On rarefaction #819
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On rarefaction #819
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Rarefaction is defined as the repeated subsampling. This is often confused with a single subsampling (to rarefy). Controversy has been fueled by this confusion with rarefy/rarefaction terminology. I believe the simpler wording here will provide better clarity, and avoid the use of 'rarefaction' when alluding to one iteration of subsampling.
Rarefaction feels out-of-place in the Transformation chapter. Rarefaction is a subsampling method/procedure, and not really a transformation on the data like TSS/CLR etc.
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Moved mention of Rarefaction away from Transformations chapter.
Rarefaction feels out of place in the Transformations section, as it is a subsampling procedure
not a transformation on data (e.g. CLR, TSS, ...)
Added section on rarefaction to Alpha diversity chapter, with terse usage example.
Pointing to longer discussion and usage example in Chapter 15.
Small proofread pass on rarefaction section in chapter 15: community similarity.
See discussion microbiome/OMA_manuscript#29
Resolves #796