Hi Joan, Shortcodes are executed by WordPress. A PHP script has no knowledge of shortcodes. shortcodes is just a mechanism so you can put a bit of text in a post or page which eventually gets filtered by WordPress (it calls the corresponding PHP unction). So there has to be a PHP function call that does the actual work. You will need to use that PHP function inside your script and it will work fine.
If the documentation of the other plugin do not state what this function name is then you can take a look at the code yourself and find it out.