Vignette Title

In graphsim: Simulate Expression Data from 'igraph' Networks

Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The html_pretty output format in package prettydoc , an alternative to html_document and html_vignette contained in the rmarkdown package, is able to generate small and nice HTML pages.

Styles

Currently html_pretty supports three page themes, cayman (the default), tactile, and architect. And there are also two syntax highlight styles: github to mimic the syntax highlight on Github, and vignette that is used by html_vignette. If no highlight parameter is given, the default style created by Pandoc will be used.

The theme and highlight styles can be given in the document metadata, for example:

output:
  prettydoc::html_pretty:
    theme: cayman
    highlight: github

Happy Knitting!

Feel free to use the knitr infrastructure with dozens of tunable options in your package vignette.

set.seed(123)
n <- 1000
x1  <- matrix(rnorm(n), ncol = 2)
x2  <- matrix(rnorm(n, mean = 3, sd = 1.5), ncol = 2)
x   <- rbind(x1, x2)
head(x)
smoothScatter(x, xlab = "x1", ylab = "x2")

You can also include code snippets of languages other than R, but note that the block header has no curly brackets around the language name.

// [[Rcpp::export]]
NumericVector timesTwo(NumericVector x) {
    return x * 2;
}

You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable().

knitr::kable(head(iris, 10))

Stay Tuned

Please visit the development page of the prettydoc package for latest updates and news. Comments, bug reports and pull requests are always welcome.

graphsim documentation built on June 8, 2025, 11:53 a.m.