if(capabilities("cairo")) knitr::opts_chunk$set(dev.args = list(type = "cairo"))

Have you ever tried to find a lightweight yet nice theme for the R Markdown documents, just like this page?

With the powerful `rmarkdown`

package, we could easily create nice HTML document
by adding some meta information in the header, for example

--- title: Nineteen Years Later author: Harry Potter date: July 31, 2016 output: rmarkdown::html_document: theme: lumen ---

The `html_document`

engine uses the Bootswatch
theme library to support different styles of the document.
This is a quick and easy way to tune the appearance of your document, yet with
the price of a large file size (> 700KB) since the whole
Bootstrap library needs to be packed in.

For package vignettes, we can use the `html_vignette`

engine to generate
a more lightweight HTML file that is meant to minimize the package size, but
the output HTML is less stylish than the `html_document`

ones.

So can we do **BOTH**, a lightweight yet nice-looking theme for R Markdown?

The answer is YES! (At least towards that direction)

The `prettydoc`

package provides an alternative engine, `html_pretty`

,
to knit your R Markdown document into pretty HTML pages.
Its usage is extremely easy: simply replace the
`rmarkdown::html_document`

or `rmarkdown::html_vignette`

output engine by
`prettydoc::html_pretty`

in your R Markdown header, and use one of the built-in
themes and syntax highlighters. For example

--- title: Nineteen Years Later author: Harry Potter date: July 31, 2016 output: prettydoc::html_pretty: theme: cayman highlight: github ---

The options for the `html_pretty`

engine are mostly compatible with the default
`html_document`

(see the documentation)
with a few exceptions:

- Currently the
`theme`

option can take the following values. More themes will be added in the future. - The
`highlight`

option takes value from`github`

and`vignette`

. - A new
`math`

parameter to choose between`mathjax`

and`katex`

for rendering math expressions. The`katex`

option supports offline display when there is no internet connection. - Options
`code_folding`

,`code_download`

and`toc_float`

are not applicable.

By default, `html_pretty`

uses MathJax to render math expressions, for example inline math
expressions $x^2 + y^2 = z^2$, and display formulas:

$$ f(x)=\frac{1}{\sqrt{2\pi}\sigma}e^{-\frac{(x-\mu)^2}{2\sigma^2}} $$

However, using MathJax requires an internet connection. If you need to create documents that can
show math expressions offline, simply add one line `math: katex`

to the document metadata:

--- title: Nineteen Years Later author: Harry Potter date: July 31, 2016 output: prettydoc::html_pretty: theme: cayman highlight: github math: katex ---

This option will enable KaTeX for rendering the math expressions, and all resource files will be included in for offline viewing. The offline document will be ~800k larger.

We demonstrate some commonly used HTML elements here to show the appearance of themes.

| | Df | Sum Sq | Mean Sq | F value | Pr(>F) | | |-----------|----|--------|---------|---------|---------|----| | Block | 5 | 343.3 | 68.66 | 4.447 | 0.01594 | * | | N | 1 | 189.3 | 189.28 | 12.259 | 0.00437 | ** | | P | 1 | 8.4 | 8.40 | 0.544 | 0.47490 | | | K | 1 | 95.2 | 95.20 | 6.166 | 0.02880 | * | | N:P | 1 | 21.3 | 21.28 | 1.378 | 0.26317 | | | N:K | 1 | 33.1 | 33.14 | 2.146 | 0.16865 | | | P:K | 1 | 0.5 | 0.48 | 0.031 | 0.86275 | | | Residuals | 12 | 185.3 | 15.44 | | | |

There are three kinds of lies:

- Lies
- Damned lies
- Statistics
- Frequentists
- Bayesian
- ...

Supported highlighters in `prettydoc`

:

`github`

: Style similar to Github`vignette`

: Style used by`rmarkdown::html_vignette`

**Bold**, *italic*, ~~don't say this~~.

Familiar `knitr`

R code and plots:

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) smoothScatter(x, xlab = "x1", ylab = "x2") head(x)

Also try some other languages, for example C++.

// [[Rcpp::depends(RcppEigen)]] // [[Rcpp::depends(RcppNumerical)]] #include <RcppNumerical.h> using namespace Numer; // f = 100 * (x2 - x1^2)^2 + (1 - x1)^2 // True minimum: x1 = x2 = 1 class Rosenbrock: public MFuncGrad { public: double f_grad(Constvec& x, Refvec grad) { double t1 = x[1] - x[0] * x[0]; double t2 = 1 - x[0]; grad[0] = -400 * x[0] * t1 - 2 * t2; grad[1] = 200 * t1; return 100 * t1 * t1 + t2 * t2; } }; // [[Rcpp::export]] Rcpp::List optim_test() { Eigen::VectorXd x(2); x[0] = -1.2; x[1] = 1; double fopt; Rosenbrock f; int res = optim_lbfgs(f, x, fopt); return Rcpp::List::create( Rcpp::Named("xopt") = x, Rcpp::Named("fopt") = fopt, Rcpp::Named("status") = res ); }

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