Sweave {utils}

R Documentation

Automatic Generation of Reports

Description

Sweave provides a flexible framework for mixing text and S code for automatic report generation. The basic idea is to replace the S code with its output, such that the final document only contains the text and the output of the statistical anlysis.

Usage

Sweave(file, driver = RweaveLatex(),
       syntax = getOption("SweaveSyntax"), ...)

Stangle(file, driver = Rtangle(),
        syntax = getOption("SweaveSyntax"), ...)

Arguments

file	Name of Sweave source file.
driver	The actual workhorse, see details below.
syntax	An object of class SweaveSyntax or a character string with its name. The default installation provides SweaveSyntaxNoweb and SweaveSyntaxLatex.
...	Further arguments passed to the driver's setup function.

Details

Automatic generation of reports by mixing word processing markup (like latex) and S code. The S code gets replaced by its output (text or graphs) in the final markup file. This allows a report to be re-generated if the input data change and documents the code to reproduce the analysis in the same file that also produces the report.

Sweave combines the documentation and code chunks together (or their output) into a single document. Stangle extracts only the code from the Sweave file creating a valid S source file (that can be run using source). Code inside \Sexpr{} statements is ignored by Stangle.

Stangle is just a frontend to Sweave using a simple driver by default, which discards the documentation and concatenates all code chunks the current S engine understands.

Hook Functions

Before each code chunk is evaluated, a number of hook functions can be executed. If getOption("SweaveHooks") is set, it is taken to be a collection of hook functions. For each logical option of a code chunk (echo, print, ...) a hook can be specified, which is executed if and only if the respective option is TRUE. Hooks must be named elements of the list returned by getOption("SweaveHooks") and be functions taking no arguments. E.g., if option "SweaveHooks" is defined as list(fig = foo), and foo is a function, then it would be executed before the code in each figure chunk. This is especially useful to set defaults for the graphical parameters in a series of figure chunks.

Note that the user is free to define new Sweave options and associate arbitrary hooks with them. E.g., one could define a hook function for option clean that removes all objects in the global environment. Then all code chunks with clean = TRUE would start operating on an empty workspace.

Syntax Definition

Sweave allows a very flexible syntax framework for marking documentation and text chunks. The default is a noweb-style syntax, as alternative a latex-style syntax can be used. See the user manual for details.

Author(s)

Friedrich Leisch

References

Friedrich Leisch: Dynamic generation of statistical reports using literate data analysis. In W. Härdle and B. Rönz, editors, Compstat 2002 - Proceedings in Computational Statistics, pages 575–580. Physika Verlag, Heidelberg, Germany, 2002. ISBN 3-7908-1517-9.

Friedrich Leisch: Sweave User Manual, 2008
http://www.stat.uni-muenchen.de/~leisch/Sweave

See Also

RweaveLatex, Rtangle

Examples

testfile <- system.file("Sweave", "Sweave-test-1.Rnw", package = "utils")

## enforce par(ask=FALSE)
options(device.ask.default=FALSE)

## create a LaTeX file
Sweave(testfile)

## This can be compiled to PDF by
## Not run: tools::texi2dvi("Sweave-test-1.tex", pdf=TRUE)
## or outside R by
## R CMD texi2dvi Sweave-test-1.tex
## which sets the appropriate TEXINPUTS path.

## create an S source file from the code chunks
Stangle(testfile)
## which can be sourced, e.g.
source("Sweave-test-1.R")

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