# -*- mode: org -*-
#+OPTIONS:  LaTeX:t

* Sweave and org-mode
  If you're reading a PDF version of this document, you should also
  look at [[file:testing.Rorg][testing.Rorg]] (the source file) and [[file:testing.org][testing.org]] (the output
  of the Sweave process).

  Keep in mind that one of the advantages of a block-based approach is
  using \texttt{C-'} to edit code in its native mode.

** Use the Sweave package for latex formatting
   Org allows us to issue commands to be included in \{LaTeX} export.
#+LATEX_HEADER:  \usepackage{Sweave}

** R blocks
   The first argument to an R block when using Sweave is the label for
   that block.

   Not all R blocks are printed.  Sweave options allow the printing of
   the evaluated code, the output of the code, both, or neither.

*** R code that is not printed
#+BEGIN_R:  hidden_block, echo=FALSE, results=HIDE
   a <- 3
   b <- 6
#+END_R

*** R code that is printed
#+BEGIN_R:  visible_block
   c <- 4
#+END_R
   
   We can use block labels to embed blocks by reference (even if they
   weren't printed before).
*** R code that references other blocks
#+BEGIN_R:  combined_block
#+R_CODEREF:  hidden_block
#+R_CODEREF:  visible_block
   a + b +c
#+END_R

** Inline references to R data
   We can evaluate R code inline.
*** Used in text
    The value of =a= is \R{a}.

*** Used in a table
    | a     | b     | c     | TOTAL         |
    |-------+-------+-------+---------------|
    | \R{a} | \R{b} | \R{c} | \R{a + b + c} |

** Single-line R commands
   If we want a line of R code to be evaluated but not printed,
   there's a convenient shorthand.  This only works for single lines
   of R code, but you can have more than one in a row.
#+R:  library(lattice)
#+R:  data(cars)

** Graphics
   We use values defined elsewhere in the buffer to produce this
   graph.  The new CAPTION and LABEL arguments work just fine.

#+CAPTION:  speed by distance
#+LABEL:  fig:speed_by_distance
#+BEGIN_R fig=TRUE, eps=FALSE, pdf=TRUE
print(xyplot(speed ~ dist, cars,
       panel = function (x, y, ...) {
         panel.xyplot(x, y, ...)
         panel.abline(h=a)
         panel.abline(v=b)
       }))
#+END_R