A generalized version of commonly used UniFrac distance. Generalized UniFrac distance contains an extra parameter controlling the weight on abundant lineages so the distance is not dominated by highly abundant lineages. The unweighted and weighted UniFrac, and variance adjusted weighted UniFrac distances are also implemented. The package also implements a permutation-based multivariate analysis of variance using MULTIPLE distance matrices.
In practice, we do not know a priori which type of change happens in the microbiome. Each distance measure is most powerful in detecting only a certain scenario. When multiple distance matrices are available, separate tests using each distance matrix will lead to loss of power due to multiple testing correction. Combing the distance matrices in a single test will improve power. PermanovaG combines multiple distance matrices by taking the maximum of pseudo-F statistics for each distance matrix. Significance is assessed by permutation.
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