Author: Eamon B. O’Dea; Harry Snelson; Shweta Bansal
Title: Using heterogeneity in the population structure of U.S. swine farms to compare transmission models for porcine epidemic diarrhoea Document date: 2015_3_27
ID: 1xxrnpg3_24
Snippet: We assumed that the random effect Z i is normally distributed. Then the likelihood is fully specified. We calculated marginal likelihoods with the Laplace approximation and numerically found the parameters that maximised it. In some cases we fixed η to 0.5, which allowed the model to be fully fit with both the lme4 35 and glmmADMB 36 packages in R. 37 To make sure our results were not sensitive to η = 0.5, we used R's optimise function to find .....
Document: We assumed that the random effect Z i is normally distributed. Then the likelihood is fully specified. We calculated marginal likelihoods with the Laplace approximation and numerically found the parameters that maximised it. In some cases we fixed η to 0.5, which allowed the model to be fully fit with both the lme4 35 and glmmADMB 36 packages in R. 37 To make sure our results were not sensitive to η = 0.5, we used R's optimise function to find the value of η in [0, 5] with highest likelihood. We performed several diagnostic checks of our fits, including checking for signs of nonlinearity with partial residual plots and for signs of temporal autocorrelation in the residuals.
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