If you only have one Rstudio instance running then open -a Rstudio file.Rmd should do the trick... if you have multiple running 
I haven't figured out how to control which it opens into. I think it defaults to whichever was opened first? Possibly something to do with the terminal running somewhat independently of the IDE? There is perhaps a clever way to identify which instance of Rstudio to send it to, but I'm unfortunately not that clever 
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