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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

The {svSweave} package provides different functions to better manage Sweave and Knitr with LyX, a document processor that creates LaTeX code. These functions are deprecated and are not detailed here. See their help page ?clean_lyx().

The package also provides functions to automatically enumerate and reference figures, tables and equations in R Markdown documents (an alternate mechanisms to {bookdown} or {quarto} that works everywhere). Indeed, this feature is missing in the basic R Markdown documents. The various {bookdown} templates provide a \@ref(label), see bookdown cross references and Quarto simply uses @label, see quarto cross references. The functions fig(), tab() and eq() provide a different mechanism to obtain a similar result: to enumerate items and to cross-reference them in the text. Here an example of a numbered figure with its caption. In order to use these function, you must load the {svSweave} package in a (setup) chunk before you use these functions:

library(svSweave)

Numbered figures

You can use fig("my caption text") to number the caption of a figure in fig.cap=. The chunk must be named too.

hist(rnorm(50))

Now, you can reference this plot in the text using fig$label (see Fig r fig$hist). It also works if the first reference appears before the figure itself[^1], see Fig r fig$boxplot.

[^1]: Take care, however, that numbering is sequential from the first call (either cross-reference, or label) in Word. You cannot cross-reference the last figure at the beginning of the document... or that last figure will be numbered "Fig. 1" there. For the other formats, it is not a problem.

boxplot(rnorm(50))

Summary: produce numbered figures from labeled R chunks by indicating fig.cap = fig("...."), and reference them using fig$label in an inline R expression.

Numbered tables

The same principle works for tables using knitr::kable(). For instance, see Table r tab$head_iris.

knitr::kable(head(iris),
  caption = tab("The few first lines of the `iris` dataset."))

A reference to cars (Table r tab$head_cars) and to iris (Table r tab$head_iris) again.

knitr::kable(head(cars),
  caption = tab("the first few lines of `cars`."), format = "pandoc")

Summary: produce numbered tables from labeled R chunks by indicating caption = tab("....") in knitr::kable(), and reference them using tab$label in an inline R expression.

Numbered equations

Finally, numbered display equations can also be constructed and cross-referenced. In the display equation, constructed with a pair of $$, you use eq(label) in an inline R expression. To reference it, you use eq$label also in an inline expression.

$$x=\frac{-b \pm \sqrt{b^2 - 4ac}}{2a} r eq(eqlabel)$$

... and I can reference Eq. r eq$eqlabel like this.

$$\sum_{i = 0}^n{x^2} r eq(sum)$$

I can cite one Eq r eq$sum, or another one Eq r eq$pythagoras.

$$a^2+b^2=c^2 r eq(pythagoras)$$

Summary: produce numbered equations by adding eq(label) inline R expression inside a display equation, and reference to it using eq$label inside an inline R expression.

These tags work in R Markdown to compile HTML, LaTeX or Word, with some glitches remaining to eliminate for LaTeX or Word.

SciViews/svSweave documentation built on May 12, 2022, 2:48 a.m.