Warships at sea can be thought of as self-contained floating cities. Its inhabitants all work at different things that keep the city going. The crew must eat; the hull must protect us from the harms of the sea; the gun must fire; our boats, power generation, and engines must always be ready; and our family's needs must be taken care of. To accomplish all this, expertise in logistics, combat, etc., must be maintained, and this is done by breaking the ship's organization into departments.
As with any warship, IROQUOIS' departments are divided into the "fighting" and the "functional". Departments are then divided into several smaller sub-departments (by trade), to ensure the necessary expertise is on board for all situations.