I wouldn't worry about this, as long as we're talking about people who know how domain names work (it's hard to know what assumptions might be made by others!). Perhaps surprisingly, domain names drill down in specificity from right to left — so
rstudio.gnuorleans.org clearly represents "the
rstudio subdomain of
gnuorleans itself being a subdomain of the
org top-level domain, and
org being a subdomain of the root of the whole internet). But if you're really concerned, you could try to come up with a name that represents the function, rather than the product. Like, this site is called
discourse.rstudio.com, but other people using the same forum software have chosen to go the other way (e.g.,: https://discourse.omnigroup.com).
Back when websites were static files in folders, there was a substantial architectural difference between subdomains (which involve DNS configuration) and subfolders (which just involved making a new directory on a physical disk). These days, so many sites are generating URLs dynamically that the distinction is less clear (e.g., the URL for this thread is being interpreted by the forum software as clues for how to locate the right resources in a database — there are no physical folders named
etiquette-question-on-naming-my-domain-to-serve-rstudio). Historically, subfolders were often considered to be easier to set up than subdomains, so sometimes people hosted entire applications (e.g.,
mysite.com/blog) that way because it was less hassle — but these days most web hosts have control panels that make configuring subdomains dead simple.
In terms of common practice, people tend to use subdomains when they want to create a substantially separate site in addition to their main site (such as
community.rstudio.com vs regular old
rstudio.com ). People tend to use subfolders (e.g.,
gnuorleans.org/rstudio) to represent parts of their main site.
The people who argue most passionately about subdomain vs subfolder are the SEO folks, and it doesn't sound like that's a consideration in your case. However, if you want a taste of that debate: