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Pass skbio arguments to compute_diversity methods #82

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AgnesBaud opened this issue Oct 1, 2021 · 0 comments
Open

Pass skbio arguments to compute_diversity methods #82

AgnesBaud opened this issue Oct 1, 2021 · 0 comments

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@AgnesBaud
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AgnesBaud commented Oct 1, 2021

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():

  1. Give the arguments during the instantiation
  2. 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

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