packrat/lib/x86_64-apple-darwin15.6.0/3.6.0/rmarkdown/NEWS.md

In adnaniazi/krauseNiazi2019Analyses: Reproducible analysis for tailfindr paper

rmarkdown 1.13

• For pdf_document(), do not override margins to 1 inch when a custom document class or geometry settings are specified in the YAML front matter (thanks, @adunning, #1550)

• The default value of the encoding argument in all functions in this package (such as render() and render_site()) has been changed from getOption("encoding") to UTF-8. We have been hoping to support UTF-8 only in rmarkdown, knitr, and other related packages in the future. For more info, you may read https://yihui.name/en/2018/11/biggest-regret-knitr/.

• The option toc_float: true for html_document now preserves the text formatting (thanks, @codetrainee, #1548).

• For the output_file argument of render(), a file extension will be automatically added if the filename does not contain an extension (e.g., render('foo.Rmd', 'html_document', output_file = 'bar') will generate bar.html); see the help page ?rmarkdown::render for details (thanks, @apreshill, #1551).

• TOC items are not correctly indented when toc_float is enabled for the html_document format (thanks, @carolynwclayton #1235 and @RLesur #1243).

• Fixed rstudio/shiny#2307 where the second execution of a shiny_prerendred document with href dependencies would cause a prerender check error (thanks, @schloerke, #1562).

• The *_files directory is not properly cleared due to the inappropriate fix for #1503 and #1472 in the last version (thanks, @wxli0 #1553, @cderv #1566).

• Added an output_extensions argument to pdf_document() to make it possible to enable/disable Pandoc extensions for the LaTeX output format (thanks, @hongyuanjia, rstudio/bookdown#687).

rmarkdown 1.12

• Fixed file extensions of output files when using non-markdown Pandoc extensions such as docx+styles (#1494, @noamross).

• Added a new argument extra_lines to latex_dependency() to allow users to add extra lines of LaTeX code after \usepackage{}. Also added a helper function latex_dependency_tikz() based on latex_dependency() (#1502, @malcolmbarrett).

• Fixed #1529: when the path of an Rmd file contains Unicode characters that cannot be represented in the system native encoding (especially on Windows), rmarkdown::render() may fail.

• Applied a correct fix to an old plotly issue ropensci/plotly#463.

• HTML widgets used to be hidden when printing ioslides to PDF in Chrome. Now they will be printed correctly.

• render(output_format = 'all') may delete the figure directories that are still needed by certain output formats when one output format doesn't need its figure directory (thanks, @rmcd1024 #1472, @cderv #1503).

• The <em> tags in the subtitle, date, and author are removed from the default HTML template (thanks, @royfrancis, #1544).

rmarkdown 1.11

• Fixed #1483, which prevented the triangle to be displayed in Firefox when <details><summary>...</summary></details> was used (#1485, @bisaloo)

• Provided rmarkdown.pandoc.args as a knitr package option in knitr::opts_knit (#1468, @noamross).

• Added the exported function pandoc_exec(), which returns the path of the pandoc binary used by the package (#1465, #1466 @noamross).

• new_session: true in _site.yml causes render_site() to render each file in a new R session, eliminating some cross-file difficulties, such as function masking (#1326, #1443 @jennybc).

• Added the LaTeX command \passthrough in the default LaTeX template for the --listings flag of Pandoc (rstudio/bookdown#591).

• The icons in flexdashboard::valueBox() are not of the full sizes due to the upgrade of FontAwesome in #1340 in the previous version (#1388, rstudio/flexdashboard#189).

• Added the ability to generate tabset dropdowns, usable by adding the .tabset-dropdown class to a header (e.g., # Heading {.tabset .tabset-dropdown}) (#1405). Thanks @stefanfritsch for contributing the necessary code for this (#1116).

• The darkly theme (a darker variant of the Bootswatch flatly theme) has been added to html_document and html_notebook (#1409, #889).

• Fixed a regression that caused scrollbars on code blocks when the syntax highlighting theme is not the default (#654, #1399).

• Fixed #1407: reactive expressions can break the section headers of Shiny R Markdown documents.

• Fixed #1431: render() with the intermediates_dir argument when the output format is powerpoint_presentation with a custom reference_doc fails to find the reference document.

• Fixed the website navbar not being able to display submenus properly (#721, #1426).

• Added checks for shiny-prerendered documents to find all html dependencies, match all execution packages, and match the major R version (#1420).

• Added an argument cache = TRUE to the internal function rmarkdown:::find_pandoc(), so that users can invalidate the cached path of Pandoc via rmarkdown:::find_pandoc(cache = FALSE) (thanks, @hammer, #1482).

• Added an RStudio project template for simple R Markdown websites, so that users can create such websites from RStudio: New Project -> New Directory -> Simple R Markdown Website (thanks, @kevinushey, #1470).

• Fixed #1471: Pandoc's (version 2.x) syntax highlighting themes don't work well with the Bootstrap style (thanks, @gponce-ars #1471, @cderv #1489).

• Fixed the warnings in #1224 and #1288 when calling render() with an absolute output_dir or intermediates_dir.

• Fixed #1300: calling render() with intermediates_dir may fail when the intermediate dir is on a difference device or filesystem.

• Fixed #1358: calling render() with intermediates_dir will fail if the Rmd document contains bibliography files that are dynamically generated.

rmarkdown 1.10

• Added a new argument slide_level to powerpoint_presentation() (#1270).

• The tinytex package has become a required dependency (to build R Markdown to PDF).

• Added compact-title variable to the LaTeX default templates to control use of LaTeX titling package; defaults to true (#1284).

• pdf_document(template = NULL) does not work (#1295).

• Restore ability to use any HTML format with R Markdown Websites (#1328).

• Add options argument to paged_table() to enable explicit passing of display options.

• Add pandoc_citeproc_convert() function for conversion of bibliography files (e.g. BibTeX files).

• Update to Font Awesome version 5.0.13 (#1340).

• Add site_resources() function for computing resource files required for a website.

• Export default_site_generator() function.

• The latex_document() format should not clean up the figure directory (thanks, @emiltb, rstudio/bookdown#582).

• Enable post processors that change the output file to specify that the base post processor should still be applied to the original output file.

rmarkdown 1.9

NEW FEATURES

• Added a new (experimental) output format powerpoint_presentation. If you want to test it, you will need Pandoc >= 2.1 (#1231).

MAJOR CHANGES

• If the tinytex package is installed, PDF output is built through tinytex::latexmk(), otherwise it is generated by rmarkdown:::latexmk(), which has been factored out and improved in the tinytex package, so it is recommended that you install the tinytex package (#1222).

BUG FIXES

• Temporary files created in render() may be cleaned up prematurely, which can cause problems with Shiny R Markdown documents (#1184).

• Further improvements regarding compatibility with Pandoc 2.0, e.g. tabbed sections don't work (https://community.rstudio.com/t/3019).

• When preserve_yaml = TRUE in md_document(), toc = TRUE fails to create the table of contents (thanks, @stla, #1216).

• Suppress confusing error messages from knitr::purl() during rmarkdown::find_external_resources() (thanks, @aronatkins #1247, and @paulobrecht #1154).

• Fixed the obscure error Error: path for html_dependency not found:, which was due to the HTML dependency of highlight.js (thanks, @bborgesr, #1213).

rmarkdown 1.8

BUG FIXES

• render_site() does not work with _site.yml that does not have the output setting (#1189).

• The variables input and output do not work in Shiny R Markdown documents (#1193).

• ioslides_presentation fails to embed images (#1197).

• With Pandoc 2.x, github_document() generates the wrong filename extension .gfm-ascii_identifiers instead of .md, and line height of code blocks in the HTML preview is too big (#1200).

rmarkdown 1.7

• Fixed an issue with df_print: paged where row names where not printed and added support for rownames.print option to control when they print.

• Add smart option for word_document() format.

• Save render intermediates when generating beamer presentations (fixes #1106).

• Fixed issues when specifying NULL/null/empty parameter values (#729 and #762).

• Better error message when unable to prerender a document. (#1125)

• shiny::renderText() does not work in Markdown section headings (#133).

• The value argument of pandoc_variable_arg() can be missing now (#287).

• Background colors and images are supported for ioslides presentations (#687).

• HTML widgets in an Rmd document cannot be rendered if another Rmd document is rendered via rmarkdown::render() in this document (#993).

• Try harder to clean up temporary files created during render() (#820).

• Wrong environment for evaluating R code chunks in Shiny R Markdown docs (#1162, #1124).

• Do not call bibtex to create the bibliography when there are no citations in the document and the output format is pdf_document() with citation_package = 'natbib' (#1113).

• render() will stop if the output format is PDF but there are any errors during building the index or bibliography (#1166).

• beamer_presentation() doesn't work when citation_package != 'none' (#1161).

• File-based inputs don't work in parameterized documents (#919).

• rmarkdown is compatible with Pandoc 2.0 now (#1120).

• render() with intermediates_dir fails with R plots (#500).

• Added two new output formats latex_document() and latex_fragment() (#626).

• Relative paths of images in HTML output should not be resolved to absolute paths (#808).

• render_site() does not support multiple output formats for a single Rmd (#793).

• Unicode characters may be scrambled when downloading the Rmd source file using the download button generated by html_document(code_download = TRUE) (#722).

• Upgraded highlight.js from v1.1 to v9.12.0 (#988, #907).

• The argument keep_md = TRUE actually preserves the Markdown output file from knitr::knit() now (as documented). Previously, it generates a new Markdown file by concatenating the YAML metadata (title, author, date) with the body of the original Markdown output file (#450).

• For md_document(), when variant == 'markdown' and perserve_yaml = TRUE, the Pandoc argument --standalone should not be used (#656).

rmarkdown 1.6

• Fixed an issue where headers with non-ASCII text would not be linked to correctly in the table of contents.

• Support code folding for bash, python, sql, Rcpp, and Stan chunks.

• Provide rmarkdown.pandoc.id_prefix as Knit option

• Fixed two issue with df_print: paged, one would prevent rendering data with lists of lists and the other where the column type would get cut off.

• Better support for citation_package: biblatex in pdf_document() (#1062).

• On certain Windows platforms, compiling LaTeX to PDF may fail because system2(stdout = FALSE) is not supported, in which case the default system2() will be used (#1061).

• Allow paged tables to render even when page load / visibility has a long delay

rmarkdown 1.5

• Fixed an issue where code within Shiny pre-rendered documents was not rendered correctly.

• Add includes parameter to html_fragment format.

• Use RStudio redirection URL to replace deprecated MathJax CDN

rmarkdown 1.4

• data.table expressions involving := are no longer automatically printed within R Markdown documents. (#829)

• Fix #910: the extra_dependencies argument of pdf_document() does not work when no code chunks contain LaTeX dependencies.

• The extra_dependencies of pdf_document() can also take a character vector of LaTeX package names, or a named list of LaTeX package options (with names being package names), which makes it much easier to express LaTeX dependencies via YAML.

• Automatically ignore packrat directory for render_site

• Fix #943: escape end tags in shiny_prerendered code contexts

• Add support for sticky tabs in html_document via tabset-sticky class

• Process Rmd files with lowercase extension (.rmd) in render_site

• Fix stack space consumption issues with large JS payloads in chunks

• Add section_divs argument to html_document and html_fragment to control generation of section tags/divs.

• Remove data-context="(data|server|server-start)" chunks from HTML served to client in shiny_prerendered

rmarkdown 1.3

• Fix v1.2 regression in ordering of CSS for ioslides_presentation.

• Fix rendering of pagedtables within html_notebook format.

• Ensure that html_prerendered UI is never cached.

• Add citeproc argument to YAML header; controls whether pandoc-citeproc is used (#831)

rmarkdown 1.2

• Add support for df_print to handle additional dplyr classes: grouped_df, rowwise_df and tbl_sql.

• Add new runtime: shiny_prerendered mode for interactive documents.

• Prepend "section-" to ids in runtime: shiny[_prerendered] to eliminate potential conflicts with shiny output ids

• Use html_dependencies for highlight.js, pagedtables, slidy, ioslides, & navigation (improved dependency behavior for runtime: shiny[_prerendered])

• Serialize runtime: shiny[_prerendered] dependencies to JSON rather than .rds

• ioslides: check for null before concatenating attr["class"] (#836)

• Add rmarkdown.onKnit/onKnitCompleted package hooks

• Non-ASCII keys in yaml file should be marked to UTF8 as well, when read into R as the name of a list (#841)

• Remove key-column special-case left alignment in pagedtables (#829)

• Replace backslashes in floating TOC headings (#849)

• Suggests rather than Imports for tibble (R 3.0 compatibility)

• Add paged_table function for printing paged tables within HTML documents

• Support {.active} attribute for setting initially active tab (#789)

• Add knit_root_dir argument to render() and YAML header, a convenience for setting knitr's root.dir option

• Improve alignment of text in sub-topics for floating TOC

• Bibliography file paths in YAML containing forward slashes could not be rendered (#875)

rmarkdown 1.1

• Fixed an issue where attempts to render an R Notebook could fail if the path contained multibyte characters.

• Fixed an issue where the default Beamer template did not provide vertical padding between paragraphs with certain versions of pandoc (<= 1.17.2).

• Try to install latexmk automatically on Windows

• Added df_print option to html_document format for optionally printing data frames using knitr::kable, the tibble package, or an arbitrary function

• Fix for render_site not showing Chinese characters correctly

• Fix for ignoring knit_meta that is explicitly passed to render

• Parameter editing: don't allow NULL to overwrite previous state

• Parameter editing: fix incorrect name for parameters with expressions

• Parameter editing: allow multiple values when the parameter is configured to use a "multiple" selector

• Switched the order in which format dependencies are added for html_document so that extra_dependencies are added at the end, after bootstrap, etc. (#737)

• pdf_document(keep_tex = TRUE) will generate the .tex document even if PDF conversion fails (#779).

• Move latex header includes to just before \begin{document}

• Special 'global' chunk label for runtime: shiny which designates a chunk to be run once and only once in the global environment (startup performance improvement for multi-user shiny documents)

• Ensure supporting files are writeable (#800)

• Make the "show code" buttons more CSS-friendly (#795)

• Exclude output_dir from site files (#803)

• Export navbar_html and yaml_front_matter functions

rmarkdown 1.0

• toc_float no longer automatically sets toc = TRUE

• Added an argument error to pandoc_available() to signal an error when (if error = TRUE) pandoc with the required version is not found.

• Added html_notebook format for creating HTML documents that include source code and output.

• Added resolve_output_format function (useful for front ends that need to mirror the default format resolution logic of render).

• Added code_download option to html_document to provide an option to embed a downloadable copy of the Rmd source code within the document.

• Added slide_level option to ioslides_presentation to set the level of heading used for individual slides.

• Added hard_line_breaks option to github_document to deal with change in behavior of GitHub's markdown renderer with respect to line breaks.

• Use "markdown_strict" rather than "markdown" for pandoc_self_contained_html when pandoc >= 1.17 (pandoc hanging bug was fixed in this version)

• Default highlighting engine for html_document now highlights bash, c++, css, ini, javascript, perl, python, r, ruby, scala, stan and xml

• Added print sub-option to toc_float to control whether the table of contents appears when user prints out the HTML page.

• Added readme option to html_vignette which automatically creates a package level README.md (for GitHub) in addition to rendering the vignette.

• Support for keep_md in html_vignette format.

• Try to install the latexmk package automatically on Windows if the executable latexmk.exe exists.

rmarkdown 0.9.6

• Ability to set opts_hooks in knitr_options() (#672)

• Added render_site and related functions for rendering collections of documents within a directory as a website.

• Ability to define html_document navigation bar using simple yaml format.

• Added pre_knit and post_knit hooks for output formats.

• Discover LaTeX dependencies and add them to the .tex preamble (#647)

• Added new all_output_formats function to enumerate all output formats registered for an Rmd.

• Change fig_caption default to TRUE for all formats

• Change fig_retina to 2 for HTML formats (no longer contingent on fig_caption)

• Ensure pandoc binary exists before binding to pandoc directory (#632)

• Handle relative paths for 'default_output_format' (#638)

• Eliminate duplicate viewport meta tag from html_document

• Added biblatex biblio-style support to the LaTeX template for Pandoc 1.15.2 (#643)

• Allow override of header font-size in html_document custom css (#652)

• Fix for horizontal scrollbars appearing w/ code folding (#654)

• Specifying toc_float in html_document now automatically sets toc = TRUE

• Enable per-header opt-out of toc-float via {.toc-ignore} attribute

• Correctly handle soft line breaks in ioslides_presentation (#661)

• Don't use text-muted for code folding btns (text visibility in non-default themes)

• Fix for rendering non-HTML formats from .md files (resolve runtime before knit)

• html_dependency_bootstrap now accepts theme = "default" argument

• Use pandoc 1.17.0.2 compatible LaTeX template when pandoc >= 1.17.0.2

• Support custom template for ioslides_presentation

• Added analytics option for ioslides_presentation for Google Analytics

• Removed the extra tag <p></p> around HTML output (typically generated by htmltools) from code chunks, to avoid invalid HTML like <p><div>...</div><p> (#685)

rmarkdown 0.9.5

• Added odt_document format for OpenDocument Text output

• Added rtf_document format for Rich Text Format output

• Added github_document format for GitHub Flavored Markdown output

• Only apply white background for themed HTML documents (#588)

• Added to the default HTML template to make it work better with mobile browsers. (#589)

• Specify --filter pandoc-citeproc after custom pandoc args

• Long lines in code blocks will be wrapped in the html_vignette() output (#595)

• Added new arguments run_pandoc = TRUE and knit_meta = NULL to render(). See the help page of render for details. (#594)

• The tufte_handout format now delegates to the tufte package and no longer provides a base template.

• Use pandoc 1.15.2 compatible LaTeX template when pandoc >= 1.15.2

• Fix issue with Beamer template and pandoc 1.15.2

• Updated embedded JQuery to v1.11.3 and Bootstrap to v3.3.5.

• Expose core HTML dependencies for use by custom R Markdown formats.

• New html_document themes: "lumen", "paper", "sandstone", "simplex", & "yeti".

• Ability to include bootstrap navbar for multi-page html_document websites

• Added support for abstract field to html_document format

• Added support for floating table of contents (via tocify) to html_document

• Added support for tabsets via use of {.tabset} class on top-level headings

• Added support for folding/unfolding of R code chunks in html_document

• Support url references in CSS files for runtime: shiny

• Change name of common options file to _output.yml

• Tweak pandoc conversion used in pandoc_self_contained_html to prevent hanging with large script elements (use "markdown" rather than "markdown-strict" as input format)

• The filename extension .bib will be removed before bibliography files are passed to Pandoc when the output is LaTeX/PDF and the citation package natbib or biblatex is used on Windows. This is because bibtex in MikTeX will always add the extension .bib to bibliography files, e.g. it treats foo.bib as foo.bib.bib. (#623)

• Render Shiny documents in a clean environment; fixes issue in which code in Shiny documents could access internal R Markdown state

rmarkdown 0.9.2

• Added a fix to #580 for Windows users.

rmarkdown 0.9.1

• Fix for a bug causing certain files to be deleted as intermediate files. (#580)

• PDF/LaTeX output no longer uses natbib as the citation package by default. If you do want to use natbib or biblatex, you may still use the argument citation_package = 'natbib' or 'biblatex'. (#577)

rmarkdown 0.9

• Fix for JS exception in slidy_presentation when served from the filesystem (don't call pushState for file:// urls)

• Escape single quotes in file paths

• Fix for missing resources when rendering a filename with shell characters

• For PDF/LaTeX output, citations are processed via natbib or biblatex instead of pandoc-citeproc. The ciation package natbib or biblatex can be chosen using the argument citation_package in pdf_document(), beamer_presentation(), and tufte_handout(). LaTeX is compiled to PDF via latexmk (https://www.ctan.org/pkg/latexmk/); if it is not installed, a simple emulation will be used (run pdflatex/xelatex/lualatex, bibtex, and makeindex a few times). You are recommended to install latexmk, and please note latexmk requires a Perl installation (this is important especially for Windows users).

• Always use the graphics package for PDF output

• Fix for the error "cannot change value of locked binding for 'metadata'" when one call of rmarkdown::render() is nested in another one (#248)

• Fix for an issue causing image paths to be rendered incorrectly in Windows when rendering an html_document with self_contained: false and a path is passed in argument output_dir. (#551)

• Add always_allow_html option for preventing errors when html_dependencies are rendered in non-HTML formats (e.g. pdf_document or word_document).

• Fix for an issue causing resources not to be discovered in some documents containing an empty quoted string ("") in an R chunk.

rmarkdown 0.8.1

• Support for table of contents in word_document (requires pandoc >= 1.14)

• Support for opts_template in knitr options

• Don't implicitly discover directories when scanning for dependent resources

• Fix for slide numbers not showing up in ioslides when served from the filesystem (don't call pushState for file:// urls)

• Remove inlining of bootstrap CSS (was workaround for bug now fixed in pandoc)

• Allow specifying an R file in calls to find_all_resources

rmarkdown 0.8

• Add support for keep_md to word_document

• Increase pandoc stack size to 512M (often required for base64 encoding e.g. larger embedded leaflet maps). Stack size can also be controlled by the pandoc.stack.size option.

• Allow YAML front matter to be terminated with ...

• Automatically generate a user-interface (via a Shiny application) for user specification of values in parameterized reports.

• Add tightlist macro for compatibility with pandoc >= 1.14

• Bugfix: Don't merge render params recursively with knit_params

• Bugfix: Handle slashes correctly on Windows for slidy_presentation when self_contained = FALSE

rmarkdown 0.7

• Add latex_engine option to beamer_presentation format

• Ensure that when LANG=en_US pandoc receives en_US.UTF-8 (prevent hang)

• Generate MathJax compatible output when using html_fragment format.

• Use pandoc built-in template for Beamer

• Use pandoc 1.14 compatible LaTeX template when pandoc >= 1.14

• Inline bootstrap.min.css to workaround pandoc 1.14 base64 encoding issue

• Add support for discovering references to external resources when the document output format is PDF

• Fix several issues causing pandoc errors when an intermediates directory is used, including during render for Shiny documents

rmarkdown 0.6

• Support for parameterized reports. Parameter names and default values are defined in YAML and can be specified via the 'params' argument to the render function

• 'md_extensions' option to enable/disable markdown extensions for input files

• Automatically discover and include dependent resources (e.g. images, css, etc.) for interactive documents.

• Added pandoc_version function.

• Use VignetteEncoding directive in html_vignette format

• Fix issues related to use of non-ASCII characters in ioslides_presentation

• Non-ASCII characters in the YAML data are not marked with the UTF-8 encoding when they are read into R, so character strings in rmarkdown::metadata may be displayed incorrectly (#420)

• Various improvements to tufte_handout format

rmarkdown 0.5.1

• Add 'dev' option to output formats to specify output device for figures

• Enable use of footnotes in titles of LaTeX documents

• Various improvements related to directory detection/handling on Windows

rmarkdown 0.4.2

• Sync to the latest LaTeX and Beamer templates from pandoc-templates

• Switched from the Bootstrap 2 web framework to Bootstrap 3. This is designed to work with Shiny >= 0.10.3, which has made the same switch

• Add CSS to restore responsive image behavior from Bootstrap 2

• Use a more subtle treatment for inline code in Bootstrap themed documents

• Improved support for multiple authors in ioslides

• Workaround for poor rendering of ioslides multi-columns lists in Safari 8

• Serve index.html as fallback default file for rmarkdown::run

rmarkdown 0.3.11

Initial release to CRAN

adnaniazi/krauseNiazi2019Analyses documentation built on June 9, 2019, 7:22 p.m.