Hydroepix is a spatially-explicit simulation framework that models waterborne spread of pathogens within and between net-pens of finfish in the same site, and to nearby farms using the free, open-source software, R. Effects of interventions such as vaccination, early detection and depopulation can be evaluated with the model.
As part of the Farming in Natural Systems (FINS) carrying capacity project, we created a graphical user-interface for Hydroepix using the R package “Shiny” to allow users without programming experience to easily adjust parameter values to compare different disease outbreak and mitigation scenarios for a predefined location. The user-interface includes reference documentation and has multiple tabs, including a simulation control tab with sliders to set 5 scenario- parameter values (top left figure). Model inputs are based on Nova Scotia data and documentation, and peer-reviewed references. Inputs are representative of provincial fish health surveillance programs and health management procedures used by salmon aquaculture companies in Atlantic Canada.
We present an example of a simulation run of the Shiny app for infectious salmon anaemia virus infection in Atlantic salmon in a hypothetical bay in Nova Scotia is to demonstrate how the user-interface works and types of outputs that can be compared. The bay includes 3 sites of 500,000 salmon separated by 6, 9, and 12 km in a triangular array (bottom left figure).
The model inputs these distances in a matrix that assumes the risk of waterborne transmission from site 1 to 2 is the same as the risk from site 2 to 1. Ocean circulation effects can be incorporated into the model using an hydroconnectivity matrix as an alternative to a distance matrix. Model outputs are plots of 1) percentage of simulations yielding a transmission event, and 2) magnitude of each outbreak event (e.g. number of infected pens). The model also tracks whether infection is acquired from a net-pen from the same site or from a distant site.