variance-covariance matrix V based on the inverse of the observed information matrix (see Appendix S1 for further details, the code used to generate the bootstrap sample is given in Code S5 and Code S6). This first stage can be loosely thought of as sampling the mean behaviour for a subgroup of possible outbreaks. To allow for variability within each subgroup, stage two involves fixing (k * ,g * )and independently generating reproductive numbers for each farm according to model (2) . Steps one and two together give R * = {R * i :i21,…,N}, an approximate bootstrap sample of the reproductive numbers for each farm. Here, 1000 samples of (k,g)pairs were drawn, and 500 sets of reproductive numbers generated for each. Finally, the approximate 95% CI for each R i is given by the 2.5 th and 97.5 th percentiles of the bootstrap distribution. The second stage of the calculation of the approximate CIs was done using Code S7 and Code S8.