R Markdown with knitr can add a prefix (usually a letter) to figure and table numbers when knitting/compling to PDF. When knitting to PDF, the following code will do the job:
```{=tex}
\renewcommand{\thetable}{S\arabic{table}}
\renewcommand{\thefigure}{S\arabic{figure}}
```
The result will be
Figure S1.1.
rather than
Figure 1.1
Is there a way to achieve the same when knitting to HTML?