How to make a figure caption in Rmarkdown?

Question

I am thinking about writing my thesis with rmarkdown and latex. I\'m getting the hang of how it all works, however, when I try to add a figure (not an R plot) to the text and re

Answer 1

Update: please check https://github.com/yihui/knitr/issues/1063.

Question: How do I make figure captions and in-text references to those figures in Rmarkdown that will display when rendered to pdf?

To get the cross-reference in the PDF produce by LaTeX you need to run LaTeX more than once. Some LaTeX IDE does it for you.

knitr is only running LaTeX once and that is the reason that you only get ??. To confirm that this was the problem I ran

library(knitr)
knitr()

in R that returned

see figure \ref{fig1}.

\begin{figure}[htbp]
\centering
\includegraphics{imagem.jpg}
\caption{picture \label{fig1}}
\end{figure}

which is a valid LaTeX code.

How do I tell pandoc what Rmarkdown is so it will render R code and plots?

Pandoc only understand Markdown (not RMarkdown). First you have to call knitr to generate the Markdown from the RMarkdown and after it call Pandoc to convert the Markdown to LaTeX.