Methods for estimating the volume of the carbon dioxide stores of an individual's respiratory tract include determining a carbon dioxide store volume at which a correlation between corresponding signals of carbon dioxide elimination and an indicator of the content of carbon dioxide in blood of the individual is optimized. The estimate of the volume of carbon dioxide stores, which comprises a model of the respiratory tract, or lungs, of the individual, may be used as a transformation to improve the accuracy of one or both of the carbon dioxide elimination and carbon dioxide content signals. Transformation, or filtering, algorithms are also disclosed, as are systems in which the methods and algorithms may be used. The methods, algorithms, and systems may be used to accurately and noninvasively determine one or both of the pulmonary capillary blood flow and cardiac output of the individual.