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Latest Sciome update: likelihood bug fix and additional testing #36

Merged

ericbair-sciome merged 36 commits into main from main-sciome

Nov 15, 2023

Collaborator

ericbair-sciome commented Nov 14, 2023

This is a minor update that fixes a bug in the full likelihood calculations and adds some additional testing for the likelihood functions.

ericbair-sciome and others added 30 commits

July 17, 2023 16:47


          Created the PrestoGP repository

095c5cd


          New file structure for generalized locs

e71fea9


          Modified package to allow for generalized locs

8a10471


          Added documentation file for generalized locs

5eafef7


          Fixed a bug in the code to generate initial values of theta

3da5580


          Parallel support for glmnet and minor bug fixes

fca8a3e


          Fixed a bug where prestogp_fit crashed when beta.hat was specified

4e26172


          Changed the initial beta estimates to decrease computation time

57fcd00


          Added multivariate prediction functionality

9b42a60


          Removed temporary files

1d6da8a


          Allow for generalized locs, bug fixes and optimizations

7e4d279


          foldid parameter for cv.glmnet and minor bug fixes

140e623


          Pull request #2: foldid parameter for cv.glmnet and minor bug fixes

544a290

Merge in STAT/prestogp from foldid to master

* commit '140e623763a78f706064587c632bb4d519120ea9':
  foldid parameter for cv.glmnet and minor bug fixes


          Update version number. foldid parameter for cv.glmnet and minor bugfixes

b8d6f84


          Fix merge conflict remnant

747f280


          Fix merge conflict remnant

8c1ceda


          Pull request #4: Fix merge conflict remnant in README

2ade51c

Squashed commit of the following:

commit 747f280
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Wed Nov 1 19:48:49 2023 -0400

    Fix merge conflict remnant


          Merge branch 'main-sciome' of github-sciome:Spatiotemporal-Exposures-…

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…and-Toxicology/PrestoGP into to-git


          Merge branch 'main' of github.com:Spatiotemporal-Exposures-and-Toxico…

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…logy/PrestoGP


          Merge branch 'main' of github.com:Spatiotemporal-Exposures-and-Toxico…

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…logy/PrestoGP


          Merge branch 'to-git' of ssh://192.168.167.103:7999/stat/prestogp int…

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…o to-git


          Merge branch 'main-sciome' of github-sciome:Spatiotemporal-Exposures-…

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…and-Toxicology/PrestoGP into to-git


          Clean up merge conflict remnants

0d13ba9


          Clean up merge conflict remnants

57a4177


          Merge branch 'master' of ssh://192.168.167.103:7999/stat/prestogp int…

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…o to-git


          Merge branch 'main-sciome' of github-sciome:Spatiotemporal-Exposures-…

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…and-Toxicology/PrestoGP into to-git


          Added new testthat tests

62f110f


          Added new testing files

a6d1d1b


          Pull request #8: Testing

31f7be3

* commit 'a6d1d1b06e9f640140bad7f03746d14ef0629af4':
  Added new testing files
  Added new testthat tests


          Merge branch 'main-sciome' of github-sciome:Spatiotemporal-Exposures-…

615e30a

…and-Toxicology/PrestoGP into to-git

shail-choksi and others added 6 commits

November 14, 2023 13:06


          Merge branch 'main' of sciome-bot-git:Spatiotemporal-Exposures-and-To…

9094abe

…xicology/PrestoGP into main-sciome


          Merge branch 'main' of sciome-bot-git:Spatiotemporal-Exposures-and-To…

b613143

…xicology/PrestoGP into main-sciome


          Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures…

79011bd

…-and-Toxicology/PrestoGP into main-sciome


          Pull request #9: Testing

84fd72f

* commit '2dd74a21380be960918b6067abec8ec163721853':
  Added a simulation file for testing
  Fixed likelihood function and added additional tests
  Fixed likelihood function and added additional test


          Testing

fb060ff

Fixed likelihood function and added additional test
Fixed likelihood function and added additional tests
Added a simulation file for testing

Squashed commit of the following:

commit 2dd74a2
Author: Eric Bair <eric.bair@sciome.com>
Date:   Mon Nov 13 19:17:43 2023 -0500

    Added a simulation file for testing

commit 6c17318
Author: Eric Bair <eric.bair@sciome.com>
Date:   Mon Nov 13 19:16:32 2023 -0500

    Fixed likelihood function and added additional tests

commit f90ce5e
Author: Eric Bair <eric.bair@sciome.com>
Date:   Mon Nov 13 19:10:57 2023 -0500

    Fixed likelihood function and added additional test


          Merge branch 'main-sciome' of github-sciome:Spatiotemporal-Exposures-…

e7fd7ea

…and-Toxicology/PrestoGP into to-git

ericbair-sciome added bug enhancement labels

ericbair-sciome requested a review from kyle-messier

November 14, 2023 19:06

ericbair-sciome self-assigned this

ericbair-sciome linked an issue

that may be closed by this pull request

Full likelihood is not matching the Vecchia likelihood in some cases #18

Closed

kyle-messier approved these changes

View reviewed changes

Collaborator

kyle-messier left a comment •

edited

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@ericbair-sciome @sciome-bot @shail-choksi

It looks like the example scripts from the NO2 analysis of Messier and Katzfuss was added. Those are probably not needed. No harm at the moment though of course.
Did this resolve the Vecchia matching full likelihood at m = n -1?
Merge with main at your discretion

ericbair-sciome merged commit f9d0185 into main

0 of 2 checks passed

Collaborator Author

ericbair-sciome commented Nov 15, 2023

The NO2 data has been in my version of the package for a while. It was used for a couple examples in the documentation (although I don't think those examples are working anyway). My inclination is to keep using for the univariate regression examples, because people who have read the paper might be interested in seeing that. But if there is a better data set to use for examples, we can always replace it later.

sciome-bot pushed a commit that referenced this pull request


          Pull request #14: Additional Testing

56cdbf2

Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit 17f5284
Merge: ea78ffa 895100d
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Dec 1 10:49:09 2023 -0500

    Pull request #12: Testing

    Merge in STAT/prestogp from testing to master

    * commit '895100db78d89c5082ddfcf1411dad69bdf1b6c5':
      Fixed another sparseNN bug and updated tests
      Fixed a bug in SparseNN
      Added more likelihood and maxmin ordering tests

commit 895100d
Merge: 7f3ca3c fb060ff
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Nov 29 17:02:10 2023 -0500

    Merge branch 'to-git' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into testing

    Conflicts:
    	DESCRIPTION
    	man/prestogp_fit-PrestoGPModel-method.Rd
    	tests/testthat/test-Log_Likelihood.R

    Fixed merge conflicts.

commit 7f3ca3c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Nov 29 16:43:40 2023 -0500

    Fixed another sparseNN bug and updated tests

commit 1ca9586
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Nov 28 18:40:36 2023 -0500

    Fixed a bug in SparseNN

commit 80a9818
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Nov 21 17:49:19 2023 -0500

    Added more likelihood and maxmin ordering tests

commit ea78ffa
Merge: 286ba5d 53e2b0d
Author: sciome-bot <software.tools@sciome.com>
Date:   Mon Nov 20 12:41:08 2023 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP

commit 53e2b0d
Author: {SET}group <127860447+Spatiotemporal-Exposures-and-Toxicology@users.noreply.github.com>
Date:   Fri Nov 17 20:54:40 2023 -0500

    Update README.md with lifecycle badge

commit 2d2e84b
Merge: f9d0185 b7c0809
Author: {SET}group <127860447+Spatiotemporal-Exposures-and-Toxicology@users.noreply.github.com>
Date:   Thu Nov 16 22:13:58 2023 -0500

    Merge pull request #15 from Spatiotemporal-Exposures-and-Toxicology/SET-actions

    partial linting (PrestoGP_Model.R) done thus far

commit b7c0809
Merge: 5705bb4 f9d0185
Author: Messier <messierkp@almbp02184136.local>
Date:   Thu Nov 16 18:43:42 2023 -0500

    fixing conflicts

commit 5705bb4
Merge: d602b8f 391e477
Author: Messier <messierkp@almbp02184136.niehs.nih.gov>
Date:   Thu Nov 16 16:54:00 2023 -0500

    Merge branch 'main' into SET-actions

commit d602b8f
Merge: 60e5fd3 4c1bf2a
Author: Messier <messierkp@almbp02184136.niehs.nih.gov>
Date:   Thu Nov 16 16:51:21 2023 -0500

    Merge branch 'SET-actions' of https://github.com/Spatiotemporal-Exposures-and-Toxicology/PrestoGP into SET-actions

commit 60e5fd3
Author: Messier <messierkp@almbp02184136.niehs.nih.gov>
Date:   Thu Nov 16 16:51:08 2023 -0500

    linting PrestoGP_Model.R

commit 4c1bf2a
Author: {SET}group <127860447+Spatiotemporal-Exposures-and-Toxicology@users.noreply.github.com>
Date:   Thu Nov 16 16:50:31 2023 -0500

    Update lint.yaml 3-linters as NULL

commit f9d0185
Merge: 391e477 e7fd7ea
Author: ericbair-sciome <149633517+ericbair-sciome@users.noreply.github.com>
Date:   Wed Nov 15 15:17:56 2023 -0500

    Merge pull request #36 from Spatiotemporal-Exposures-and-Toxicology/main-sciome

    Latest Sciome update: likelihood bug fix and additional testing

commit e7fd7ea
Merge: fb060ff 84fd72f
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Nov 14 13:16:41 2023 -0500

    Merge branch 'main-sciome' of github-sciome:Spatiotemporal-Exposures-and-Toxicology/PrestoGP into to-git

commit 286ba5d
Merge: f52ebbb 84fd72f
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Nov 14 13:11:48 2023 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP

commit 84fd72f
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Nov 14 13:10:52 2023 -0500

    Pull request #9: Testing

    * commit '2dd74a21380be960918b6067abec8ec163721853':
      Added a simulation file for testing
      Fixed likelihood function and added additional tests
      Fixed likelihood function and added additional test

commit f52ebbb
Merge: 4e0e1ec 2dd74a2
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Nov 14 13:10:51 2023 -0500

    Pull request #9: Testing

    * commit '2dd74a21380be960918b6067abec8ec163721853':
      Added a simulation file for testing
      Fixed likelihood function and added additional tests
      Fixed likelihood function and added additional test

commit 79011bd
Merge: b613143 9094abe
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Nov 14 13:09:25 2023 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP into main-sciome

commit b613143
Merge: 615e30a 391e477
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Nov 14 13:06:44 2023 -0500

    Merge branch 'main' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP into main-sciome

... and 20 more commits

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bug enhancement