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For nearly a century, the initial reproduction number (R0) has been used as aone number summary to compare outbreaks of infectious disease, yet there is no`standard' estimator for R0. Difficulties in estimating R0 arise both from howa disease transmits through a population as well as from differences instatistical estimation method. We describe eight methods used to estimate R0and provide a thorough simulation study of how these estimates change in thepresence of different disease parameters. As motivation, we analyze the 2009outbreak of the H1N1 pandemic influenza in the USA and compare the results fromour eight methods to a previous study. We discuss the most important aspectsfrom our results which effect the estimation of R0, which include thepopulation size, time period used, and the initial percent of infectiousindividuals. Additionally, we discuss how pre-processing incidence counts mayeffect estimates of R0. Finally, we provide guidelines for estimating pointestimates and confidence intervals to create reliable, comparable estimates ofR0.

Exploring the nuances of R0: Eight estimates and application to 2009 pandemic influenza