I think the above rooms would be a good springboard, and i guess the number of rooms could really expand depending on what level of detail you want to incorporate.
For example, the office listed above could be expanded upon to a great degree. For example, whether its a civilian or military ship, people need to get paid, so an office for payroll would be necessary. Or an onboard legal team for dealing with disciplinary actions on ship, or legal representation if someone gets in trouble on leave. For larger ships, a staffing and human resources office would be necessary also. Essentially, any office that you would need on a ground side base would also need to be included on ship.
Hydroponics could help alleviate strain on life support plants, and also contribute to food supplies.
Though I suppose this isn't technically a 'room' there is a device called a Bussard ram scoop; effectively a giant magnetic funnel which scoops free hydrogen from vacuum; could help reduce the need for large onboard fuel tanks, but is very vulnerable to enemy fire (they have to be outside the hull to work).
As to the different types of living quarters, I might suggest moving away from that model. Maybe one for military and one for civilian; reason being it doesn't necessarily add much to the game, nor is it really necessary. A janitor doesn't need any different sleeping arrangements than a medic, or a scientist. As opposed to military, which tend to segregate themselves from civilians for sake of discipline.
A chapel could help promote unit morale.
Security rooms could help to restrict enemy boarder movement.
If there's going to be an option to do fleet engagements, then a Flag bridge might be usefull; essentially a second bridge where an admiral can sit and control the fleet, while the ship's captain controls the ship.
Armory; can't remember if this is already in or not, but a small arms locker.
Magazines: Storage rooms dedicated to holding ship's munitions (missiles, artillery and KEW shells, etc)
A brig.
Communications rooms which would control the actual communication arrays (radio antennas, laser emitters, etc).
Dedicated drone control section.
While the Workshop was mentioned, you could expand its functions a bit. It could be used to manufacture items onboard (new weapons, replacement parts, trade goods, etc).
The medical section could be elaborated on a bit also. While a sick bay could deal with general underway colds and sniffles, a dedicated operating room would deal with more serious issues. A medical lab section could handle the diagnostics.
Essentially, depending on the purpose of the ship, it would have more specialized facilities to go with it. A hospital ship would essentially have everything a hospital has, plus everything a spaceship needs to fly safely. A freighter would be basically an empty shell with crew quarters, entertainment and engines. A warship would, by necessity, be very large to accommodate weapons, military sensors, magazines, powerful engines, a small onboard hospital, a bureaucratic support section, various command and control elements, etc.
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