Q:

R: how to center output in R markdown

I know I can set fig.align = 'center' if I want to center my figure. But what if I want to center my output in a pdf document? 

A:

The following code worked for me.
\center Centered Text \center

And, if you need to put it in bold, as my case, you can use the underline (two at the beggining, two at the end):
\center __Centered Text__ \center

A:

Hopefully it is not too late to add my answer.
You can use html tags in Rstudio Markdown documents.
To center a text you just need to:
<center> TEXT TO CENTER </center>

This works for me when knitting Rstudio Markdowns.

