1

I have a RMarkdown file and a LaTeX snippet containing bunch of latex \newcommand calls I want to place in separate file (since I want to reuse them across multiple RMarkdown files). Here's a small reproducible example: test.rmd

---
title: "Test"
---

# Test Document

## Math

$$
\begin{bmatrix}
1 & 2 & 3 \\
4 & 5 & 6 \\
7 & 8 & 9
\end{bmatrix}
$$

$$
\bmat
1 & 2 & 3 \\
4 & 5 & 6 \\
7 & 8 & 9
\emat
$$

and the LaTeX snippet:

\newcommand{\bmat}{\begin{bmatrix}}
\newcommand{\emat}{\end{bmatrix}}

I wish to add the LaTeX snippet in the document header and compile test.rmd to a standalone HTML document. How do you do this?

I have made two attempts, in attempt (1) the compiler is ignoring header-includes in the metadata, and in attempt (2) the \newcommand{\bmat}{... is shown in the browser as plain-text. Both of these attempts work when compiling to PDF (i.e. replacing rmarkdown::html_document by rmarkdown::pdf_document). I suspect this is because MathJax works very differently from LaTeX compilers but I haven't found a very clear explanation on StackOverflow or docs about this...

Attempt 1

Define common.yaml YAML metadata file for Pandoc

---
urlcolor: blue
header-includes: |
  \newcommand{\bmat}{\begin{bmatrix}}
  \newcommand{\emat}{\end{bmatrix}}
---

then I compile test.rmd by doing

Rscript -e "rmarkdown::render('test.rmd',quiet=TRUE,output_format=rmarkdown::html_document(pandoc_args=c('--metadata-file=/current/working/dir/common.yaml')))"

Attempt 2

Define header.tex header file for Pandoc

\newcommand{\bmat}{\begin{bmatrix}}
\newcommand{\emat}{\end{bmatrix}}

then I compile test.rmd by doing

Rscript -e "rmarkdown::render('test.rmd',quiet=TRUE,output_format=rmarkdown::html_document(pandoc_args=c('--include-in-header=/current/working/dir/header.tex')))"
CloudIcarus
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1 Answers1

0

I figured out the answer to my question. Do attempt (2), except header has to be an HTML file, say header.html with contents

\(
\newcommand{\bmat}{\begin{bmatrix}}
\newcommand{\emat}{\end{bmatrix}}
\)

Note the use of \( and \). Now I can use

Rscript -e "rmarkdown::render('test.rmd',quiet=TRUE,output_format=rmarkdown::html_document(pandoc_args=c('--include-in-header=/current/working/dir/header.html')))"

Note that it's not possible to add \usepackage in the snippet as mentioned here.

CloudIcarus
  • 83
  • 5