8000 change the subsampling method to use pymbar.timeseries.subsampleCorrelatedData() · Issue #39 · alchemistry/alchemlyb · GitHub
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change the subsampling method to use pymbar.timeseries.subsampleCorrelatedData() #39

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shuail opened this issue Nov 14, 2017 · 1 comment
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change the subsampling method to use pymbar.timeseries.subsampleCorrelatedData() #39

shuail opened this issue Nov 14, 2017 · 1 comment
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release 0.2.0

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@shuail
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shuail commented Nov 14, 2017

Proposed to change the subsampling method to avoid using the pandas slicing for subsampling, this issue is corresponding to the pull request #38

The pandas slicing method requires the steps to be integer which is rounded from the statistical inefficiency of a time series. This will sometimes make different time series indistinguishable from each other in terms of their subsampling positions. Proposed to switch to the pymbar subsampleCorrelatedData function.
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orbeckst commented Nov 16, 2017 •
edited by shuail
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The discussion on PR #38 lead to the following consensus (see comments by @davidlmobley @shuail and myself leading up to #38 (comment)):

  • use pymbar.timeseries.subsampleCorrelatedData() for fractional g or ceil(g)
  • add a keyword to allow the user to switch between conservative=True and False
  • make the default conservative=True

@orbeckst orbeckst changed the title change the subsamping method? change the subsamping method to use pymbar.timeseries.subsampleCorrelatedData() Nov 16, 2017
@orbeckst orbeckst changed the title change the subsamping method to use pymbar.timeseries.subsampleCorrelatedData() change the subsampling method to use pymbar.timeseries.subsampleCorrelatedData() Nov 16, 2017
orbeckst pushed a commit that referenced this issue Nov 22, 2017
@shuail @orbeckst
use pymbar.timeseries.subsampleCorrelatedData() (Issue #39)
91ee8c2 
- change the subsampling code to use the pymbar module to get the
  subsampled indexes, the original method use the slicing function in
  pandas which requires the slicing step to be integer
@orbeckst orbeckst mentioned this issue Nov 22, 2017
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orbeckst added a commit that referenced this issue Nov 22, 2017
@orbeckst
added kwargs to select subsampling strategy in statistical_inefficieny()
51ed87a 
- kwarg conservative=True (default)
- test that series for statistical ineffiency calculation and the data
  are sampled on the same times (otherwise the slicing would be wrong)
- added tests
- added notes and warning to the docs
- fixes #39
orbeckst added a commit that referenced this issue Nov 23, 2017
@orbeckst
Merge pull request #41 from alchemistry/issue-39-subsampling
799e800 
change subsampling with statistical_inefficiency() (#39)
@orbeckst orbeckst added this to the release 0.2.0 milestone Jan 17, 2018
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