing is needed in the browser as with usual KaTeX or MathJaX methods. (thanks, @jeroen, #2304).
anchor_sections can now be easily customized using style or depth element for anchor_sections. For example:

yaml output: html_document: anchor_sections: style: symbol # use symbol style ("hash", "symbol", "icon") depth: 2 # max depth to apply anchor on (default to max which is 6)

Customizing using a CSS rule is still possible. Detailed explanation and examples have been added to the help page ?html_document.

Improved the highlighting mechanism in formats that supports highlight argument:
- It is now possible to pass a custom theme file .theme in highlight argument for customizing the syntax highlighting style used by Pandoc.
- In addition to Pandoc's own supported themes, two more themes are bundled in the package: highlight: arrow a theme optimized for accessibility and color constrast (thanks to @apreshill), and highlight: rstudio to mimic the RStudio editor theme.
- For HTML output only, added optional downlit support in html_document() for R syntax highlighting and autolinking. Use highlight_downlit = TRUE to activate it (same argument as in distill). This features require the downlit package.
Templates for html_document() and ioslides_presentation() gained a new CSS rule to display single line <summary> content inline (rstudio/rstudio#10589).
md_document() gained a new standalone argument, which is FALSE by default unless toc = TRUE. This allows to output authors, date and other metadata per the Pandoc's template. Due to limitation in how Pandoc is handling metadata blocks in its extensions yaml_metadata_block, preserve_yaml = TRUE now deactivate any extension to let rmarkdown directly handle the keeping of YAML block - this means it does not set standalone = TRUE by default. Meanwhile, github_document() gained the preserve_yaml argument (thanks, @florisvdh, #2297).
Added available_templates() to list all the templates from a specific package that can be used with rmarkdown::draft().
Following support in Pandoc 2.15, powerpoint_presentation() gained a incremental argument as other slide formats. As a reminder, setting incremental = TRUE will make lists to display incrementally. See more in Pandoc's MANUAL.
Added support for Pandoc's dir variable in HTML templates. This is the second Language Variables after lang.
Added a global option rmarkdown.html_dependency.header_attr (TRUE by default). It can be set to FALSE to opt-out the HTML dependency html_dependency_header_attrs() in documents based on html_document_base() (thanks, @salim-b rstudio/bookdown#865, @maelle r-lib/downlit#1538).
Rendering using runtime: shiny_prerendered or runtime: shinyrmd now natively supports custom templates. Previously since 2.8, developers had to add a special comment, , conditionally to shiny-prerendered variable. (See also NEWS from 2.8 for the previous behavior). The new behavior inserts required special comment  as a last element of $header-includes$ . If templates rely on the old behavior and require some contents between $header-includes$ and , consider including them with $header-includes$ (thanks, @atusy, @gadenbuie #2249).
A shiny prerendered document with only a empty server context does not error anymore. Document will be rendered with a empty server function and server.R file will be ignored. To use server.R, no server context should be present in the Rmd document (thanks, @jcheng5, #2305).
Fixed a regression with rendering shiny_prerendered document (thanks, @aronatkins, @gadenbuie, #2218).
Fixed an issue in beamer_presentation() where header-includes would be overwritten by includes = list(in_header =) (thanks, @samcarter, #2294). Same fix as for pdf_document() (#1359).
Fixed broken links to section headers when number_sections = TRUE is specified in md_document and github_document (thanks, @atusy, #2093).
draft() now works with devtools::load_all() and testthat when used in other packages.
Lua Filters: Added two more functions in shared.lua for other package to use:
- Added type() function backward compatible following Pandoc 2.17 changes.
- Added print_debug() for easier logging during debug.

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Published by yihui almost 4 years ago

rmarkdown - rmarkdown 2.11

Relative paths in parent directories in the css argument of html_document() were incorrectly normalized to absolute paths by #2095 in v2.8. Now relative paths in parent directories will no longer be converted to absolute paths (thanks, @daijiang, yihui/xaringan#331).
It is possible to specify the version of jQuery via a global option now, e.g., options(rmarkdown.jquery.version = 2) (note that the default major version is 3). This is mainly for advanced users and developers to test different versions of jQuery.
pandoc_citeproc_convert() now handles correctly bib file containing specific UTF-8 characters on non default UTF-8 systems like Windows (thanks, @mitchelloharawild, #2195).
Shiny prerendered documents are now pre-rendered in a child environment to avoid allowing the results of static code chunks to exist in the Shiny app environment (@gadenbuie, #2203).
The previously unexported function convert_ipynb() is exported now (thanks, @acircleda).

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Published by yihui over 4 years ago

rmarkdown - rmarkdown 2.10

md_document() will now handle correctly preserve_yaml value for all variants and all pandoc versions (#2190).
- with preserve_yaml = TRUE, markdown output will keep the YAML metadata block from the Rmd file.
- with preserve_yaml = FALSE, markdown output will have no YAML metadata block.

This fixes a breaking change in Pandoc 2.13 regarding gfm, commonmark and commonmark_x which now supports yaml_metadata_block by default (#2118).

New supported syntax for Shiny prerendered documents: you can now use server: shiny or server: type: shiny.
Ability to inject additional functions into Shiny prerendered server scope using the "server-extras" context.
Fixed the syntax highlighting issue with R's pipe operator |> (thanks, @edzer, rstudio/bookdown#1157).

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Published by yihui over 4 years ago

rmarkdown - rmarkdown 2.9

Fix a regression in version 2.8 when a url is used in css argument (thanks, @vnijs, #2163).
All HTML dependencies are now correctly supported, included those with only an href component but not file component in their src attribute. Previously, rmarkdown would throw the error 'path for html_dependency not provided' when rendering documents containing HTML dependencies with href components (thanks, @crazycapivara, @matthewstrasiotto, #1805, #1948, #2151).
Fix an error thrown with output format using a file_scope function (like in bookdown) (thanks, @rfaelens, #2149).
Fix an issue with copy_ressource = TRUE in html_document_base where very long HTML documents were truncated during post processing (thanks, @oliviermeslin, #2145).
When run()-ing a runtime: shiny document, an extra temp folder will be used in the output path. With the extra temp random folder in the path, predictable output file names may be used. (#2137)
When run()-ing a runtime: shiny document with a {bslib} theme, the global theme value wasn't being restored properly. (#2160)
Floating ToC in html_document can now hide headings with unnumbered and unlisted classes (thanks, @atusy, #1993).
Fix prefix handling in R Markdown website's navbar for Fontawesome V5 and compatibility with V4. For icon only available in V5, the full prefix + name should be use, especially with new fab prefix (e.g. fab fa-r-project). If no prefix is used (e.g fa-home instead of fas fa-home), the fa prefix will be added for V4 compatibility as it has been deprecated in V5. We advice to use the full prefix + name for icons following Fontawesome documentation. (#1994)
rmarkdown::site_generator() can hang session waiting for input when the site field is not found in the YAML frontmatter of index.Rmd (thanks, @kevinushey @mirh, #2043).

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Published by yihui over 4 years ago

rmarkdown - rmarkdown 2.8

Fix a issue with Pandoc 2.5 and latex-div.lua - documents can now be rendered as expected without error (thanks, @davidwales, #2121).
Fix an issue with styling and code folding button behavior when default is code-folding: show. The Button can now be correctly style according to state as aria-expanded attributes is correctly updated. Also, new classes has been added on the button to allow styling during transition: btn-collapsing and btn-expanding are respectively applied during transition Show to Hide and Hide to Show. (This follow Bootstrap behavior for the collapsible block) (thanks, @steveharoz, #2085).
Fix an issue with citation_package having no effect when using .md file as input to render() with latex and PDF output formats (thanks, @andrewheiss, #2113).
A new internal option rmarkdown.knit.ext has been added to control the extension of the intermediary knit output during a rendering. It defaults to md to produce *.knit.md. Only useful for very advanced usage (#2098).
render() won't produce any *.utf8.md intermediary file anymore. This was a leftover from previous versions of rmarkdown. Since knitr 1.24 and rmarkdown 2.0, only UTF-8 input files are allowed. (#2098).
Fix an Invalid cross-device link error when tempdir() is used for intermediates_dir in render() (thanks, @gorgitko, #2096).
Fix a regression in HTML default template with floating toc incorrectly placed on small size window (thanks, @grimbough, #2071)
Provided a runtime: shiny fix for output formats that pass a modified bslib::bs_theme() object to html_document_base()'s theme (thanks, @cpsievert, #2049).
Rendering using runtime: shiny_prerendered or runtime: shinyrmd will now produce valid HTML by not inserting anymore the full document as body in the resulting shiny apps (thanks, @dakep, #1912). Header content usually containing html dependencies will be inserted in the HTML document at the end of the head before </head>, unless the rendered HTML contains  special comment (see htmltools::renderDocument()). A new Pandoc variable is set in for shiny prerendered document to allow conditional insertion of such content in the the HTML template using $if(shiny-prerendered)$ . This has been done in all HTML template in this package. Users of custom template should make this change to provide support for this runtime. See rmarkdown default template (default.html) for an example (#2064).
Added tectonic as a supported LaTeX engine for generating PDF output (thanks, @dpryan79, #2078). You can specify to use this by adding engine: "tectonic" to your output format in YAML, such as pdf_document.
When no output_format is provided in any way but an output_file is provided in render(), the default format will be determined based on the extension: "pdf_document" for .pdf, or "word_document" for .docx. Otherwise, it will be "html_document" as previous version (thanks, @pearsonca, #1569).
Added a new global option rmarkdown.render.message. When set FALSE, render() will not output the message starting by Output created: allowing RStudio IDE to open a preview of the document. This is useful for package developers that would need to emit there own output message for there custom format. See ?render_site for more info on this special message (#2092).
Internal changes regarding Lua filters. They have now an explicit Pandoc version minimal requirement: A filter will be skipped with a warning printed by the Lua filter if this requirement is not met. For now, all filters work for Pandoc 2.1 and above (thanks, @atusy, #2088). There is also now a new mechanism to have a share Lua filter script loadable by other Lua files: render() will set the RMARKDOWN_LUA_SHARED env var to the path of Lua filter shared.lua so that other filters can access functions defined in it using dofile(os.getenv 'RMARKDOWN_LUA_SHARED'). This is for internal usage only to avoid duplication (thanks, @tarleb, #2103).
html_document_base gains a css argument, to which html_document's css argument is now passed. This also fix an issue when .sass or .scss files are used with this css argument when self_contained: FALSE. Moreover, sass caching mechanism can now be used when passing .sass or .scss files to the css argument (thanks, @cpsievert, #2095).
The fig_crop option of PDF document formats (such as pdf_document and beamer_presentation) supports the value "auto" now, which means fig_crop = TRUE when figure cropping tools pdfcrop and ghostscript are available.
The default value of the fig_crop option of PDF output formats has been changed from TRUE to "auto" (#2077).
rmarkdown::tufte_handout has been deprecated and will be removed in the future from this package. It has been moved to the tufte package since rmarkdown 0.9.5 (released on 2016-02-22). Please use tufte::tufte_handout instead.

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Published by yihui almost 5 years ago

rmarkdown - rmarkdown 2.7

html_document (and html_document_base)'s theme parameter now understands bslib::bs_theme() objects/arguments, meaning that one may opt-into Bootstrap 4 and more easily create custom themes. For examples, see https://github.com/rstudio/rmarkdown/pull/1706, and for context, see https://rstudio.github.io/bslib/ (thanks, @cpsievert, #1706).
Files with .scss/.sass extension (i.e., Sass files) provided to html_document's css parameter are now compiled to CSS using the {sass} package. Also, if theme is a {bslib} object, these Sass files may utilize Sass code inside the theme (thanks, @cpsievert, #1706).
Fix an issue with line numbering in code chunks when .numberlines with Pandoc's highlighting (thanks, @aosavi, #1876).
Fix an issue with shiny runtime and global.R (thanks, @liaojiahui-r, rstudio/flexdashboard#298).
Accept latex="{options}", latex=1, or latex=true for Latex Divs.
Add output_format_filter function to default_site_generator(). Enables custom site generators to customize or even entirely replace the output format right before rendering of each page.
Automatically exclude renv directory for render_site() (thanks, @jmbuhr, #1996)
Do not force options(htmltools.preserve.raw = TRUE) when this option has been set, otherwise it is impossible for other packages to turn this option off, e.g., yihui/xaringan#293.
knitr_options_pdf() will now throw a warning when fig_crop = TRUE but is disabled because required tools pdfcrop and/or ghostscript are missing (thanks, @netique, #2016).
Eliminated the unnecessary padding in code blocks in the html_document output with Bootstrap 4 themes (thanks, @atusy, #2019).
github_document() will produce a working TOC even if some headers start with number (#2039).
Fix an issue with knit_print.data.frame. The ... arguments are no more passed to print() to avoid passing knit_print() arguments options and encoding to custom print() methods (#2047).

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Published by yihui about 5 years ago

rmarkdown - rmarkdown 2.6

Encoding is correctly handled now in html_vignette when checking for identical title and vignette index entry (thanks, @py-b, #1978).
clean_site() now default to preview = TRUE and will no more remove files without notice. This change will affect the "Clean All" button in the "Build" pane for website project. clean_site(preview = FALSE) must be run to effectively remove files (#1973).
The intermediate .tex file is now correctly deleted if keep_tex = FALSE when the R Markdown document is not rendered from the working directory (thanks, @vqv, #1308).
Fix a bug causing certain resources files to be deleted as intermediate files when intermediates_dir is the same as the input (thanks, @bellma-lilly, #1248).
Fix issues with anchor_sections = TRUE and learnr (thanks, @gadenbuie, #1938).
Enable use of server.R and global.R alongside runtime: shinyrmd documents.
pkg_file_lua() now works with devtools::load_all() and testthat when used in other packages.
Fix pandoc_convert(citeproc = TRUE) not supressing the --natbib or --biblatex options (thanks, @atusy, #1932).
pandoc-citeproc is now activated if a bibliography field is defined in another YAML block instead of the first YAML block (thanks, @bwiernik, #1364).
Specify that htmltools::htmlPreserve() should use the pandoc raw attribute rather than preservation tokens when pandoc >= v2.0. Note that this option will have the intended effect only for versions of htmltools >= 0.5.0.9003.
anchor_sections in html_documents() now defaults to FALSE. It was introduced in previous version with a default to TRUE, but it is reverted now after hearing feedbacks from the community (thank you!). The # is still used as the character for the anchor but you can easily change that using CSS rules. Examples have been added to the help page ?html_document.
Using Pandoc's default for --email-obfuscation now. Previously, it was set to none explicitly, which is the default for Pandoc 1.17.2+ anyway. Only users with a Pandoc version before 1.17.2 may see a change in the content of the html source file produced if the document contains email addresses. This change allows to pass the Pandoc's command line flag if you want to set it to another value (thanks,@seankross, #1969).

yaml output: html_document: pandoc_args: ["--email-obfuscation", "javascript"]

See Pandoc's manual for the meaning of this option.

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Published by yihui about 5 years ago

rmarkdown - rmarkdown 2.5

Tables without header rows (wich can be possible in Pandoc's simple table) are now formatted correctly when using html_document() format (thanks, @fkohrt, #1893).
html_document gains the anchor_sections argument, which is TRUE by default, so that readers can get links to section headers easily---when you mouse over a section hader, you will see a hash symbol # at the end of the header, which contains the anchor link to this header. You can click on this link and get the URL in the addres bar of your web browser, or right-click on it and copy the URL from the context menu. The hash symbol is defined by the CSS rule a.anchor-section::before {content: '#';}. You can customize it by overriding this rule (e.g., via the css argument of html_document) and use any other symbols or icons, e.g., content: "\02AD8;" (thanks, @atusy, #1884).
pkg_file_lua() should have thrown an error if the expected Lua file does not exist.
Provide files_dir and intermediates_dir as attributes on return from render() when run_pandoc = FALSE.
Supports new Pandoc 2.11 --citeproc flags usage instead of pandoc-citeproc external filter. pandoc_convert() and pandoc_citeproc_convert() will now use the correct flags according to the Pandoc version used. The logic is exported in pandoc_citeproc_args(). See Pandoc release note for more information about the new citeproc processing (#1916).
Fixed the code highlighting when code block is hidden. Previous version introduced a regression where non default code highlighting was still shown when code_folding is activated and code block is hidden (thanks, @matthewcarlucci, #1921).
The minimal required version for the xfun package (v0.15) has been specified for R Markdown Notebooks to work properly (thanks, @jmcphers, #1923).
Fixed a bug in convert_ipynb() when the language is not specified in the .ipynb file (thanks, @acca3003, #1925).
Introduce runtime: shinyrmd as a more user friendly alias for runtime: shiny_prerendered.

- R
Published by yihui over 5 years ago

rmarkdown - rmarkdown 2.4

Lua filters handling has been improved internally with some user-facing changes (#1899):
- New exported function pandoc_lua_filter_args() to return the Pandoc command-line argument to add a Lua filter.
- New argument lua_filters in pandoc_options() to pass the Lua filter paths to use with a format. This allow output format authors to add filters for a custom format using the pandoc argument of output_format() and to get filters from a format using fmt$pandoc$lua_filters.
- The Lua filters of an output format are now passed to Pandoc in render(). By default, they are passed to Pandoc before any other format-defined or user-defined Pandoc arguments (usually via the pandoc_args option of an output format). This ensures that filters of an output format are executed first. To change the default, you need to deal with it in a custom format (i.e., modify the elements in fmt$pandoc$lua_filters, such as reordering them).
- New exported function pkg_file_lua() to get the full system path of a Lua filter included in a package source within the inst/rmarkdown/lua folder (thanks, @atusy, #1903).
Fixed the path separators for the css parameter in YAML frontmatter for HTML output files under Windows. Previously, forward slashes in css paths were converted to backslashes (thanks, @jonathan-g, #1862).
Since rmarkdown 1.16, Pandoc's fenced Div's are converted to LaTeX environments when the output format is LaTeX, e.g., ::: {.center data-latex=""} is converted to \begin{center}. The attribute data-latex of the Div was mandatory, even if it is empty. In rmarkdown 2.2, we silently drop this requirement, which means ::: {.center} is converted to \begin{center}. This turns out to be a bad idea, because users have no control over which Div's to be converted to LaTeX environments. Previously, they could opt-in by the data-latex attribute, but with rmarkdown 2.3, all Div's are converted to LaTeX environments unconditionally. What's more, this change led to bugs like https://stackoverflow.com/q/62340425/559676 and https://github.com/rstudio/bookdown/issues/883. Therefore the data-latex attribute became mandatory again in this version. If the LaTeX environment does not need arguments, you may use data-latex="".
The two Lua fitlers pagebreak.lua and latex-div.lua (introduced in rmarkdown 1.16) are also applied to the output format beamer_presentation now (thanks, @XiangyunHuang, #1815).
When customizing formats with the output_format function, pre_knit, opts_hooks, and knit_hooks can now refer to rmarkdown::metadata. Previously, rmarkdown::metadata returned list() in these functions (thanks, @atusy, #1855).
rmarkdown::find_external_resources() now discovers external template files. This in turn fixes the rendering issue of html_document with the shiny runtime and intermediate_dir set (thanks, @atusy, @cderv, #1865).
Added the number_sections argument to following formats: github_document, ioslides_presentation, md_document, odt_document, powerpoint_presentation, rtf_document, slidy_presentation, word_document. These are powered by a Lua filter and requires Pandoc > 2.0. It will silently have no effect has before with previous pandoc version (thanks @atusy 1893). Pandoc >= 2.10.1 adds --number-sections for docx format, and thus word_document prefers the native feature to the Lua filter (thanks, @jooyoungseo, #1869).
For the output format pdf_document, the option fig_crop will not be enabled unless both the programs pdfcrop and ghostscript are found (thanks, @dalupus, yihui/knitr#954).
Fixed a bug that a chunk with a class fold-hide hides the rest of the chunks even the output format setting html_document(code_folding = "show") (thanks, @atusy, #1906).
Updated documentation for render() to make it clearer how options are set for the output_format parameter (thanks, @jonathan-g, #1907 and rstudio/bookdown#930).
Ported some CSS styles (e.g., underlines, small caps, and multi-column layouts) from the latest Pandoc's HTML template into rmarkdowns HTML templates (thanks, @atusy, #1878, #1908).

- R
Published by yihui over 5 years ago

rmarkdown - rmarkdown 2.3

Addressed an accessibility issue in highlighted code blocks of HTML output for screen reader users: screen readers no longer read out an unnecessary code line id values (thanks, @jooyoungseo and @atusy, #1833).
Added file_scope option to output format definition. This enables handling of duplicate numeric footnote identifiers (e.g. across bookdown chapters) via the pandoc --file-scope option (#1837).
Added the customizable lang attribute to ioslides_presentation output (thanks, @jooyoungseo, #1841).
Added publish_site() function for "one-button" publishing of R Markdown websites.
When the df_print option is kable and the output format is not HTML, <div class="kable-table"> is no longer added to the kable() output, because recent versions of Pandoc will convert the div to a LaTeX environment when the output format is LaTeX (thanks, Laurens, https://stackoverflow.com/q/62340425/559676).
html_vignette() only warns against differences in the vignette title and the vignette index entry for R >= 3.6.0 (thanks, @krlmlr, #1832).
html_document() can apply code_folding on any chunk engines if the foldable class is added to a source code block via the chunk options (class.source or attr.source). You may apply this feature to all the source code blocks, for example, by setting knitr::opts_chunk$set(class.source = "foldable") at the beginning of your document (thanks, @atusy, #1835).

- R
Published by yihui over 5 years ago

rmarkdown - rmarkdown 2.2

Exported the internal function find_pandoc(), and also added two arguments, dir and version, so that users can provide a custom directory under which this function may find Pandoc, as well as an expected version of Pandoc to be found (thanks, @connorp, #1785).
pandoc_metadata_arg() is a new Pandoc helper function to generate --metadata argument for Pandoc command line (thanks, @cderv, #1789).
The output format html_vignette() now warns against differences in the vignette title specified in the title field in the YAML metadata and the one specified inside \VignetteIndexEntry{}. Normally they are expected to be identical (#1789).
Fixed a bug with encoding when rendering html_notebook containing HTML widgets (thanks, @cderv, #1799).
TOC title can now be specified for html_document via the top-level option toc-title in the YAML frontmatter (thanks, @atusy, #1771).
Floating TOC can now distinguish upper/lower-cases (thanks, @atusy, #1783).
When code_folding='show' for the output format html_document, code blocks can be individually hidden initially by specifying the chunk option class.source='fold-hide' (thanks, @atusy, #1798).
For LaTeX/PDF output formats pdf_document, beamer_presentation, and context_document, the argument citation_package = 'none' was deprecated, and citation_package = 'default' should be used instead if citations are to be processed by pandoc-citeproc (thanks, @njbart, rstudio/bookdown#754).
output_format() can now inherit keep_md and clean_supporting from base_format when NULL is passed to these arguments. Previously, you must explicitly specify keep_md and/or clean_supporting as TRUE or FALSE in output_format() since they could not inherit the corresponding options of base_format. This behavior was not consisent with other arguments of output_format() (thanks, @atusy, #1823).
The smart argument of most output formats has been removed, because Pandoc's smart extension is enabled by default, and setting smart: false for an output format did not really have any effect (which could be considered a bug, but we want to get rid of this option since it existed only for a historical reason for Pandoc 1.x, and Pandoc 2.x has been released for more than two years). If you want to disable the smart extension, you can use the option md_extensions: -smart of the output format (thanks, @atusy, #1774).
pdf_document() should not specify the geometry variable when the documentclass variable is passed to Pandoc (thanks, @jpcirrus, #1782).
render() now respects the YAML metadata in the R script when rendering the script with Pandoc 2.8 or later (thanks, @nsoranzo #1740, @cderv #1741).
For pandoc_convert(), when the argument to = 'pdf', it will be changed to 'latex' internally (thanks, @JohannesFriedrich, #1802).
render(run_pandoc = FALSE) no longer cleans up the Markdown file (typically knitted from Rmd) (thanks, @BrianDiggs, #1812).

- R
Published by yihui over 5 years ago

rmarkdown - rmarkdown 2.1

Added the returned output from shiny::runApp() within rmarkdown::run() (thanks, @schloerke, #1760).
YAML header is now correctly parsed in html_notebook's intermediate .knit.md file so that features like adding bibliography works again (thanks, @everdark, @cderv, #1747).
ioslides_presentation template no longer generates an empty <h2> tag when subtitle is not specified in YAML (thanks, @jooyoungseo #1735, @cgrudz #1663).
No longer center the #header element in the html_vignette() output (thanks, @EmilHvitfeldt, #1742).
Ensure the tempdir() exists (via tempdir(TRUE)) when writing HTML dependencies to a temporary file, because this directory might be erased by accident (thanks, Kurt Hornik, and also @karawoo #1743).
Added the slide_level argument to slidy_presentation() (https://stackoverflow.com/q/59157211/559676).
Removed the jQuery dependency in html_document_base() (#1723). To avoid bugs like #1723, Pandoc 2.8 users have to upgrade to Pandoc 2.9+.
For pdf_document, horizontal rules generated by Pandoc (before v2.8) stopped working in recent versions of TeX Live, and the same fix as the one to https://github.com/jgm/pandoc/issues/5801 (i.e., hard-code \linethickness to 0.5pt) was applied in rmarkdown (thanks, @cderv, https://stackoverflow.com/a/58646915/559676).

- R
Published by yihui about 6 years ago

rmarkdown - rmarkdown 2.0

For the output format pdf_document(), we no longer adjust the vertical spacing of the title area. This means there will be a larger spacing above the document title in PDF. If you prefers the old (smaller) spacing, please download https://github.com/rstudio/rmarkdown/blob/f6961af/inst/rmd/latex/compact-title.tex and include it to the preamble via the includes option of pdf_document. However, please note that this means you won't be able to have multiple authors in the author field of the YAML frontmatter, unless you use a custom LaTeX template. With the default LaTeX template, you will run into the error in #1716. Besides, the compact-title option in YAML is no longer supported.
R code in the header-includes field in the YAML frontmatter stopped working in the previous version of rmarkdown. The code should be evaluated before passing to Pandoc (thanks, @mcol #1709, @cderv #1710).
The encoding argument is no longer passed to the intermediates_generator of R Markdown output formats. The intermediates_generator function can only accept arguments input_file and intermediates_dir now (see ?rmarkdown::output_format). This is a breaking change to developers. If you are an output format developer, you have to remove the encoding argument in your intermediates_generator if your output format uses this function.
The encoding argument is no longer passed to the render element of the site generator (see ?rmarkdown::render_site).
The encoding argument has been removed from many of the internal functions in the rmarkdown package. Now all input files are assumed to be encoded in UTF-8. If you see an error message like "Error in FUN(arg = ...): unused argument (arg = ...)", please file an issue (with a reproducible example) to https://github.com/rstudio/rmarkdown.
Added a new output format context_document() to support ConTeXT output (thanks, @RLesur #1725, @jooyoungseo #1713).
render_site() can render R scripts in addition to Rmd files if you set autospin: true in _site.yml (thanks, @zeehio, #1564).
Added ext argument to md_document(). Its default value is ".md". This argument is intended to be used together with variant argument (e.g., variant = "context" and ext = ".pdf") (thanks, @atusy, #1715).
ioslides_presentation() stylesheet is updated for printing. Browsers are notified that the presentation should preferentially be printed in landscape orientation and without margin (thanks, @RLesur, #1718).
Reverted the fix #1703 and applied an alternative fix to #1700, because the original fix brought a new bug #1714 (thanks, @pablobernabeu @cderv @everron @aronatkins).
Tabsets don't work with Pandoc 2.8 (thanks, @mnazarov, #1723).
The pdf_document format failed to work if the header-includes field in YAML is an empty list (thanks, @cderv, #1728).

- R
Published by yihui about 6 years ago