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Make minor edits #26

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented Jun 20, 2022

resolves #25

I made some minor edits directly in the R Markdown document. I'm not super tied to them -- feel free to discard anything you don't like.

I have one important question about open/closed OptiFit -- see comment below.

Comment on lines +330 to +334
the OptiFit algorithm @sovacool2022. The OptiFit algorithm was run with the open
method so that any sequences that did not map to the existing OTU
clusters would form new OTUs.
<!-- Did you then remove the columns corresponding to the additional OTUs?
Typically you'd want to run the closed method for this use-case, right? -->
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Typically for this use-case you'd want the closed method so your shared file will have the same OTUs as the reference. Did you then remove those columns before ML?

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I originally had consistency but Pat specifically changed to "stability"

The reverse happened to me with the OptiFit method paper 😆 @pschloss

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