Support Numbered Equations (and solve some math rendering issues) #335
Description
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