Some skbio diversity methods allow other arguments/options, in addition to the dataframe argument, to compute the diverse diversity indexes.
For example, there is a base argument to compute Shannon Index, a bias_corrected argument for Chao1 Index, and a validate argument for all Phylogenetic Diversity Indexes (Faith's PD and both UniFrac)
These arguments were available in moonstone when you were directly calling the compute_diversity/compute_beta_diversity methods, but were not available through the analyse_groups() method.
Two ways to make them available when calling analyse_groups():
Give the arguments during the instantiation
~Give the arguments when calling analyse_groups() and pass them through the different methods and properties called up to the compute_diversity/compute_beta_diversity methods = more flexible~
We chose to do the first option (at least for now)(#81) for consistency with the rest of moonstone and because, from experience, this kind of flexibility is not needed
Description
Some skbio diversity methods allow other arguments/options, in addition to the dataframe argument, to compute the diverse diversity indexes. For example, there is a base argument to compute Shannon Index, a bias_corrected argument for Chao1 Index, and a validate argument for all Phylogenetic Diversity Indexes (Faith's PD and both UniFrac)
These arguments were available in moonstone when you were directly calling the compute_diversity/compute_beta_diversity methods, but were not available through the analyse_groups() method.
Two ways to make them available when calling analyse_groups():
We chose to do the first option (at least for now)(#81) for consistency with the rest of moonstone and because, from experience, this kind of flexibility is not needed