"JR" is short for "Japan Railways" and we Japanese commonly use this
name.
JR has a network of railroads covering the all country of Japan, and
owes
Shinkansen.
It was originally "Japan National Railways (JNR)".
JNR was one of public authorities in Japan, but it was privatized and
divided into 6 companies by districts and a freight company in 1987.
The companies differ from region to region, but you are not a cause for
concern.
You can buy a ticket for any station in Japan, and many trains run
across the companies.
The network of JR covers the country of Japan.
The core of the network is Shinkansen after all.
Tokaido-San'yo ,Tohoku-Joetsu-Nagano and Kyushu Shinkansen were
constructed parallel to each traditional line. Basically on their
routes, the trains on Shinkansen are limited
express and the ones on traditional line are local.
On Yamagata and Akita Shinkansen, the high-speed trains from Tohoku
Shinkansen and local trains run on the same line.
Also many limited expess trains run on traditional line.
The train schedule across the country is planned with a focus on
Shinkansen.
The main four islands of Japan is connected by rail.
Hokkaido and Kyushu are linked by tunnels to Honshu. Shikoku is linked
by a bridge to Honshu.
To Hokkaido and Kyushu, some overnight sleeper trains run from Tokyo
and Osaka.
To Shikoku, many limited express trains run from Okayama.
Below is a map of the JR network. The red lines are Shinkansen, the blue ones are the lines on which limited express runs, and the thin black ones are local lines.
Around Tokyo and Osaka, there are a lot of commuter lines and many
trains run frequently.
Especially, the loop lines in Tokyo and Osaka are very convenient.
("Yamanote Line" in Tokyo, "Osaka Loop Line" in Osaka)
JR map in the greater Tokyo (pdf)
To get on the JR train, you have to buy a ticket to your destination.
In addition, you need to buy some optional tickets.
If you get on a limited express or Shinkansen, you need this ticket.
Basically this is for reserved seat. But most limited
express or Shinkansen trains have several non-reserved cars.
So if you get on a non-reserved car, you need "Non Reserved Limited
Express Ticket". It is 510 yen cheaper than Limited Express Ticket.
Most limited express and Shinkansen trains have a few Green Cars.
"Green Car" is like first-class car, and has spacious seats.
If you get on a green car, you need "Green Car Ticket". If it is a
limited express train, you need Limited
Express Ticket, too.
Several sleeper trains starts from Tokyo and Osaka every day.
Most of such trains are limited express.
So if you get on a sleeper car, you need "Berth Ticket" and "Limited
Express Tichet".
Two types of sleeper are A-type (high-grade type) and B-type (ordinary
type), so of course a berth ticket of A-type is more
expensive than one of B-type.
You can buy JR tickets at any JR station or travel company.
At JR station, you can buy a short-distance ticket at the ticket
machine.
And you can buy the long-distance ticket, limited express ticket and so
on at the ticket office "Midori no Madoguchi" (means office counter
with green sign).
Most urban stations have the ticket office, but many country stations
don't have one.
In such case, you can also buy the tickets from the conductor in the
train.
Recently the ticket machine into which the user can put own resarvation
data and get the reserved-seat tickets is increasing at the urban
stations.
You are checked your tickets at ticket wicket before you enter the
platform. The station staff punches or stamps on your ticket.
At many urban stations, automatic ticket gates are install.
If you insert your ticket, the gate opens. Go through the wicket, but
never leave the tickets on the machine.
When you arrive at your destination, you insert your ticket into the
gate.
The gate opens, but the ticket is taken up.
This is an economical ticket that you can use all trains, buses and
ferries of JR.
However, it is not available to get on only "Nozomi" of Tokaido-San'yo
Shinkansen. (If you want to get on Nozomi, buy the tickets for it.)
There are two types.
They are for Green Seat and for Ordinary Seat.
And there are three type of duration.
They are 7-days, 14-days and 21-days.
You can't buy this ticket in Japan.
You have to buy in advance at major travel agency or Japanese airline's
office (JAL or ANA) in your country.
When you buy the ticket, you can get a "Exchange Order" ticket. So you
exchange it for Japan Rail Pass when you visit Japan.
When you exchange in Japan, you must show your passport.
The exchage offices are in the main cities in Japan.
This is an economical ticket that you can use the trains in JR East
company.
The area of JR East contains Tohoku district, Kanto district, Tokyo
metropolitan district, Nagano and Izu Peninsula.
This is available for Tohoku-Yamagata-Akita and Joetsu-Nagano
Shinkansen, but not Tokaido-San'yo Shinkansen.
You can buy like "Japan Rail Pass". And if you show your passport and
return air ticket, you can get it in Japan.
There are three types (5-day, 10-day, Flexible 4-day).
JR
East Pass and some other passes
This is an economical ticket that you can use the trains in JR Hokkaido
company for 3 or 5 days. The available area is the most lines in
Hokkaido island.
There are two types: for Green Seat and for Ordinary Seat.
How to buy this is same to Japan Rail Pass.
This is an economical ticket that you can use the trains in JR West
company.
There are two types: Kansai Area and San'yo Area.
The former is the area around Osaka city and you select the duration
1-4 days.
The latter is available to San'yo Shinkansen and San'yo Line in
addition to Kansai area. You select the duration 4 or 8 days.
JR
West Rail Pass and some other passes
This is an economical ticket that you can use the trains in JR Kyushu
company for 3 or 5 days. The available area is the most lines in
Kyushu island.
There is only one type for Ordinary Seat.
How to buy this is same to Japan Rail Pass.