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Basic rarefaction curve based on vegan::rarecurve - #226

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Basic rarefaction curve based on vegan::rarecurve#226
vsuksi wants to merge 1 commit into
microbiome:develfrom
vsuksi:rarefaction-curve

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@vsuksi

@vsuksi vsuksi commented Apr 13, 2026

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@vsuksi

vsuksi commented Apr 13, 2026

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Is it important to integrate with mia::getAlpha and niter to be able to visualize multiple alpha indices and make it more general? Initial testing suggests that would not be feasible in terms of performance because first we'd rarefy the assay and then compute the diversity indices. Just observed richness is motivated in that it's intuitive and most sensitive for quality control.

The most overlap I found was with using iNEXT::iNEXT() and iNEXT::ggiNEXT() which is ggplot2-based. Perhaps most relevant downside is that extrapolation can not be turned off and extrapolating species richness curves seems questionable for sequencing data without special singleton estimator (Chao et al. 2016), which is not implemented in iNEXT. One option could be to instruct user to do iNEXT::iNEXT with nboot = FALSE and ggiNEXT.

@vsuksi vsuksi mentioned this pull request Apr 13, 2026
@antagomir

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getAlpha integration is not critical; If it is possible utilize existing methods that's even better - you could see what works best, then we get some experience with it and can improve later if it turns out to be necessary?

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