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sparseNN produces incorrect nearest neighbors in some cases #38

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ericbair-sciome opened this issue Nov 28, 2023 · 2 comments · Fixed by #39
Closed

sparseNN produces incorrect nearest neighbors in some cases #38

ericbair-sciome opened this issue Nov 28, 2023 · 2 comments · Fixed by #39
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bug Something isn't working version 1.0 Features that should be included in the initial PrestoGP release

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@ericbair-sciome
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ericbair-sciome commented Nov 28, 2023 •
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I noticed that the nearest neighbors produced by sparseNN were different from the nearest neighbors produced by GPvecchia in some cases. I wrote a new function of my own to find nearest neighbors. It gave the same output as GPvecchia. That suggests that the nearest neighbors produced by sparseNN are sometimes wrong.
@ericbair-sciome ericbair-sciome added bug Something isn't working version 1.0 Features that should be included in the initial PrestoGP release labels Nov 28, 2023
@ericbair-sciome ericbair-sciome self-assigned this Nov 28, 2023
@ericbair-sciome ericbair-sciome changed the title SparseNN produces incorrect nearest neighbors in some cases sparseNN produces incorrect nearest neighbors in some cases Nov 28, 2023
@kyle-messier
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@ericbair-sciome @brian-bk22 @sciome-bot Does this need to be discussed? I remember there being some workaround in the GPvecchia to avoid randomness in determining the nearest neighbor set.

@ericbair-sciome
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No, this is a separate issue. I had noticed some small differences between the nearest neighbors produced by sparseNN and GPvecchia in the past. I assumed it was due to the artificial noise that GPvecchia adds to the data to avoid ties. But I did some more careful testing, and found that sparseNN simply misses some neighbors in unusual situations. Luckily, this was a rare bug that doesn't seem to meaningfully change any of our output. And I already fixed it anyway. @sciome-bot is reviewing my changes. I'll create a pull request (and close this bug) once the latest version is on GitHub.

@ericbair-sciome ericbair-sciome linked a pull request Dec 1, 2023 that will close this issue
Sciome update: sparseNN bug fix and new tests #39
Merged
sciome-bot added a commit that referenced this issue Feb 8, 2024
@sciome-bot
Pull request #39: Removed test vignette, fixed lint issues
95fef8c 
Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit bab8357
Merge: 55c0e8e 5394772
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:19:24 2024 -0500

    Pull request #38: Removed vignette, fixed lint issues

    Merge in STAT/prestogp from eb-dev to master

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Merge: 7e330f3 076c0a1
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Date:   Thu Feb 8 14:18:48 2024 -0500

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Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

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Date:   Wed Feb 7 23:25:05 2024 -0500

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commit f49d076
Merge: 439790c 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Feb 7 23:19:54 2024 -0500

    Pull request #35: Eb dev

    Merge in STAT/prestogp from eb-dev to master

    * commit '59baf720737abe59a04c98705c950ef1c7b63321':
      Fixed some documentation issues
      Removed C++11 compiler flag
      Added RandomFields data sets to PrestoGP
      Added knitr to Suggests in DESCRIPTION
      Documentation, R-cmd-check fixes, binomial regression

commit 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

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commit 662907d
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

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commit cf2aadb
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 13:40:24 2024 -0500

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Date:   Wed Jan 31 01:31:53 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Jan 14 10:58:49 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 14:05:12 2024 -0500

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Date:   Sat Jan 13 12:37:28 2024 -0500

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Date:   Sat Jan 13 12:11:56 2024 -0500

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Date:   Fri Jan 12 19:37:55 2024 -0500

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Date:   Fri Jan 12 19:36:05 2024 -0500

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... and 25 more commits
sciome-bot pushed a commit that referenced this issue Apr 5, 2024
@shail-choksi
Implement imputation beta
05e7dfb 
Squashed commit of the following:

commit cae8439
Merge: c15c519 6bafe5c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Apr 5 16:38:34 2024 -0400

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Date:   Thu Feb 8 14:19:24 2024 -0500

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Date:   Wed Feb 7 23:19:54 2024 -0500

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    Merge in STAT/prestogp from eb-dev to master

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

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commit cf2aadb
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 13:40:24 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 01:31:53 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Jan 14 10:58:49 2024 -0500

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... and 30 more commits
sciome-bot pushed a commit that referenced this issue Apr 9, 2024
@shail-choksi
Pull request #43: Fix documentation issue blocking R CMD check and re…
6c79863 
…vert execute permission on all files

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Merge: c15c519 6bafe5c
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Date:   Thu Feb 8 14:24:34 2024 -0500

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Date:   Thu Feb 8 14:19:24 2024 -0500

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Date:   Thu Feb 8 14:18:48 2024 -0500

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Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

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Merge: 13a6f44 f49d076
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Feb 7 23:25:05 2024 -0500

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Merge: 439790c 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Feb 7 23:19:54 2024 -0500

    Pull request #35: Eb dev

    Merge in STAT/prestogp from eb-dev to master

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      Documentation, R-cmd-check fixes, binomial regression

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 13:40:24 2024 -0500

    Added knitr to Suggests in DESCRIPTION

... and 35 more commits
sciome-bot pushed a commit that referenced this issue Apr 25, 2024
@shail-choksi
Remove dependency on sysreqs to fix sanitizer action
d1dd01b 
Squashed commit of the following:

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Author: sciome-bot <software.tools@sciome.com>
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Date:   Fri Apr 5 16:38:34 2024 -0400

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Date:   Thu Feb 8 14:24:34 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:19:24 2024 -0500

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Date:   Thu Feb 8 14:18:48 2024 -0500

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Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

    Resolved merge conflict

commit b431df4
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

    Removed vignette, fixed lint issues

commit 7e330f3
Merge: 13a6f44 f49d076
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Feb 7 23:25:05 2024 -0500

    Merge branch 'master' of ssh://sciome-bot/stat/prestogp

commit f49d076
Merge: 439790c 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Feb 7 23:19:54 2024 -0500

    Pull request #35: Eb dev

    Merge in STAT/prestogp from eb-dev to master

    * commit '59baf720737abe59a04c98705c950ef1c7b63321':
      Fixed some documentation issues
      Removed C++11 compiler flag
      Added RandomFields data sets to PrestoGP
      Added knitr to Suggests in DESCRIPTION
      Documentation, R-cmd-check fixes, binomial regression

... and 37 more commits
sciome-bot pushed a commit that referenced this issue Dec 29, 2024
@ericbair-sciome @shail-choksi
Pull request #38: Removed vignette, fixed lint issues
bab8357 
Merge in STAT/prestogp from eb-dev to master

* commit '53947729624b47fa1920ef39bd23d86f6e5cd7b7':
  Removed vignette, fixed lint issues
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Sciome update: sparseNN bug fix and new tests NIEHS/PrestoGP
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