In practice, with method 2 rather than estimating separate q ijt terms for every day t (which would over-parameterize the model), we apply constraints. We consider constraints where i) q ijt terms from the same ward and same study phase are required to take the same value; ii) q ijt are the same across all time periods within each ward; iii) q ijt terms from the same study phase are constrained to take the same value and do not vary across study wards; and iv) q ijt terms are the same for different MRSA types, q i1t~qi2t . These constraints imply a series of nested models, and we apply likelihood ratio tests to determine whether there is evidence to reject the hypotheses that these equality constraints represent.