I'm trying to adapt an unofficial University of South Florida Latex document class and template file which are available from http://shell.cas.usf.edu/~saito/grad/ into an Rmarkdown template similar to the thesisdown and huskydown packages. After playing with that for a while I was able to get a package that has a custom template (https://github.com/ailich/bulldown) and can be installed with remotes::install_github("ailich/bulldown"). The document will knit, but if I add any headers to the child documents (e.g. # Chapter 1) I get the error "! Undefined control sequence. l.49 \hypertarget". I've included a text file which lists the steps I took to create this R package/template and the edits I had to make to various files. Does anyone know how to fix this issue or why it would occur? I'm not very familiar with Latex so I've had trouble debugging this.
Rmarkdown – Adapting LaTeX Class and Template File to an Rmarkdown Template
bookdownrmarkdown
Related Solutions
Option 1: Export figure and then include it again
In a similar manner to this answer to Plotly as png in knitr/rmarkdown the current hack is to export the figure and then load in the produced file. As a small example (which you could adapt) there is
---
title: "Diamond prices"
author: "Oliver"
date: "6^th^ May 2020"
output:
pdf_document:
fig_caption: yes
header-includes:
- \usepackage{cleveref}
fontsize: 12pt
always_allow_html: yes
---
# Making a plot
```{r, echo=FALSE, include=FALSE}
options(shiny.testmode = TRUE)
library(knitr)
library(plotly)
data("diamonds")
```
```{r , echo=FALSE, include=FALSE}
fig <- plot_ly(diamonds, x = ~carat, y = ~price, type="scatter", mode="markers", color = ~clarity, width =200, height = 150)
orca(fig, file="diamonds.png")
```
We can see in \Cref{fig:fig_prices_of_diamonds} how expensive diamonds can be.
which produces
Option 2: Use webshot
Based on comments in this answer to Change output width of plotly chart size in R Markdown PDF output an alternative is to capture the image automatically using wesbot. Simply run the following once in the R console to install webshot (and PhantomJS which webshot in turn uses):
install.packages('webshot')
webshot::install_phantomjs()
One you have this you can adapt the above example to use instead:
```{r fig:fig_prices_of_diamonds, echo=FALSE, include=TRUE, fig.cap="\\label{fig:fig_prices_of_diamonds}The prices of diamonds increases perhaps?"}
plot_ly(diamonds, x = ~carat, y = ~price, type="scatter", mode="markers", color = ~clarity, width =400, height = 250)
```
We can see in \Cref{fig:fig_prices_of_diamonds} how expensive diamonds can be.
which is much cleaner code.
I would like to include title/date/author/supervisor(costum command) in the rmd yaml header. How do I achieve this?
So simple:
---
title: A theme
subtitle: A modern beamer and Rmarkdown template
date: \today
author: XY
supervisor: YZ
institute: Institution or Company of High Esteem
output: beamer_presentation
---
# test
This is a test.
If you compile this, this produce a title frame and the only thing ignored of the YALM header is YZ.
The reason is that there are not any $supervisor$ variable nor $if(supervisor)$ <whatever> $else$ <whatever> $endif$ in the default template. This link the second question:
Does anyone know of a good example/walk-through for integrating costum tex templates?
cd /usr/share/pandoc/data/templates # In Linux Mint
nano default.beamer # change "nano" to your favorite editor
OK, ok, some simpler to start: simplest.template:
\documentclass{beamer}
\begin{document}
\begin{frame}
$body$
\end{frame}
\end{document}
Test.Rmd:
---
output:
pdf_document:
template: simplest.template
---
This is the body.
Too simple? Ok, ok, I know, ... some less simple: the supervisor.template:
\documentclass{beamer}
\begin{document}
\begin{frame}
$if(supervisor)$ Supervisor: $supervisor$
$else$ I have not a supervisor $endif$
\end{frame}
\end{document}
Test2.Rmd:
---
supervisor: YZ
output:
pdf_document:
keep_tex: yes
template: supervisor.template
---
This is ignored text.
... And so on.
Best Answer
This can be accomplished with
"-r", "markdown-auto_identifiers"It can be specified in the YAML with
or in a function like
bookdown::pdf_bookusing thepandoc_argsargumentpandoc_args = c(pandoc_args, "--top-level-division=chapter", "-r","markdown-auto_identifiers")