Analyzing a PHP script

I am learning a PHP programming and I am looking at a script which has 316 folders and 1,461 files. It takes up around 18MB on a disk and it is a tube site script (with pic galleries, members, importing content, things like this).

I started learning one week ago and I am reading the entire php.net website, some other books (including books about Netbeans, Eclipse and PhpStorm) and since this is not an easy task I started looking at some already written code in the afternoons (and evenings).

I have this script in Netbeans and I am going over the code in the files. I got familiar with the directory structure and I am also going over the code in the files. What I am not sure about, I check on php.net.

Are there any better tools for something like this? Analyzing and learning the script (understanding it, knowing how it is written and so on). I was trying to see if there is some kind of stats on what variables are used the most often, what functions, what are the biggest and most important files in the script (maybe most referred to from other parts or something like this).

How an advanced and experience person could approach something like this. I personally add my own Idea to the code...