How to convert Rmarkdown file to working latex file

Question

I have written a manuscript I would like to submit to a journal in Rmarkdown. The journal accepts word and latex files, so I am looking for a way to generate a working .tex file out of my .Rmd file.

I have read some posts that allude to this being possible (e.g., How to generate LaTeX file without preamble in R markdown?) and this is getting me some of the way, but I am still having problems.

For example, using the method mentioned in the post above, I can convert a test .Rmd into something with a .tex filetype. This is the test Rmarkdown (just the usual template for new files):

---
title: "Test document"
author: "Me"
date: "23 7 2020"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

This compiles fine to PDF as it should. Then, in the console I run:

knitr::knit("test.Rmd")

to get a markdown file test.md in my working directory, and then I can apparently convert this .md file to .tex with

rmarkdown::pandoc_convert("test.md", to = "latex", output = "test.tex")

This produces a .tex file that, when I double click on it, pops up a PDF view of the file that looks fine. Taking a look at the file though, it is incomplete or at least unfamiliar to me:

\hypertarget{r-markdown}{%
\subsection{R Markdown}\label{r-markdown}}

This is an R Markdown document. Markdown is a simple formatting syntax
for authoring HTML, PDF, and MS Word documents. For more details on
using R Markdown see \url{http://rmarkdown.rstudio.com}.

When you click the \textbf{Knit} button a document will be generated
that includes both content as well as the output of any embedded R code
chunks within the document. You can embed an R code chunk like this:

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{summary}\NormalTok{(cars)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00
\end{verbatim}

\hypertarget{including-plots}{%
\subsection{Including Plots}\label{including-plots}}

You can also embed plots, for example:

\begin{figure}
\centering
\includegraphics{figure/pressure-1.png}
\caption{plot of chunk pressure}
\end{figure}

Note that the \texttt{echo\ =\ FALSE} parameter was added to the code
chunk to prevent printing of the R code that generated the plot.

As far as I can tell, it is missing the preamble, \begin{document}, \end{document}, and I have no idea what is going on with hypertarget bit of the section headers. Unsurprisingly, it does not "re-compile" when I hit run in MiKTeX. The verbatim bits for the code chunks look to be what I'm after, though.

So, is there a way to generate a .tex file that compiles out of an .Rmd file? Or will I have to manually write the preamble and all that? If the answer to my problem is "read up pandoc", then fair enough, I will have to bite the bullet and finally have a look at it. But I find it hard to imagine that there is no good (easy) way to prepare submittable manuscripts in Rmarkdown.

Answer 1

Pandoc generates LaTeX snippets by default, i.e., not a full document. This can be changed by calling pandoc with the --standalone option:

rmarkdown::pandoc_convert(
  "test.md",
  to = "latex",
  output = "out.tex",
  options = "--standalone"
)

You can let R do the work and shorten your commands to

render("test.Rmd", output_format = "latex_document")

A project of interest might be rticles.