Changes

The second one makes <code>Times-Roman</code> an "alias" (?) for font stored in the file called <code>tir</code> (probably with some extension?). The third argument specifies the encoding (it might be qx, for instance, or something else) and possibly another options, like <code>features=smallcaps</code> (for opentype fonts). Encoding is used by pdfTeX only - XeTeX and LuaTeX both use Unicode (Mojca - thanks for this point!). Other possibilities include <code>mapping</code> and <code>handling</code>, but don't ask me about these;).