Not quite sure what you want to achieve. If I knit the following Rmd file in the RStudio environment the result is a pdf file and a tex file with preamble. You can remove the preamble from the tex file.
In that case, just use knit and pandoc_convert directly from the console or a script. E.g.,
knitr::knit("test.Rmd")
rmarkdown::pandoc_convert("test.md", to = "latex", output = "test.tex")
The knit command will produce test.md. The pandoc_convert command will produce test.tex, which by default will be a tex file without any preamble or \begin{document} ... \end{document} paraphernalia.
I’ve been curious about using LaTeX in RStudio and this has helped a lot. Thank you.
Out of curiosity, how would the plot command be written in the body of the Rnw file?
I have some examples of Rmd files that produce PDF files with none or more LaTeX.
See the github repository HanOostdijk/rmd_pdf_examples.
The bookdown package has a lot of functionality for 'citations, bibtex, references'. The names suggest that is useful only for books but it can also be used for articles. Chapter 2 of bookdown: Authoring Books and Technical Documents with R Markdown sections 6 and 8 describe how to use references and citations and the latexpdf part describes some specifics for the use of LaTeX.
This is great information. Thank you. I will definitely be looking into those references. Hopefully this will help me merge my workflow into one arena.