R: Clean up, weave or tangle Sweave files produced by LyX with...

clean_lyx {svSweave}

R Documentation

Clean up, weave or tangle Sweave files produced by LyX with the SciViews Sweave module

Description

These functions process ⁠.Rnw`` files produced by LyX and the SciViews Sweave module (not the standard Sweave module provided with LyX <= 2.0.0!). The SciViews-LyX extension defines ⁠rchunk' commands to contain R chunks (embedded R code processed by Sweave). Unfortunately, LyX use to write two lines feeds for each line of code, introducing extra lines in the R chunks. Moreover, tabulations are interpreted as 8 spaces, while R code use to consider a tabulation as equivalent to 4 spaces. clean_lyx() corrects these little problems, and it should not affect R noweb files produced by a different software.

Usage

clean_lyx(RnwCon, RnwCon2 = RnwCon, encoding = "UTF-8")

cleanLyxRnw(RnwCon, RnwCon2 = RnwCon, encoding = "UTF-8")

tangle_lyx(
  file,
  driver = Rtangle(),
  syntax = getOption("SweaveSyntax"),
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  annotate = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

tangleLyxRnw(
  file,
  driver = Rtangle(),
  syntax = getOption("SweaveSyntax"),
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  annotate = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

purl_lyx(
  file,
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

purlLyxRnw(
  file,
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

weave_lyx(
  file,
  driver = RweaveLatex(),
  syntax = getOption("SweaveSyntax"),
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

weaveLyxRnw(
  file,
  driver = RweaveLatex(),
  syntax = getOption("SweaveSyntax"),
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

knit_lyx(
  file,
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

knitLyxRnw(
  file,
  encoding = "UTF-8",
  width = 80,
  useFancyQuotes = TRUE,
  logFile = file.path(tempdir(), ".lyxSweave.log"),
  ...
)

Arguments

`RnwCon`	A connection object or a character string corresponding to the path to a R noweb file to be read.
`RnwCon2`	Idem, but where the cleaned up R noweb file should be written (by default, on the same file or connection).
`encoding`	The encoding of the `.Rnw` file. It is UTF-8 by default, but you can change it here.
`file`	The Sweave source file.
`driver`	The actual function to do the process, see `Sweave()`.
`syntax`	`NULL` or an object of class 'SweaveSyntax' or a character string with its name, see `Sweave()`.
`width`	The width used for outputs, 80 characters by default.
`useFancyQuotes`	Do we use fancy quotes in R outputs?
`annotate`	Is the R code extracted from the `.Rnw` file annotated?
`logFile`	The file to use to log results of weaving/tangling the document.
`...`	Further arguments passed to the driver's setup function of `Sweave()` or `Stangle()`.

Value

For clean_lyx(), a list for Sweave options found in the document; NULL for the other functions: these functions are invoked for their side effects. The function weave_lyx() uses the standard Sweave driver (but it uses knitr for LyX documents that use the SciViews Knitr module), while knit_lyx() does the same, but using the knitr driver. Similarly, purl_lyx() is the knitr counterpart of tangle_lyx() standard tangling function.

Author(s)