JR means Japan Railways. There are several branches of the Japan Railways Group depending on the location, for example, Japan Railways East (JR East) covers Tohoku and Kanto, where Tokyo is located. Similarly, JR West serves the Kansai route and JR Kyushu covers Kyushu.
If you are staying in a hotel or a hostel, you will usually get an indication to get to the nearest train station.
If you are inside the station, you will find signs that indicate the location of the JR lines. Note that if you arrive at the station by subway, you must leave the subway section, that is, insert your ticket or use your IC card to go through the ticket doors, before arriving at the JR section.
Tickets can be purchased at these machines located next to or near the ticket doors. You can use them in English by selecting the button that says "English", commonly located, in the upper left or right corner.
When you approach the screen, it will illuminate (unless someone is using it immediately before you, in which case it is already active) and you will see boxes with numbers on the screen. These are the ticket prices. To find out how much it takes to get to your destination, just look at the map.
This map is generally on the ticket vending machines and is a diagram of all the lines you can take from where you are and how much the ticket costs to reach each station. The station where it is located is usually the largest square in the diagram and, if you stay on the same line and know how many stops you will travel, you can count the squares in the direction (for example, towards Shinjuku station or away from the Shinjuku station). If you are transferring, you must locate the corresponding line connected to the line you are currently in and then go from there. If you get confused don't worry, you can check the information desk and they will gladly help you or you can purchase a ticket at the lowest price and simply make a fare adjustment when you arrive at your destination. You can reload the difference when it arrives.
Once you have calculated how much you have to pay, touch the box on the screen and follow the instructions (insert your money). You can also select for how many people you are buying by clicking on the buttons on the left side with the "people" icon. The price of tickets for children is lower, so you can also adjust it. You can also purchase each ticket separately.
There are also different "brands" of IC Cards, such as Suica and Pasmo (purchased in Tokyo for JR and non-JR companies, respectively). In Tokyo, Suica and Pasmo can be obtained at vending machines or at station counters. For machines, it should be noted that it will dispense Suica or Pasmo cards (Suica and Pasmo are romanized, so you can see this on the machine even if it is in Japanese). When you buy your first Suica or Pasmo, you will be charged a fee for the card (500 yen), as well as for the amount you initially charge.
If a ticket is used, then it must be entered at the gates of the station and picked up on the other side. You should not lose the ticket as it is necessary to re-enter it at the exit doors of the next station.
Once you pass through the entrance door and have found the correct platform, you will notice that there are numbers on the opposite wall or on the platform screen. These numbers indicate where the doors of each car will open, and this is where people line up. The intermediate train cars are usually the busiest and the chances of getting a seat are greater if you are in the first or last car. Of course, this also depends on the line where you are and the time the train is taking.
The line is made as usual. When the incoming train stops, you will have to wait until everyone has gone down. This is sometimes really fascinating to see, especially if the train is completely crowded. Once you get on the train, it is recommended to move to the sides of the car to free space in the middle.
Then when you arrive at the desired station, re-enter the ticket at the exit door, but this time the ticket will stay inside the machine and will have reached its destination.