A system configured to determine the functional residual capacity of a subject, comprising: sensors in communication with gas at or near an airway of a subject; a processor that receives output signals generated by the sensors; a concentration module configured to determine concentrations of molecular species in gas inhaled and exhaled by the subject, wherein the concentrations are determined from the output signals received by the processor from the sensors; a composition change module configured to automatically identify an inhalation composition change from concentrations determined by the concentration module, wherein an inhalation composition change is a change of at least a predetermined magnitude in the concentration of at least one molecular species in gas inhaled by the subject during temporally proximate breaths; an alveolar volume module configured to determine an alveolar tidal volume of a respiration of the subject from the output signals received by the processor from the sensors; and a functional residual capacity module configured to determine the functional residual capacity of the subject based on - a change in concentrations determined by the concentration module for breaths subsequent to the automatically identified inhalation composition change, - a cumulative alveolar ventilation of the subject subsequent to the automatically identified inhalation composition change, and - an analysis of the concentration of the molecular species in the gas exhaled by the subject as a function of the cumulative alveolar ventilation of the subject, said analysis comprising implementing a model of the lungs of the subject as a set of n chambers, where n > 1, in a data matching or search algorithm that fits the model of the lungs of the subject to the concentration of the molecular species exhaled by the subject as a function of said cumulative alveolar ventilation of the subject, wherein the determination of the functional residual capacity by the functional residual capacity module is triggered by the automatically identified inhalation composition change. sensors in communication with gas at or near an airway of a subject; a processor that receives output signals generated by the sensors; a concentration module configured to determine concentrations of molecular species in gas inhaled and exhaled by the subject, wherein the concentrations are determined from the output signals received by the processor from the sensors; a composition change module configured to automatically identify an inhalation composition change from concentrations determined by the concentration module, wherein an inhalation composition change is a change of at least a predetermined magnitude in the concentration of at least one molecular species in gas inhaled by the subject during temporally proximate breaths; an alveolar volume module configured to determine an alveolar tidal volume of a respiration of the subject from the output signals received by the processor from the sensors; and a functional residual capacity module configured to determine the functional residual capacity of the subject based on - a change in concentrations determined by the concentration module for breaths subsequent to the automatically identified inhalation composition change, - a cumulative alveolar ventilation of the subject subsequent to the automatically identified inhalation composition change, and - an analysis of the concentration of the molecular species in the gas exhaled by the subject as a function of the cumulative alveolar ventilation of the subject, said analysis comprising implementing a model of the lungs of the subject as a set of n chambers, where n > 1, in a data matching or search algorithm that fits the model of the lungs of the subject to the concentration of the molecular species exhaled by the subject as a function of said cumulative alveolar ventilation of the subject, - a change in concentrations determined by the concentration module for breaths subsequent to the automatically identified inhalation composition change, - a cumulative alveolar ventilation of the subject subsequent to the automatically identified inhalation composition change, and - an analysis of the concentration of the molecular species in the gas exhaled by the subject as a function of the cumulative alveolar ventilation of the subject, said analysis comprising implementing a model of the lungs of the subject as a set of n chambers, where n > 1, in a data matching or search algorithm that fits the model of the lungs of the subject to the concentration of the molecular species exhaled by the subject as a function of said cumulative alveolar ventilation of the subject, wherein the determination of the functional residual capacity by the functional residual capacity module is triggered by the automatically identified inhalation composition change.