Help for package svSweave

Type:

Package

Version:

1.0.0

Date:

2022-05-10

Title:

'SciViews' - 'Sweave', 'Knitr' and R Markdown Companion Functions

Description:

Functions to enumerate and reference figures, tables and equations in R Markdown documents that do not support these features (thus not 'bookdown' or 'quarto'. Supporting functions for using 'Sweave' and 'Knitr' with 'LyX'.

Maintainer:

Philippe Grosjean <phgrosjean@sciviews.org>

Depends:

R (≥ 2.6.0)

Imports:

utils, knitr, rmarkdown

Suggests:

covr, testthat, spelling

License:

GPL-2

URL:

https://github.com/SciViews/svSweave, https://www.sciviews.org/svSweave/

BugReports:

https://github.com/SciViews/svSweave/issues

RoxygenNote:

7.1.1

VignetteBuilder:

knitr

Encoding:

UTF-8

Language:

en-US

NeedsCompilation:

Packaged:

2022-05-10 08:39:56 UTC; phgrosjean

Author:

Philippe Grosjean

[aut, cre]

Repository:

CRAN

Date/Publication:

2022-05-10 09:30:02 UTC

svSweave: 'SciViews' - 'Sweave', 'Knitr' and R Markdown Companion Functions

Description

Details

The SciViews 'svSweave' package provides additional function to use Sweave or knitr with LyX and SciViews-LyX. There are also functions to reference tables, figures or equations inside a R markdown.

Important functions

fig(), tab() or eq() to enumerate and reference figures, tables and equations in R Markdown documents.
new_labelling() to create new items iterators.
clean_lyx(), weave_lyx(), knit_lyx(), tangle_lyx(), purl_lyx() to clean up, weave or tangle Sweave files produced by LyX with the SciViews Sweave or Knitr modules.

Author(s)

Maintainer: Philippe Grosjean phgrosjean@sciviews.org (ORCID)

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)

Philippe Grosjean

Create a figure id from a chunk label

Description

This function looks at the current chunk label and returns id="fig:label" that is usable in the ⁠out.extra=⁠ field of the R chunk. It allows to refer to a figure generated from a chunk with this label. Use out.extra=chunk_id() to set the id, or use fig_id_auto().

Usage

fig_id(label)

fig_id_auto()

Arguments

label

The label to use. If provided, it supersedes the chunk label.

Value

A string to set the id like id="fig:label". For fig_id_auto(), the function installs a hook in 'knitr' to add an id automatically for each plot make by changing ⁠out.extra=⁠.

Examples

fig_id("my_label")

Reference figures, tables and equations in R Markdown documents

Description

These functions return closures that allow for constructing a series of numbered items and to reference them. The number is create the first time a label is encountered, and provided again for further use of the same label.

Usage

new_labelling(
  type = c("arabic", "roman"),
  string_html = paste0("<style>.++++-%%%%::after{content:\"####\"}</style>",
    "<span class=\"figheader\">Figure\\ ####: </span>@@@@"),
  string_latex = "@@@@",
  string_word = "[Figure\\ ####:]{#++++:%%%%} @@@@",
  string_ref_html = "<a class=\"++++-%%%%\" href=\"#++++:%%%%\"></a>",
  string_ref_latex = "\\ref{++++:%%%%}",
  string_ref_word = "[####](#++++:%%%%)",
  name = "fig"
)

newLabelling(
  type = c("arabic", "roman"),
  string_html = paste0("<style>.++++-%%%%::after{content:\"####\"}</style>",
    "<span class=\"figheader\">Figure\\ ####: </span>@@@@"),
  string_latex = "@@@@",
  string_word = "[Figure\\ ####:]{#++++:%%%%} @@@@",
  string_ref_html = "<a class=\"++++-%%%%\" href=\"#++++:%%%%\"></a>",
  string_ref_latex = "\\ref{++++:%%%%}",
  string_ref_word = "[####](#++++:%%%%)",
  name = "fig"
)

fig(
  caption = "",
  label = knitr::opts_current$get("label"),
  ref = NULL,
  reset = FALSE
)

tab(
  caption = "",
  label = knitr::opts_current$get("label"),
  ref = NULL,
  reset = FALSE
)

eq(label, ref, reset = FALSE)

Arguments

type

The type of numbering (arabic or roman).

string_html

The string prototyping the legend, with ⁠++++⁠ being the name (fig by default) ⁠@@⁠ being a placeholder for the text, ⁠####⁠ as a placeholder for the number, or ⁠%%%%⁠ as a placeholder for the label.

string_latex

Idem for LaTeX.

string_word

Idem for Word.

string_ref_html

Idem for reference in HTML format.

string_ref_latex

Idem for reference in LaTeX format.

string_ref_word

Idem for reference in Word format.

name

The name to use before the number, e.g., "Fig." to get "Fig. 1" as cross-reference text for the first figure. If you provide name = NULL, only the number is produced.

caption

The test of the caption.

label

A short string uniquely identifying the item within the collection. To set a label in and equation, give a name instead of a string.

ref

The reference to the label.

reset

If TRUE, the collection is reset. Useful if you want to restart numbering at the beginning of each chapter.

Details

A new labelling type is created using new_labelling() which is a function factory (a function that creates functions).

Value

The function returns a caption if ⁠text =⁠ is provided, or an anchor if it is missing. If ⁠text=⁠ contains a name, it returns a link. Same for the ⁠label=⁠ for eq(): if it is a text, a couple label + tag to place inside display equations is produced, and if it is a name, a link is provided. new_labelling() creates a new labelling function, which has the same arguments as fig().

Author(s)

Philippe Grosjean

Examples

# These function are supposed to be used in an R Markdown document
# see the svSweave vignette
# Produce a caption that contains the required code to number and reference
# a figure in HTML documents
fig("A caption", label = "a_label")
# Produce a reference to that figure
fig$a_label

Define a function as being 'subsettable' using $ operator

Description

For labelling items like fig(), tab() or eq(), implements the $ method to retrieve a reference and build a link to the element.

Usage

## S3 method for class 'subsettable_labelling_ref'
x$name

Arguments

x

A subsettable_labelling_ref function.

name

The value to use for the ⁠ref=⁠ argument.

Examples

eq(pythagoras) # Create a label / tag pair for R Markdown display equations
eq$pythagoras  # Create a link to the equation somewhere else in the document

svSweave: 'SciViews' - 'Sweave', 'Knitr' and R Markdown Companion Functions

Description

Details

Important functions

Author(s)

See Also

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

Description

Usage

Arguments

Value

Author(s)

See Also

Create a figure id from a chunk label

Description

Usage

Arguments

Value

Examples

Reference figures, tables and equations in R Markdown documents

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Define a function as being 'subsettable' using $ operator

Description

Usage

Arguments

Examples