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Jaccard index #706

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antagomir opened this issue Mar 12, 2025 · 0 comments · Fixed by #709
Closed

Jaccard index #706

antagomir opened this issue Mar 12, 2025 · 0 comments · Fixed by #709

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@antagomir
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antagomir commented Mar 12, 2025 •
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vegan default for Jaccard index is with binary=FALSE

That is different from the classical Jaccard index.

See OMA issue #681 and PR #682.

I suggest that we chance mia default to the original Jaccard index in getDissimilarity / addDissimilarity (and elsewhere if necessary) and then update the OMA example accordingly. The manpage and OMA example should mention that mia default is different from vegan default and mention why.

Imo it is not a problem if the outcome is different from vegan when there is a good justification to it.
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Calculate binary Jaccard by default microbiome/mia
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@antagomir