## Table of Contents

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

## Themes for R Markdown

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 prettydoc Engine

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

## Options and Themes

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.

## Offline Math Expressions

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.

## Elements

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

### Headers

#### Level 4

##### Level 5

### Tables

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 |

### Lists

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`

### Markups

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

### Code

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")
```

```
## [,1] [,2]
## [1,] -0.56047565 -0.60189285
## [2,] -0.23017749 -0.99369859
## [3,] 1.55870831 1.02678506
## [4,] 0.07050839 0.75106130
## [5,] 0.12928774 -1.50916654
## [6,] 1.71506499 -0.09514745
```

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
);
}
```