R_rmarkdown_reference.R

#' ---
#' title: "rmarkdown::render snippets"
#' subtitle: "R code snippets for scripts enhanced with rmarkdown `#'` markup"
#' author: "Lorenzo Gaborini"
#' date: ""
#' output: 
#'   html_document:
#'     toc: true
#'     toc_float: 
#'       collapsed: false
#'     self_contained: true
#' ---
#' \newcommand{\tuple}[1]{\langle #1 \rangle}

#+ include=FALSE
knitr::opts_chunk$set(clean = FALSE)
knitr::opts_knit$set(progress = FALSE)

#' # Setup chunk options
#' 
library(knitr)

#' Remove knitr progress bar during page build:
#+ eval=FALSE
knitr::opts_knit$set(progress = FALSE)

#' Enable knitr cache:
#+ eval=FALSE
knitr::opts_chunk$set(cache = TRUE, 
                      clean = FALSE, 
                      autodep = TRUE, 
                      cache.comments = FALSE,
                      cache.path = 'cache/')

#' Clear knitr cache:
#+ eval=FALSE
knitr::opts_chunk$set(cache.rebuild = TRUE)

#' Auto pretty print:
#+ eval=FALSE
library(printr)

#' # Chunks without R comments
#' 
#' rmarkdown::render supports echoing R code used to build a chunks.  
#' R comments can be suppressed in echoed code using chunk option `tidy`.
#' 
#' ## Within global options
#' 
#' Change all chunks in the current document:
#' 
#+ eval=FALSE
knitr::opts_chunk$set(tidy = TRUE, tidy.opts = list(comment = FALSE))

#' ## Using a chunk template
#' 
#' Change only selected chunks.
#' 
#' Within global options, we can specify a chunk template:
knitr::opts_template$set(nocomments = list(tidy = TRUE, tidy.opts = list(comment = FALSE)))
#' Template usage: set `opts.label` for a new chunk  
#' `#+ opts.label="nocomments"`
#' 
#' ## Results
#' 
#' Without template:

#+ eval=FALSE
choose.method <- 'ML'
# choose.method <- 'fixed'
# choose.method <- 'exact'

#' With template:
#' 
#+ opts.label="nocomments"
choose.method <- 'ML'
# choose.method <- 'fixed'
# choose.method <- 'exact'



#' # pandoc markdown extensions
#' 
#' `pandoc` markdown extensions are supported: see [reference](http://rmarkdown.rstudio.com/authoring_pandoc_markdown.html#pandoc_markdown).
#' 
#' ## TeX's `newcommand`  
#' 
#' Set just after YAML header!
#' 
#' `\newcommand{\tuple}[1]{\langle #1 \rangle}`  
#' 
#' `$\tuple{a, b, c}$` inserts: $\tuple{a, b, c}$
#' 

#' 
#' # R matrices to $\LaTeX$
#' 
#' This function converts an R matrix to LaTeX inline code:
bmatrix <- function(x, digits = NULL, display = TRUE, pre = '', post = '', ...) {
   library(xtable)
   default_args = list(
      include.colnames = FALSE,
      only.contents = TRUE,
      include.rownames = FALSE,
      hline.after = NULL,
      comment = FALSE,
      print.results = FALSE
   )
   passed_args = list(...)
   calling_args = c(list(x = xtable(x, digits = digits)),
                    c(passed_args,
                      default_args[setdiff(names(default_args), names(passed_args))]))
   if (display){
      pre.tag <- '$$'
      post.tag <- '$$'
   } else {
      pre.tag <- ''
      post.tag <- ''
   }

   return(cat(
      pre.tag,
      pre,
      "\\begin{bmatrix}\n",
      do.call(print.xtable, calling_args),
      "\\end{bmatrix}",
      post,
      post.tag
   ))
}

#' The call:  
#' must use chunk option `results='asis'`
#+results='asis'
bmatrix(diag(2))

#' ## Adding a prefix to the line
#' 
#' ### The wrong ways
#' 
#' With TeX prefix on separate line:  
#' $A =$
#+results='asis', echo=FALSE
bmatrix(diag(2))

#' With TeX displaymath prefix on separate line:
#' $$A =$$
#+results='asis', echo=FALSE
bmatrix(diag(2))

#' Inline equations
#' **not working**
#' `r bmatrix(diag(2))`
#' 
#' Inline equations 2: 
#' inlinemath **not working**
#' $`r bmatrix(diag(2))`$
#' 
#' Inline equations 3: 
#' displaymath **not working**
#' $$`r bmatrix(diag(2))`$$
#' 


#' ### The correct way
#' 
#' Using `bmatrix` with prefix, and `+results='asis'`:
#+results='asis'
bmatrix(diag(2), pre='A =')

#' ### Constant matrices
#' 
#' We can inline $\LaTeX$ constant matrices using pure $\LaTeX$ markup:
#' 
#' $$\mathbf{X} = \left[\begin{array}
#' {rrr}
#' 1 & 2 & 3 \\
#' 4 & 5 & 6 \\
#' 7 & 8 & 9
#' \end{array}\right]
#' $$


#' 
#' # Completely ignore rmarkdown chunks
#' 
#' Sometimes `include=FALSE` is not sufficient, one would like to omit sections from the resulting report.  
#' It is possible to ignore entire chunks and markdown text (i.e. lines starting with `#'`).
#' 
#' Just add C++ style comments:
1

#' Below, an ignored markdown line with R code:
#' 

# /*
#' ignored markdown line
2
# */
#' Above, ignored markdown chunk:
#' 
3