Table 1.

Model parametrisation

Parameter	Value	Notes
Date of new cases	Date of the onset of symptoms, offset by incubation period
Incubation period	9 days	[3, 6, 29]
Serial interval	Average = 9.8 days Standard deviation = 3.875 days	Gamma-distributed [3]
Smoothing window	5 days	Chosen from sensitivity analysis (see Supplementary material)
Imported cases	Whenever the probable place of infection was not in Spain	Manually labelled first case in each region as imported (method requirement)

Summary of the parameter values used in the method of Cori et al. [23] to estimate the effective reproduction number.