Sweave: Automatic Generation of Reports

Description

Sweave provides a flexible framework for mixing text and R/S code for automatic report generation. The basic idea is to replace the code with its output, such that the final document only contains the text and the output of the statistical analysis: however, the source code can also be included.

Usage

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

Arguments

file

Path to Sweave source file. Note that this can be supplied without the extension, but the function will only proceed if there is exactly one Sweave file in the directory whose basename matches file.

driver

the actual workhorse, (a function returning) a named list of five functions, see ‘Details’ or the Sweave manual vignette.

syntax

NULL or an object of class SweaveSyntax or a character string with its name. See the section ‘Syntax Definition’.

encoding

The default encoding to assume for file.

…

further arguments passed to the driver's setup function: see section ‘Details’, or specifically the arguments of the R...Setup() function in RweaveLatex and Rtangle, respectively.

Syntax Definition

Sweave allows a 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 further details.)

If syntax = NULL (the default) then the available syntax objects are consulted in turn, and selected if their extension component matches (as a regexp) the file name. Objects SweaveSyntaxNoweb (with extension = "[.][rsRS]nw$") and SweaveSyntaxLatex (with extension = "[.][rsRS]tex$") are supplied, but users or packages can supply others with names matching the pattern SweaveSyntax.*.

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 an S source file that can be run using source. (Code inside \Sexpr{} statements is ignored by Stangle.)

Stangle is just a wrapper to Sweave specifying a different default driver. Alternative drivers can be used: the former CRAN package cacheSweave and the Bioconductor package weaver provide drivers based on the default driver RweaveLatex which incorporate ideas of caching the results of computations on code chunks.

Environment variable SWEAVE_OPTIONS can be used to override the initial options set by the driver: it should be a comma-separated set of key=value items, as would be used in a \SweaveOpts statement in a document.

Non-ASCII source files must contain a line of the form

  \usepackage[foo]{inputenc}

(where foo is typically latin1, latin2, utf8 or cp1252 or cp1250) or they will give an error. Re-encoding can be turned off completely with argument encoding = "bytes".

References

Friedrich Leisch (2002) Dynamic generation of statistical reports using literate data analysis. In W. H<U+00E4>rdle and B. R<U+00F6>nz, editors, Compstat 2002 - Proceedings in Computational Statistics, pages 575--580. Physika Verlag, Heidelberg, Germany, ISBN 3-7908-1517-9.

Examples

Run this code

# NOT RUN {
testfile <- system.file("Sweave", "Sweave-test-1.Rnw", package = "utils")
# }
# NOT RUN {
## enforce par(ask = FALSE)
options(device.ask.default = FALSE)

## create a LaTeX file - in the current working directory, getwd():
Sweave(testfile)

## This can be compiled to PDF by
## tools::texi2pdf("Sweave-test-1.tex")

## or outside R by
##
## 	R CMD texi2pdf Sweave-test-1.tex
## on Unix-alikes which sets the appropriate TEXINPUTS path.
##
## On Windows,
##      Rcmd texify --pdf Sweave-test-1.tex
## if MiKTeX is available.

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

# }

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