Understanding the early dynamics of the 2014 porcine epidemic diarrhea virus (PEDV) outbreak in Ontario using the incidence decay and exponential adjustment (IDEA) model

Greer, Amy L.; Spence, Kelsey; Gardner, Emma

Initially, we estimated the best-fit R 0 and d parameters for the farm-to-farm transmission component of the PEDV outbreak (February 20 -April 30, 2014) by fitting the previously described IDEA model to cumulative incidence curves using the R statistical computing environment [29] . The IDEA model is not parameterized in terms of calendar date but rather generation time (epidemic generations) and therefore the observed case data were aggregated based on an estimated generation time of seven days. We also fit the IDEA model to the time series data describing cumulative cases over time in an iterative fashion. We did this by fitting the model to a dataset that included progressively more outbreak generations and comparing model fits using maximum likelihood estimates (MLE) for different combinations of values for R 0 and d. Lastly, we used the results from the iterative fitting procedure to examine the ability of the IDEA model to predict the projected time course of the observed epidemic using only model based estimates generated from the analysis of a small number of generations.