Verification-diversity outputs

Hi,

I just want to verify something. I calculated simpson diversity in qiime2 and then exported the results to R. I wanted to makes sure, that in fact, this metric is calculated on the rarefied table.

Thanks

Hi @Fabs!
Once the data are exported/in R, there is no way to verify. However, if you remember which artifact you exported, you can just check out the artifact provenance! Open in https://view.qiime2.org/ and click on the provenance tab to see all commands and artifacts that were used to generate that artifact in :qiime2: , starting with the imported data.

You can use that to make sure you used subsample to subsample your feature table at even depth.

I hope that helps!

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That’s a handy tool.

Fortunately, I do remember which artifacts I used, since I remember we entered a rarefying depth in core-metrics, I decided to calculate simpson diversity the same way (on a rarefied table). I just wanted to make sure that, that is in
fact the correct way of doing the calculation.

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yes, as long as you used subsample then your table is rarefied at even depth!

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