merge upstream

Author: rstudio

DESCRIPTION

@@ -6,6 +6,7 @@ Date: 2014-03-14
 Author: Who wrote it
 Maintainer: Who to complain to <yourfault@somewhere.net>
 Description: More about what it does (maybe more than one line)
-License: What license is it under?
+License: GPL-3
 Imports:
     rmarkdown
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,10 +1,12 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(acm)
 export(acs)
 export(ctex_template)
 export(elsevier)
+export(frontiers_article)
 export(jss_article)
 export(plos_article)
 export(rjournal_article)
+export(tufte_ebook)
 export(use_r_abstract)

R/frontiers_article.R

@@ -0,0 +1,39 @@
+#' @export
+frontiers_article <- function(keep_tex = TRUE,
+                              includes = NULL){
+  template <- system.file("rmarkdown", "templates", "frontiers_article",
+                          "resources", "template.tex",
+                          package = "rticles")
+  base <- rmarkdown::pdf_document(template = template,
+                                  keep_tex = keep_tex,
+                                  includes = includes,
+                                  highlight = "tango")#,
+                                  # pandoc_args = c("--latex-engine=xelatex"))
+
+  # Mostly copied from knitr::render_sweave
+  base$knitr$opts_knit$out.format <- "sweave"
+
+  base$knitr$opts_chunk$prompt <- TRUE
+  base$knitr$opts_chunk$comment <- NA
+  base$knitr$opts_chunk$highlight <- FALSE
+
+  hook_chunk <- function(x, options) {
+    if (knitr:::output_asis(x, options)) return(x)
+    paste0('\\begin{CodeChunk}\n', x, '\\end{CodeChunk}')
+  }
+  hook_input <- function(x, options) {
+    paste0(c('\\begin{CodeInput}', x, '\\end{CodeInput}', ''),
+           collapse = '\n')
+  }
+  hook_output <- function(x, options) {
+    paste0('\\begin{CodeOutput}\n', x, '\\end{CodeOutput}\n')
+  }
+
+  base$knitr$knit_hooks$chunk   <- hook_chunk
+  base$knitr$knit_hooks$source  <- hook_input
+  base$knitr$knit_hooks$output  <- hook_output
+  base$knitr$knit_hooks$message <- hook_output
+  base$knitr$knit_hooks$warning <- hook_output
+  base$knitr$knit_hooks$plot <- knitr:::hook_plot_tex
+  base
+}

R/jss_article.R

@@ -11,6 +11,11 @@ jss_article <- function() {
   base$knitr$opts_chunk$comment <- NA
   base$knitr$opts_chunk$highlight <- FALSE
 
+  base$knitr$opts_chunk$dev.args <- list(pointsize = 11)
+  base$knitr$opts_chunk$fig.width <- 4.9 # 6.125" * 0.8, as in template
+  base$knitr$opts_chunk$fig.height <- 3.675 # 4.9 * 3:4
+  base$knitr$opts_chunk$fig.align <- "center"
+
   hook_chunk <- function(x, options) {
     if (knitr:::output_asis(x, options)) return(x)
     paste0('\\begin{CodeChunk}\n', x, '\\end{CodeChunk}')
@@ -28,6 +33,7 @@ jss_article <- function() {
   base$knitr$knit_hooks$output  <- hook_output
   base$knitr$knit_hooks$message <- hook_output
   base$knitr$knit_hooks$warning <- hook_output
+  base$knitr$knit_hooks$plot <- knitr:::hook_plot_tex
 
   base
 }

R/tufte_ebook.R

@@ -0,0 +1,91 @@
+
+#' Tufte e-Book format (PDF)
+#'
+#' Template for creating an e-book based on the style of
+#' Edward R. Tufte and Richard Feynman.
+#'
+#' @inheritParams pdf_document
+#'
+#' @param latex_engine LaTeX engine for producing PDF output. Options are
+#'   "pdflatex", "lualatex", and "xelatex".  Note that lualatex may have
+#'   problems with text spacing, and that pdflatex may have memory issues
+#'   when using tikzDevice.
+#'
+#' @export
+tufte_ebook <- function(  toc = TRUE,
+                          toc_depth = 3,
+                          number_sections = TRUE,
+                          fig_width = 4,
+                          fig_height = 2.5,
+                          fig_crop = TRUE,
+                          highlight = "default",
+                          keep_tex = FALSE,
+                          latex_engine = "xelatex",
+                          includes = NULL,
+                          pandoc_args = NULL,
+                          ...
+                          ) {
+
+  # resolve default highlight
+  if (identical(highlight, "default"))
+    highlight <- "pygments"
+
+  # get the tufte handout template
+  template <-  system.file(
+    "rmarkdown/templates/tufte_ebook/resources/tufte-ebook.tex",
+    package = "rticles"
+  )
+
+  # call the base pdf_document format with the appropriate options
+  format <- rmarkdown::pdf_document(fig_width = fig_width,
+                                    fig_height = fig_height,
+                                    fig_crop = fig_crop,
+                                    highlight = highlight,
+                                    keep_tex = keep_tex,
+                                    latex_engine = latex_engine,
+                                    includes = includes,
+                                    pandoc_args = pandoc_args,
+                                    toc = toc,
+                                    toc_depth = toc_depth,
+                                    template = template,
+                                    number_sections = number_sections,
+                                    ...
+                                    )
+
+
+  # create knitr options (ensure opts and hooks are non-null)
+  knitr_options <- rmarkdown::knitr_options_pdf(fig_width, fig_height, fig_crop)
+  if (is.null(knitr_options$opts_knit))
+    knitr_options$opts_knit <- list()
+  if (is.null(knitr_options$knit_hooks))
+    knitr_options$knit_hooks <- list()
+
+  # set options
+  knitr_options$opts_chunk$tidy <- TRUE
+  knitr_options$opts_knit$width <- 45
+
+  # set hooks for special plot output
+  knitr_options$knit_hooks$plot <- function(x, options) {
+
+    # determine caption (if any)
+    caption <- ifelse(is.null(options$fig.cap),
+                      "",
+                      paste("\\caption{", options$fig.cap, "}\n", sep = ""))
+
+    # determine figure type
+    if (isTRUE(options$fig.margin))
+      figtype <- "marginfigure"
+    else if (isTRUE(options$fig.fullwidth))
+      figtype <- "figure*"
+    else
+      figtype <- "figure"
+
+    # return the latex
+    paste(sprintf('\\begin{%s}\n \\includegraphics{%s}\n%s\\end{%s}\n',
+                  figtype, x, caption, figtype))
+  }
+
+  # override the knitr settings of the base format and return the format
+  format$knitr <- knitr_options
+  format
+}

README.md

@@ -1,6 +1,8 @@
 ### Overview
 
-The **rticles** package includes a set of [R Markdown](http://rmarkdown.rstudio.com) templates that enable authoring of R related journal and conference submissions. Available templates include:
+The **rticles** package includes a set of [R Markdown](http://rmarkdown.rstudio.com) templates that enable authoring of R related journal and conference submissions, and creating e-books. Available templates include:
+
+- [Tuftish e-book] e-books formatted based on the style of Edward R. Tufte and Richard Feynman
 
 - [JSS](http://www.jstatsoft.org/) articles
 

inst/rmarkdown/templates/acm/resources/template.tex

@@ -1,10 +1,14 @@
 \documentclass{acm_proc_article-sp}
+\usepackage[utf8]{inputenc}
 
 \renewcommand{\paragraph}[1]{\vskip 6pt\noindent\textbf{#1 }}
 \usepackage{hyperref}
 \usepackage{graphicx}
 \usepackage{url}
 
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
 $if(title)$
 \title{$title$}
 $endif$

inst/rmarkdown/templates/acs/resources/template.tex

@@ -1,7 +1,10 @@
 \documentclass[journal=$journal$,manuscript=$type$]{achemso}
+\usepackage[utf8]{inputenc}
 \usepackage[version=3]{mhchem}
 \usepackage{amsmath}
 \newcommand*\mycommand[1]{\texttt{\emph{#1}}}
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 $for(author)$
 \author{$author.name$}
 $if(author.aff)$

inst/rmarkdown/templates/ctex/resources/default.latex

@@ -34,6 +34,10 @@ $endif$
 $if(monofont)$
     \setmonofont[Mapping=tex-ansi]{$monofont$}
 $endif$
+$if(CJKmainfont)$
+    \usepackage{xeCJK}
+    \setCJKmainfont[$CJKoptions$]{$CJKmainfont$}
+$endif$
 \fi
 % use upquote if available, for straight quotes in verbatim environments
 \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
@@ -45,10 +49,29 @@ $endif$
 $if(geometry)$
 \usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
 $endif$
+\ifxetex
+  \usepackage[setpagesize=false, % page size defined by xetex
+              unicode=false, % unicode breaks when used with xetex
+              xetex]{hyperref}
+\else
+  \usepackage[unicode=true]{hyperref}
+\fi
+\usepackage[usenames,dvipsnames]{color}
+\hypersetup{breaklinks=true,
+            bookmarks=true,
+            pdfauthor={$author-meta$},
+            pdftitle={$title-meta$},
+            colorlinks=true,
+            citecolor=$if(citecolor)$$citecolor$$else$blue$endif$,
+            urlcolor=$if(urlcolor)$$urlcolor$$else$blue$endif$,
+            linkcolor=$if(linkcolor)$$linkcolor$$else$magenta$endif$,
+            pdfborder={0 0 0}}
+\urlstyle{same}  % don't use monospace font for urls
 $if(lang)$
 \ifxetex
   \usepackage{polyglossia}
   \setmainlanguage{$mainlang$}
+  \setotherlanguages{$for(otherlang)$$otherlang$$sep$,$endfor$}
 \else
   \usepackage[shorthands=off,$lang$]{babel}
 \fi
@@ -59,9 +82,9 @@ $if(natbib)$
 $endif$
 $if(biblatex)$
 \usepackage{biblatex}
-$if(biblio-files)$
-\bibliography{$biblio-files$}
-$endif$
+$for(bibliography)$
+\addbibresource{$bibliography$}
+$endfor$
 $endif$
 $if(listings)$
 \usepackage{listings}
@@ -80,7 +103,7 @@ $if(tables)$
 \usepackage{longtable,booktabs}
 $endif$
 $if(graphics)$
-\usepackage{graphicx}
+\usepackage{graphicx,grffile}
 \makeatletter
 \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
 \def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
@@ -99,9 +122,9 @@ $if(strikeout)$
 % avoid problems with \sout in headers with hyperref:
 \pdfstringdefDisableCommands{\renewcommand{\sout}{}}
 $endif$
-\setlength{\parindent}{0pt}
-\setlength{\parskip}{6pt plus 2pt minus 1pt}
 \setlength{\emergencystretch}{3em}  % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 $if(numbersections)$
 \setcounter{secnumdepth}{5}
 $else$
@@ -122,6 +145,16 @@ $for(header-includes)$
 $header-includes$
 $endfor$
 
+% Redefines (sub)paragraphs to behave more like sections
+\ifx\paragraph\undefined\else
+\let\oldparagraph\paragraph
+\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+\let\oldsubparagraph\subparagraph
+\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+
 \begin{document}
 $if(title)$
 \maketitle
@@ -151,15 +184,15 @@ $endif$
 $body$
 
 $if(natbib)$
-$if(biblio-files)$
+$if(bibliography)$
 $if(biblio-title)$
 $if(book-class)$
 \renewcommand\bibname{$biblio-title$}
 $else$
 \renewcommand\refname{$biblio-title$}
 $endif$
 $endif$
-\bibliography{$biblio-files$}
+\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
 
 $endif$
 $endif$

inst/rmarkdown/templates/ctex/skeleton/skeleton.Rmd

@@ -12,7 +12,7 @@ output:
     number_sections: yes
     template: !expr rticles::ctex_template()
     toc: yes
-classoption: "hyperref`r if (.Platform$OS.type != 'windows') ',nofonts'`"
+classoption: "hyperref,"
 ---
 
 # 引言
@@ -33,14 +33,9 @@ classoption: "hyperref`r if (.Platform$OS.type != 'windows') ',nofonts'`"
 
 # 字体和选项
 
-LaTeX包[**ctex**](http://ctan.org/pkg/ctex)支持若干种字体选项，例如winfonts、adobefonts等，这些选项要么不跨平台通用，要么不免费。那么中文字体问题咋整？下面我们介绍两个解决办法：
+LaTeX包[**ctex**](http://ctan.org/pkg/ctex)支持若干种字体选项，如果你是**ctex**老用户，请注意这里我们要求的最低版本是2.2，你可能需要升级你的LaTeX包。从版本2.0开始，**ctex**支持根据不同操作系统自动选择中文字体，简直是为人类进步作出了巨大贡献，我们再也不必费尽口舌向用户解释“啊，你用Windows啊，那么你该使用什么字体；啊，你用Mac啊，又该如何如何”。
 
-1. 装鸵鸟，把头埋沙子里，自己默念一百遍“别人都不用Windows，我只管我的系统上的字体能用就好了”；
-2. 找一个大家都能用的中文字体，当然它得是免费的^[从隔壁王大爷那里“免费”复制过来的不算免费]，不然无法推广；
-
-## 管它什么跨平台
-
-如果不管跨平台通用，那问题会非常简单。下面是Windows用户所需要的YAML元数据，主要设置三项参数：文档类为`ctexart`（当然也可以是别的类），`latex_engine`为XeLaTeX（真的，别纠结你的旧爱PDFLaTeX了），`template`为这个**rticles**包所带的LaTeX模板（当然你也可以用你自定义的模板）。
+下面的YAML元数据应该能满足多数用户的需求，主要设置三项参数：文档类为`ctexart`（当然也可以是别的类），`latex_engine`为XeLaTeX（真的，别纠结你的旧爱PDFLaTeX了），`template`为这个**rticles**包所带的LaTeX模板（当然你也可以用你自定义的模板）。
 
 ```yaml
 ---
@@ -54,29 +49,7 @@ output:
 
 这里`template`参数用了一点YAML黑魔法，主要是R包yaml发明的，`!expr`表示这个取值是通过运行R代码得到的，若不知道`rticles::ctex_template()`是什么意思，在R里面运行一下就知道了。其它参数都是普通的`pdf_document`参数，参见文档**rmarkdown**包的文档，这里就不赘述了。
 
-关于Mac和Linux用户，目前有两种选择：要么复制别人的中文字体，例如Adobe中文字体，然后用`classoption`指定选项`adobefonts`，例如：
-
-```yaml
----
-classoption: adobefonts
-# 其它选项都跟上面一样
----
-```
-
-要么下载[Fandol字体](http://ctan.org/pkg/fandol)^[http://ctan.org/tex-archive/fonts/fandol]，它号称是免费的，不过我们也没太搞清楚它的来头。把那些.otf字体文件下载下来之后一个个安装上，苹果用户猛击鼠标安装即可，Linux用户可以把字体保存到`~/.fonts`文件夹下，然后命令行切换到那里，运行`fc-cache -fv`。YAML元数据中唯一需要修改的地方就是`classoption: nofonts`，这样ctex包会自动使用Fandol字体。
-
-```yaml
----
-classoption: nofonts
-# 其它选项都跟上面一样
----
-```
-
-未来Mac用户也许还有第三种选择，就是用macfonts选项，不过截止到记者写稿之日，这个选项还没有发布到CTAN上，想吃螃蟹的用户只能去ctex的SVN库中去找。
-
-## 不，我要普渡众生
-
-客官若是想要找一种普渡众生的方案，我们给您最好的建议就是早点发财或成名，然后号召某中文字体生产厂商开源一种好看的中文字体，或斥资买断再开彼源兮，这样我们灰头土脸的小码农们也好大胆放心宣传。
+Windows和Mac用户应该都已经有自带的中文字体了。Linux用户可以另外下载[Fandol字体](http://ctan.org/pkg/fandol)^[http://ctan.org/tex-archive/fonts/fandol]，它号称是免费的，不过我们也没太搞清楚它的来头。把那些.otf字体文件下载下来保存到`~/.fonts`文件夹下，然后命令行切换到那里，运行`fc-cache -fv`。
 
 # R代码段