Since QR codes are images there are several ways to put them in a PDF. The two primary ways are as a bitmapped image or as PostScript. Bitmapped images originally were in TIFF form, but as far as I know, modern PDFs can handle things like PNG directly.
PostScript (and SVG) are the better option, since they're actual graphic commands and render cleanly regardless of how you zoom in or out or print. Bitmapped images can become blurred or distorted when scaled. PostScript, incidentally, is the "machine language" of PDFs and EPS.
PostScript is a programming language, so if desired you could actually generate a rendering program PS function for QR output and feed it a string of bit values. Or, take the easy way out and just render a matrix of black and white rectangles.
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