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Before you can understand what choices to make in creating a game, it helps to know some of the terminology used in OOTP.
A saved game is one 'universe' of baseball in OOTP. A saved game could contain one league, five leagues, one league with multiple 'subleagues,' or any other combination of leagues and subleagues. In fact, in OOTP, there is no limit to the combinations of leagues you can put into one saved game, other than your computer's performance. Each game you create generates a distinct directory on your computer's hard drive, located in data/saved_games. Saved game directories end in .lg, for example, My League.lg.
A league consists of one group of baseball teams, players, and the rules for how that league operates. A saved game can contain one or more leagues. OOTP supports four types of leagues: standard leagues, historical leagues, fictional leagues, and imported leagues (from previous versions of OOTP). Each of these is described in League Types. Although there is no limit to the number of leagues your saved game can have, the more leagues your saved game has, the higher the toll on your computer's memory and hard disk space.
A subleague is a group of teams within a league. A league can have one or two subleagues. For example, if you create a league called My League and divide it into a Northern League and Southern League, the latter two are subleagues of My League.
A division is a group of teams within a subleague. A league can contain between 1 and 50 divisions. Each division can contain between 2 and 50 teams.
Within a saved game, related leagues are grouped together into hierarchies called league systems. League systems can have from 1 to n leagues, and each league in a saved game belongs to a league system. There can be multiple league systems in a single saved game. "League system" is not a term referred to in the user interface, but it is helpful in better understanding how leagues relate to each other.
Parent Leagues and Affiliated (Child) Leagues
A league can be considered to be a parent league or an affiliated league. A parent league is any league that has no leagues above it in its league system. There can only be one parent in a league system. It's important to note that a parent league is NOT necessarily a "Major League." You could just as easily have a AA league that is a parent league.
Parent leagues can have affiliated leagues, which are leagues that are below the parent in its league system. In one typical setup, the Major League is the "parent league," and the AAA, AA, and A leagues are "affiliated leagues." An affiliated league cannot have more than one parent league.
In OOTP, the most important reason to understand this parent/affiliate relationship is because most league settings cascade from parent leagues down to affiliated leagues. In most cases, you cannot modify an affiliated league's settings, because they are obtained automatically from the parent league.
A minor league is usually an affiliated league rolling up to a parent league, usually called a "major league." However, it is possible to have a minor league that is independent. Independent minor leagues behave just like any parent league. Minor leagues typically involve a lower level of play than major leagues. OOTP supports five levels of minor league play: Triple A, Double A, Single A, Short Season A, and Rookie. Each minor league you create must be classified using one of these five levels. However, the classifications have no real impact on game play. As with all leagues, you can customize your minor leagues to perform in the manner that suits you best. There is no limit to the number of minor leagues you can have. You can learn more about adding minor leagues in the screen on Adding Minor Leagues.
Note: Minor league teams do not necessarily need to be affiliated with a major league team, although that is often the case.
In addition, there are two special kinds of affiliated leagues called feeder leagues - college feeder leagues and high school feeder leagues. These leagues are designed to feed players into your minor leagues. You can learn more about feeder leagues here.
One way to map out the relationships between these elements is shown below.
An actual game might look something like this: