polyRAD will now work in diversity panels where individuals vary in ploidy. Additionally, a much less convoluted approach is taken for triploid F1 populations derived from diploid x tetraploid crosses.
Resolves #17
Approach
Slots containing genotype likelihoods, prior probabilities, and posterior probabilities are now formatted as two-dimensional lists, with possible inheritance modes across the genome in the first genome, and individual ploidies in the second dimension. This change in data structure has necessitated small changes across most of the code, and RADdata objects are not backwards compatible across this change.
Purpose
polyRAD will now work in diversity panels where individuals vary in ploidy. Additionally, a much less convoluted approach is taken for triploid F1 populations derived from diploid x tetraploid crosses.
Resolves #17
Approach
Slots containing genotype likelihoods, prior probabilities, and posterior probabilities are now formatted as two-dimensional lists, with possible inheritance modes across the genome in the first genome, and individual ploidies in the second dimension. This change in data structure has necessitated small changes across most of the code, and RADdata objects are not backwards compatible across this change.