MDPI issue with equation numbering

[etiennebr]

Equation labels are not translated \label{eq:eq} when knitting with mdpi_article, but they are with bookdown::pdf_document2.

Here's the Rmd

This is an equation
\begin{equation}
(\#eq:eq)
c = a \cdot b
\end{equation}
  
see \@ref(eq:eq)

And 
$$
(\#eq:eq2)
a = c \cdot b
$$
  
see \@ref(eq:eq2)

Knit with bookdown::pdf_document2

Knit with rticles::mdpi_article

It seems like there is some processing not happening. I don't have a deep knowledge of knitr, so I suspect it might simply be that the mdpi_article and pdf2_document are unrelated, and mdpi in fact uses pdf_document for rendering, but in any case, I'd like to reference equations in a mdpi paper, so this might be a feature request. Also, per rstudio/bookdown#190 (comment), it seems like the second equation should also be translated to \begin{equation} ... \end{equation} (at least for ebooks), so I wondered if one of my packages was outdated, but apparently not (see session info below, but knitr_1.30, rmarkdown_2.3, bookdown_0.20, rticles_0.16.1 all seemed fine).

Here are the rendered .tex

With bookdown::pdf_document2 yields in .tex

This is an equation
\begin{equation}
\label{eq:eq}
c = a \cdot b
\end{equation}

see \eqref{eq:eq}

And
\[
\label{eq:eq2}
a = c \cdot b
\]

see \eqref{eq:eq2}

With rticles::mdpi_article, the tex is:

This is an equation \begin{equation}
(\#eq:eq)
c = a \cdot b
\end{equation}

see @ref(eq:eq)

And \[
(\#eq:eq2)
a = c \cdot b
\]

@dleutnant, any idea? @cderv, I'm happy to dive a bit deeper in rticles/knitr if you can point me in a general direction where this could be fixed, or how to have a step-by-step look at the knitting process because I'm completely new to this code.

session info

xfun::session_info('rticles')
#' R version 3.6.3 (2020-02-29)
#' Platform: x86_64-pc-linux-gnu (64-bit)
#' Running under: Ubuntu 18.04.5 LTS, RStudio 1.3.1073
#' 
#' Locale:
#'   LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8       
#'   LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
#'   LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
#'   LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       
#' 
#' Package version:
#'   base64enc_0.1.3 digest_0.6.25   evaluate_0.14   glue_1.4.2      graphics_3.6.3 
#'   grDevices_3.6.3 highr_0.8       htmltools_0.5.0 jsonlite_1.7.1  knitr_1.30     
#'   magrittr_1.5    markdown_1.1    methods_3.6.3   mime_0.9        rlang_0.4.7    
#'   rmarkdown_2.3   rticles_0.16.1  stats_3.6.3     stringi_1.5.3   stringr_1.4.0  
#'   tinytex_0.26    tools_3.6.3     utils_3.6.3     xfun_0.17       yaml_2.2.1    

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[etiennebr]

Using base_format: rticles::mdpi_article as a base format pretty much resolves the issue

output:
  bookdown::pdf_book: 
    base_format: rticles::mdpi_article

But

$$
(\#eq:eq2)
a = c \cdot b
$$

is still rendered to

\[
\label{eq:eq2}
a = c \cdot b
\]

But I guess it's an issue for bookdown, rather than rticles.

[cderv]

Hi @etiennebr,

this is indeed the official way for now to add bookdown features to any other format. It is document in the book:

• https://bookdown.org/yihui/bookdown/latexpdf.html
• https://bookdown.org/yihui/bookdown/a-single-document.html

we may in the future move the referencing feature in rmarkdown directly to make it available more broadly without doing this.

So you just need to change the output: field in the yaml

it seems like the second equation should also be translated to \begin{equation} ... \end{equation}

Pandoc will not do the conversion. It will transform $$ to the bracketed syntax: https://pandoc.org/MANUAL.html#extension-tex_math_dollars

And it seems for bookdown referencing of equation you need to explicitly use \begin{equation} as described in the documentation https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#equations

It seems $$ works for HTML though - Maybe we could support the $$ syntax for pdf output. This is indeed a bookdown issue.

[cderv]

Also, bookdown features is to provided same referencing mechanism for different type of output.

With rticles, the output format is only tex for now so I think it is expected that reference mechanism from tex be used directly maybe.

This is an equation
\begin{equation} \label{eq:1}
c = a \cdot b
\end{equation}
  
see \ref{eq:1}

But I can see the advantage of having one syntax, and that the equation preview in rstudio works.

[etiennebr]

@cderv, thanks for all the pointers.

we may in the future move the referencing feature in rmarkdown directly

Is there an issue I can track?

Maybe we could support the $$ syntax for pdf output

Opened #959

[cderv]

Is there an issue I can track?

Not yet. It is just an idea for now. Nothing yet planned. I am referencing issues that points toward that being a good idea. And testing the idea in the wild ! 😉

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