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