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adw96 / DivNet

diversity estimation under ecological networks
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DivNet runtime #28

Closed mooreryan closed 3 years ago

mooreryan commented 5 years ago

Do you have any info on the runtime/memory usage of the divnet function? In the vignettes it says it takes a while with lots of taxa, but I was wondering if you had any more specific info.

For example, I was trying to run it on data ~300 samples by ~10,000 taxa/ASVs with covariates, but it kept crashing. Is there a limit on taxa or samples that we should keep in mind?

paulinetrinh commented 3 years ago

@mooreryan wanted to confirm that using the implementation of DivNet-rs resolves this issue with wide datasets.

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mooreryan commented 3 years ago

It works for a subset of the problems DivNet R package solves. But it's a working solution for large datasets, so that's something!

paulinetrinh commented 3 years ago

Thanks Ryan! For all users, please refer to the README link to DivNet-rs on how you might use your wide dataset with DivNet. We will be adding more to our README on what DivNet methods/options are available to users via DivNet-rs. Stay tuned!