Lay summary
The first questions asked at the beginning of an epidemic are: ""What is the infection reproduction number?"", and ""What is the case fatality ratio?"". By linking rigorous mathematical models with the estimation procedure, it is possible to provide estimates of these statistics adjusted for the most serious sources of bias, which are the inclusion of imported cases in the data; the so-called truncation error; and the effects of age structure. We will develop a scheme whereby these statistics can be estimated at an early stage of an epidemic and revised as more data become available. A model will then be used to assess the performance of control strategies against influenza. The scheme will be demonstrated with regard to the 2009 epidemic of H1N1 and will be used for any future wave of H1N1 or epidemic of an emerging virus. Results will be used to make recommendations for strategic epidemic planning.