Support Numbered Equations

[GitHunter0]

Hi @gadenbuie ,

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

Xaringan for some reason does not have it natively but it is an indispensable feature in many fields...

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

Thank you

[gadenbuie]

Do you have any ideas about how this would work or what the API would look like?

[GitHunter0]

Hey @gadenbuie , yes I have.

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 (which might need to be corrected in the original package) or by the limitation of in_header: "www/mathjax-equation-numbers.html" solution.
Xaringan Cross-Reference.pdf

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

[gadenbuie]

Thanks for writing this up! Unfortunately, I don't think this feature is a good fit for xaringanExtra. There's a lot of lower-level things that are needed to make this work, and xaringanExtra tends towards features that are possible mostly in the browser or with a small amount of messing with knitr hooks.

I do think that the setting up the mathjax configuration to enable cross-referencing might be something xaringan itself would consider. You could try describing the issue at https://github.com/yihui/xaringan to see if they're open to it there.

[GitHunter0]

Thanks man, I appreciate the feedback.
Yihui is usually extremely busy but I will try to open this issue there.

[GitHunter0]

The issue was opened here yihui/xaringan#335