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Filter #122

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@johnchase johnchase commented Jun 19, 2019 •
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  • Adds the option to filter zero counts from a sourcetracker analysis (When both a given sink and source have zero counts)
  • Removes the left out sample from the feature assignment tables when run with LOO=True Previously this was populated with all zeros

johnchase added 4 commits June 17, 2019 16:16
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first pass at filtering zeros
9096fc8
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more changes
e39fba1
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ENH: Adds feature filtering
558b201 
Sourcetracker will now filter and features that are zero values in _all_
source features _and_ in a give sink. (i.e. each sink is analyzed
independently)
@johnchase
Added command line functionality and refactored parallel functionalit…
f3724a5 
…y to be more efficient
@johnchase johnchase requested review from wdwvt1 and lkursell June 19, 2019 00:28
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@wdwvt1 We haven't really discussed this in detail. If this is not appropriate to add to master, we can close the pull request and I can maintain the code in another repo.

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coveralls commented Jun 19, 2019 •
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Coverage Status

Coverage increased (+0.4%) to 100.0% when pulling d5a673c on filter into 4f52d7f on master.

@johnchase johnchase self-assigned this Aug 22, 2019
@johnchase johnchase requested a review from jkliu September 21, 2019 21:39
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Flake8 errors, will fix soon

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jkliu commented Sep 23, 2019 •
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Tested branch on a dataset that was previously returning the incorrect columns/features when using filter_zero_counts=True for filtering. Rerunning branch on the same dataset now returns a feature assignment table with a set of columns/features that is a subset to the set of columns/features that went into gibbs()

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@wdwvt1 wdwvt1 Awaiting requested review from wdwvt1

@lkursell lkursell Awaiting requested review from lkursell

@jkliu jkliu Awaiting requested review from jkliu

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