An R package to calculate probability of freedom from disease in a population based on surveillance data.
At SVA, we perform calculations of probability of freedom from disease based on ongoing surveillance activities in animal populations that over a period of time have had negative results. This is referred to a Demonstrating Disease Freedom (DDF) and the tools and results from this are very important as a foundation for affecting and maintaining trade relationships as well as trade restrictions to avoid future introductions.
These calculations have been successfully done in @risk software which is add-on toolset to the Microsoft Excel spreadsheet package. In order to make these calculations more reproducible and based on openly available tools, this package is being produced in R. The vision is ultimately to have an adaptable tool that can quickly be used to perform these calculations for various surveillance systems.
As a first step, we will define a tool to calculate the probability of freedom from 4 diseases in Sweden (BVDV, IBR, Bovine Leucosis, and Paratuberculosis). This first step will fulfil the requirements to report these results. The tool may be adaptable for other calculations, but at this point, absolute adaptability is not the main focus.
A few fake datasets are included in the package in order to build the tools. Their structure is similar to those that will be used for the actual calculations but their contents are simulated, so don't draw conclusions from their content.