Creating Pretty Documents from R Markdown

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

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

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.
- cayman: Modified from the Cayman theme.
- tactile: Modified from the Tactile theme.
- architect: Modified from the Architect theme.
- leonids: Modified from the Leonids theme.
- hpstr: Modified from the HPSTR theme.
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")

head(x)

##             [,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
    );
}