A ventilator system for assisting the respiratory function of a patient under the direction of a clinician, comprising: a supply pump and a control module in communication with a data circuit and a gas circuit having a plurality of valves (50, 52) and supply and exhaust ports, the control module including a display, input device, and a memory in communication with the data circuit; a sensor array in communication with the data circuit that includes at least one oximeter, at least one capnometer, at least one pressure sensor, and at least one flow meter in communication with at least one of the supply and exhaust ports; a command module resident in the memory operative to command the control module to adjustably actuate the pump and the plurality of valves to establish at least one pressure, volume or flow rate in the gas circuit; at least one initialization parameter database resident in the memory to be communicable with the display and configured to store at least one model patient data array element that includes at least an FiO2 quantity, a high pressure, a low pressure, a high time, and a low time; wherein the command module is configured to receive settings from the clinician via the input device and is configured to command the control module to actuate the supply pump and commence respiratory assistance to the patient whereby the gas circuit communicates with the patient using one each of the FiO2 quantity, the high and low pressure, and the high and low time; wherein the command module is configured to communicate with the sensor array to measure a patient actual data array elements of at least one of (i) a patient SpO2 quantity, (ii) a patient etCO2 quantity, (iii) a peak expiratory flow rate, (iv) an end expiratory lung volume and (v) a spontaneous breathing frequency; wherein the command module comprises an initial setup module with an optimal end expiratory lung volume assessment mode configured to monitor a number of key patient parameters to ascertain and periodically compute an optimal end expiratory lung volume, an adjustment and maintenance module with an oxygenation mode, a recruitment mode and a ventilation mode, and a weaning module, and wherein the command module is configured to compare the patient actual data array to the at least one model patient data array and compute at least one of an SpO2 goal value, an etCO2 goal value, and the optimal end expiratory lung volume, which SpO2 goal value, etCO2 goal value and optimal end expiratory lung volume are used to determine whether the patient should be initially weaned, undergo recruitment and increased oxygenation, or be maintained in an unaltered state of ventilation to achieve the SpO2 goal value, the etCO2 goal value, and the optimal end expiratory lung volume. a supply pump and a control module in communication with a data circuit and a gas circuit having a plurality of valves (50, 52) and supply and exhaust ports, the control module including a display, input device, and a memory in communication with the data circuit; a sensor array in communication with the data circuit that includes at least one oximeter, at least one capnometer, at least one pressure sensor, and at least one flow meter in communication with at least one of the supply and exhaust ports; a command module resident in the memory operative to command the control module to adjustably actuate the pump and the plurality of valves to establish at least one pressure, volume or flow rate in the gas circuit; at least one initialization parameter database resident in the memory to be communicable with the display and configured to store at least one model patient data array element that includes at least an FiO2 quantity, a high pressure, a low pressure, a high time, and a low time; wherein the command module is configured to receive settings from the clinician via the input device and is configured to command the control module to actuate the supply pump and commence respiratory assistance to the patient whereby the gas circuit communicates with the patient using one each of the FiO2 quantity, the high and low pressure, and the high and low time; wherein the command module is configured to communicate with the sensor array to measure a patient actual data array elements of at least one of (i) a patient SpO2 quantity, (ii) a patient etCO2 quantity, (iii) a peak expiratory flow rate, (iv) an end expiratory lung volume and (v) a spontaneous breathing frequency; wherein the command module comprises an initial setup module with an optimal end expiratory lung volume assessment mode configured to monitor a number of key patient parameters to ascertain and periodically compute an optimal end expiratory lung volume, an adjustment and maintenance module with an oxygenation mode, a recruitment mode and a ventilation mode, and a weaning module, and wherein the command module is configured to compare the patient actual data array to the at least one model patient data array and compute at least one of an SpO2 goal value, an etCO2 goal value, and the optimal end expiratory lung volume, which SpO2 goal value, etCO2 goal value and optimal end expiratory lung volume are used to determine whether the patient should be initially weaned, undergo recruitment and increased oxygenation, or be maintained in an unaltered state of ventilation to achieve the SpO2 goal value, the etCO2 goal value, and the optimal end expiratory lung volume.