Tyo Metro Special Open Ticket

My first time to Japan. I see that i can purchase a 1 or 2 day Metro pass.
I am not familiar with this. Does this include JR (yamate line) or just subways?
I am going to tsukiji/akihabara/shinjuku/
ueno /ginza /hibiya areas as a tourist. Is this the cheapest method for moving around?

It is explained here:
http://www.japan-guide.com/e/e2017.html

Does this include JR (yamate line) or just subways?

It covers only the eight "Tokyo Metro" subway lines. It does not cover the "Toei" subway lines and it does not cover the JR lines or any other railway lines.

I personally don't like the ticket because it is so restrictive on the lines you can use. And many foreign tourists are not easily able to distinguish the Toei from the Metro Tokyo lines. Furthermore, you will need to ride the subway for around 4 times or more per day in order to make it pay off. But I estimate that the average tourist propbably rides the subway only 2-3 times per day, although it depends on travel style.

If you stay in Tokyo several days, I would rather go for a prepaid card, which is valid on all trains in Tokyo (but you pay single fare for each trip):
http://www.japan-guide.com/e/e2359_002.html

Does this include JR (yamate line) or just subways?
Only Metro-run subways.

I am going to tsukiji/akihabara/shinjuku/
ueno /ginza /hibiya areas
All places have Metro station nearby. But it mostly depends on where you stay.