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biocore / American-Gut

American Gut open-access data and IPython notebooks
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5 alpha diversity #166

Closed wasade closed 8 years ago

wasade commented 8 years ago

This depends on #165, please do not review/merge until #165 has gone in.

wasade commented 8 years ago

:boom: tests are passing here as well once #165 gets merged

wasade commented 8 years ago

Tests are stochastically failing. My guess is that the Travis CI instances do not handle multiple cores well, so taking a stab with the ability to limit cores.

mortonjt commented 8 years ago

Travis is a bit finicky. If you set the env variable to 1, that may be good enough.

mortonjt commented 8 years ago

I think this is good to go once the tests pass

wasade commented 8 years ago

@mortonjt, looks good :)

wasade commented 8 years ago

Is this good to merge?

rob-knight commented 8 years ago

Quick question, are we planning to add deblurring or a similar technique to make sure results distributed back to participants have plausible numbers of taxa? Or is the focus on things like Shannon entropy and PD?

On Oct 22, 2015, at 8:11 PM, mortonjt notifications@github.com wrote:

Merged #166 https://github.com/biocore/American-Gut/pull/166.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/166#event-443387861.

EmbrietteH commented 8 years ago

Speaking of deblurring...is it published yet? If not, I might be a bit hesitant to include it until it is, but perhaps I'm just being overly cautious.

Embriette R. Hyde, PhD Postdoctoral Scholar Project Manager, American Gut Project Rob Knight Lab Department of Pediatrics University of California, San Diego Phone: 832-845-7532

On Fri, Oct 23, 2015 at 10:02 AM, Rob Knight notifications@github.com wrote:

Quick question, are we planning to add deblurring or a similar technique to make sure results distributed back to participants have plausible numbers of taxa? Or is the focus on things like Shannon entropy and PD?

On Oct 22, 2015, at 8:11 PM, mortonjt notifications@github.com wrote:

Merged #166 https://github.com/biocore/American-Gut/pull/166.

— Reply to this email directly or view it on GitHub < https://github.com/biocore/American-Gut/pull/166#event-443387861>.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/166#issuecomment-150634312.

wasade commented 8 years ago

We haven't delivered alpha diversity, so was just including this right now so we had at least some measures available. Deblurring would be fantastic going forward.

On Fri, Oct 23, 2015 at 11:06 AM, EmbrietteH notifications@github.com wrote:

Speaking of deblurring...is it published yet? If not, I might be a bit hesitant to include it until it is, but perhaps I'm just being overly cautious.

Embriette R. Hyde, PhD Postdoctoral Scholar Project Manager, American Gut Project Rob Knight Lab Department of Pediatrics University of California, San Diego Phone: 832-845-7532

On Fri, Oct 23, 2015 at 10:02 AM, Rob Knight notifications@github.com wrote:

Quick question, are we planning to add deblurring or a similar technique to make sure results distributed back to participants have plausible numbers of taxa? Or is the focus on things like Shannon entropy and PD?

On Oct 22, 2015, at 8:11 PM, mortonjt notifications@github.com wrote:

Merged #166 https://github.com/biocore/American-Gut/pull/166.

— Reply to this email directly or view it on GitHub < https://github.com/biocore/American-Gut/pull/166#event-443387861>.

— Reply to this email directly or view it on GitHub <https://github.com/biocore/American-Gut/pull/166#issuecomment-150634312 .

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/166#issuecomment-150634933.