id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-314295-itr3b63z	Cori, Anne	A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics	2013-09-15		.txt	text/plain	5253	244	49	The Wallinga and Teunis method (13) is generic and requires only case incidence data and the distribution of the serial interval (the time between the onset of symptoms in a primary case and the onset of symptoms of secondary cases) to estimate R over the course of an epidemic. The aim of our study was to develop a generic and robust tool for estimating the time-varying reproduction number, similar in spirit to earlier methods, but implemented with ready-to-use software and without the drawbacks mentioned above. After describing our approach, we apply it to data from selected historical outbreaks of pandemic influenza, severe acute respiratory syndrome (SARS), measles, and smallpox. In such diseases, and when the infectiousness profile after symptoms is independent of the incubation period, the distributions of the serial interval and the generation time are identical (Web Appendix 9), and our estimates are exact (albeit with t defined as the time of symptom onset of a primary case and a time lag in our estimates of R t equal to the incubation period).	./cache/cord-314295-itr3b63z.txt	./txt/cord-314295-itr3b63z.txt