Updated polyRAD to use the beta-binomial distribution for estimating genotype likelihood rather than the binomial distribution. The depthSamplingPermutations slot also now contains the log of n choose k, rather than simply n choose k, making this version of polyRAD backwards-incompatible with RADdata objects from previous versions. An overdispersion argument has been added to all pipelines, and there is a function to assist users in optimizing the value for this argument. A function for adding even priors has also been added; it is not currently incorporated into any pipeline, but may be useful for future testing purposes.
Updated polyRAD to use the beta-binomial distribution for estimating genotype likelihood rather than the binomial distribution. The depthSamplingPermutations slot also now contains the log of n choose k, rather than simply n choose k, making this version of polyRAD backwards-incompatible with RADdata objects from previous versions. An overdispersion argument has been added to all pipelines, and there is a function to assist users in optimizing the value for this argument. A function for adding even priors has also been added; it is not currently incorporated into any pipeline, but may be useful for future testing purposes.