Nothing in this study challenges the central role of the individual reproduction number as an epidemiological measure; because the empirical measures of reproduction number proposed here and in [12, 27, 29] use incident observed cases as the base, all of the complication in defining the 'typical' or 'eigen' case for structured models discussed most clearly in [24] are neatly sidestepped. What this study does highlight is that much complexity is hidden in effectively defining and estimating the generation time distribution for a structured population. In the case studied here, generation times between individuals are shorter for within household transmission than between household transmission, particularly for more infectious pathogens, and this resulted in systematic biases associated with estimating the reproduction number while ignoring this effect, which were quite substantial in the case of highly infectious measles virus.