A method for controlling operation of a system for controlling the atmosphere within a confined space. The system has an electrical control having a display and electrically controlled components. The components include an air compressor, a filter, an air heater, a separator for dividing air into streams of oxygen and nitrogen, and flow control valves for varying the purity of the nitrogen stream. The system also includes sensors for indicating the temperature leaving the heater and the temperature within the confined space. A sensor indicates the pressure upstream of the control valves. An oxygen sensor and a carbon dioxide sensor are included. The method includes the steps of energizing the system and simultaneously operating the electrical control to perform the steps of: (1) operating the compressor to an on or off position responsive to inputs from the oxygen sensor and the carbon dioxide sensor; (2) operating the flow control to achieve setpoint oxygen and carbon dioxide levels in the atmosphere, in response to inputs from the oxygen sensor and the carbon dioxide sensor; (3) operating the air heater to maintain a preset value; (4) monitoring the oxygen sensor, and, compensating the output when a predetermined temperature of the atmosphere is indicated; (5) monitoring the carbon dioxide sensor, and compensating the output when a predetermined change in the temperature of the carbon dioxide sensor occurs; and (6) monitoring system components, and, indicating on the display when unsafe or out of range conditions occur.