Support Numbered Equations (and solve some math rendering issues)

[GitHunter0]

Hey @yihui , how are you?

Please, would you consider adding support for numbered equations & cross-reference?

I was surprised Xaringan didn't have it natively since it is an indispensable feature in many fields.

That would be a great contribution to the package in my opinion.

If so, below I'm sharing my thoughts about the feature while also highlighting some math rendering issues I found:

I believe there are 2 important compatibilities the API should have: bookdown and plain Latex.

The bookdown package introduced cross-reference capabilities to R Markdown and it would be really desirable the syntax used by it to be accepted in xaringan too. Here is a MWE:

---
title: "Bookdown HTML Article - Cross-Reference"
output:
  bookdown::html_document2:
    toc: true
    toc_depth: 5
    number_sections: true
    toc_collapsed: false
    toc_float:
      collapsed: false
      smooth_scroll: false
    anchor_sections: TRUE
---



# Equations Label & Cross-Reference

## Single Equation

- Unlabeled equation
$$\int\limits_a^b f(x)dx = \frac{F(x)}{\frac{\binom{n}{n}}{\binom{k}{k}}} \Biggr|^b_a = F(b)-F(a)$$
- Labeled equation
$$
\mathrm{cov}(\epsilon_s, \epsilon_t) =
\left\lbrace
\begin{align}
 & \sigma^2  \quad \mathrm{if}  \; s = t \\
 & 0         \quad \mathrm{else} \\
\end{align}
\right. 
(\#eq:eqname0) 
$$

- See equation \@ref(eq:eqname0) above.


## Block of Equations

- Labeled system of equations
$$
\begin{align}
\left( \sum_{i=1}^{n}{i} \right)^2 &= \left( \frac{n(n-1)}{2}\right)^2 = \frac{n^2(n-1)^2}{4} (\#eq:eqname1) \\
\frac{\partial f}{\partial x}(x=3) &= y^2  \\
y &= \frac{(x-\mu)}{(max-min)} \\
\end{align}
$$
- See system of equations \@ref(eq:eqname1) above.


# Tables Caption & Cross-Reference


## kable() Table

`Bookdown` default table caption only works with `kable()`

See table \@ref(tab:tables-mtcars)

```{r tables-mtcars}
knitr::kable(iris[1:5, ], caption = 'A caption', longtable=TRUE)
```

## Custom Tables

See Table \@ref(tab:mytab).

Table: (\#tab:mytab) Your table caption.

| Sepal.Length| Sepal.Width| Petal.Length|
|------------:|-----------:|------------:|
|          5.1|         3.5|          1.4|
|          5.2|         3.6|          1.5|

# Figures Caption & Cross-Reference

## Plot

See figure \@ref(fig:car)

```{r "car", fig.cap = 'Title of the plot', fig.fullwidth=TRUE}
plot(cars)
```

## Image

See figure \@ref(fig:myfig)
```{r "myfig", fig.cap = 'Title of the plot', fig.fullwidth=TRUE}
knitr::include_graphics("www/myfigure1.png")
```

See attached PDF with the output:
Bookdown.HTML.Article.-.Cross-Reference.pdf

It should also ideally allow the standard Latex API for cross-referencing. As a matter of fact, this repository already did that as explained here.
However, its cross-reference system just works for equations and not for tables and figures.

Here is a MWE:

---
title: "Xaringan Cross-Reference"
output:
  xaringan::moon_reader:
    self_contained: false
    css: [default, metropolis, metropolis-fonts]
    # css: [default, shinobi, metropolis-fonts] # custom themes
    lib_dir: libs
    nature:
      highlightStyle: arta
      highlightLines: true
      countIncrementalSlides: false
    includes:
      # this allows equation numbering:
      in_header: "www/mathjax-equation-numbers.html"
editor_options: 
  chunk_output_type: console
---

```{r include=FALSE }
## Global Chunk settings ----
knitr::opts_chunk$set(warning=FALSE, message=FALSE)	 
```


# ___ Equations Label & Cross-Reference ___

---

# Single Equation

- Unlabeled equation
$$\int\limits_a^b f(x)dx = \frac{F(x)}{\frac{\binom{n}{n}}{\binom{k}{k}}} \Biggr|^b_a = F(b)-F(a)$$
- NOTE: `xaringan` renders (n n)/ (k k) denominator too small (considerably smaller than `ioslides` for example). Is there a way to correct that?

- Labeled equation
$$
\mathrm{cov}(\epsilon_s, \epsilon_t) =
\left\lbrace
\begin{align}
 & \sigma^2  \quad \mathrm{if}  \; s = t \nonumber\\
 & 0         \quad \mathrm{else} \label{eq:eqname0} \\
\end{align}
\right. 
$$


- NOTE: `xaringan` does not render equation \eqref{eq:eqname0} above correctly and also the equation number is not displayed.

---

# A Single Equation that works

- Labeled Equation
$$
\begin{align} 
y = \frac{(x-\mu)}{(max-min)} \label{eq:eqnameY} \\
\end{align}
$$
- See equation \eqref{eq:eqnameY} above.

---

# Block of Equations

NOTE: these sometimes render correctly and label/cross-reference works and sometimes they don't, I have no idea why. 

- Labeled system of equations
$$
\begin{align}
\left( \sum_{i=1}^{n}{i} \right)^2 &= \left( \frac{n(n-1)}{2}\right)^2 = \frac{n^2(n-1)^2}{4} \nonumber \\
\frac{\partial f}{\partial x}(x=3) &= y^2  \label{eq:eqname1}  \\
y &= \frac{(x-\mu)}{(max-min)} \nonumber \\
\end{align}
$$
- See system of equations \eqref{eq:eqname1} above. 
- See system of equations \ref{eq:eqname1} above.

---

# ___ Tables Caption & Cross-Reference ___

---

# kable() Table

`Bookdown` default table caption only works with `kable()`

See table \ref{tab:tables-mtcars}

```{r tables-mtcars}
knitr::kable(iris[1:5, ], caption = 'A caption', longtable=TRUE)
```

---

# Latex Tables

- This works in LaTeX and ideally should work in `xaringan` too

See table \ref{tab:my-tab1} below.

\begin{table}[htbp!]
\centering
\caption{\label{tab:my-tab1} Caption}
\begin{tabular}{ccccc}   
1 & 2 & 3 & 4 & 5 \\   
6 & 7 & 8 & 9 & 10 \\ 
\end{tabular} 
\end{table}
---

# ___ Figures Caption & Cross-Reference ___


---

# Image

- This works in LaTeX and ideally should work in `xaringan` too

See Figure \ref{fig:image1} below:

\begin{figure}[h!]  
\includegraphics[scale=0.5]{www/myfigure1.png}
\caption{Figure Title}\label{fig:image1}
\end{figure}

Where the file mathjax-equation-numbers.html content is:

<script type="text/x-mathjax-config">
  MathJax.Hub.Config({
    TeX: { equationNumbers: { autoNumber: "AMS" } },
  });
</script>
<style>
.mjx-mrow a {
  color: black;
  pointer-events: none;
  cursor: default;
}
</style>

We can see in attached PDF with the output below that many things failed, either by xaringan's math rendering issues or by the limitation of in_header: "www/mathjax-equation-numbers.html" solution.
Xaringan.Cross-Reference.pdf

It would be really great if xaringan could solve those issues and also avoid the necessity to declare external files in YAML metadata.

Thank you