Parallel createUMultivariate and test fixes #78
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Collaborator
sciome-bot
commented
Dec 6, 2024
•
sciome-bot
commented
- Parallel createUMultivariate using OpenMP
- Added BH dependecy for boost math functions
- Minor tweaks to further optimize imputation
- Test fixes for latest version of R
Merge in STAT/prestogp from master to to-git Squashed commit of the following: commit 93a0e4f Merge: abf92aa 55d9113 Author: sciome-bot <[email protected]> Date: Fri Dec 6 13:07:51 2024 -0500 Merge branch 'master' into to-git commit 55d9113 Merge: 49819ab 1416407 Author: Eric Bair <[email protected]> Date: Fri Dec 6 12:59:52 2024 -0500 Pull request #61: Optimizations, test fixes and BH dependency * commit '1416407582bda359d58681890fa5853b8f25b48d': Fixed some lint issues New data files for tests Parallel createUMultivariate, fixed tests, and other minor updates Removed R lib dependency in matern1 commit 1416407 Author: Eric Bair <[email protected]> Date: Thu Dec 5 03:38:13 2024 -0500 Fixed some lint issues commit 0bc1a1e Author: Eric Bair <[email protected]> Date: Wed Dec 4 23:44:19 2024 -0500 New data files for tests commit 58e06c1 Author: Eric Bair <[email protected]> Date: Wed Dec 4 23:43:42 2024 -0500 Parallel createUMultivariate, fixed tests, and other minor updates commit 6ebe45b Author: Eric Bair <[email protected]> Date: Thu Nov 14 17:56:19 2024 -0500 Removed R lib dependency in matern1 commit 49819ab Merge: 67c103b e215b77 Author: Eric Bair <[email protected]> Date: Fri Nov 1 12:33:35 2024 -0400 Pull request #57: Eb dev Merge in STAT/prestogp from eb-dev to master * commit 'e215b772485d2dfcaa151e9b31b78fff5bf64f2a': Added new .Rd files Improved show/accessor methods commit e215b77 Author: Eric Bair <[email protected]> Date: Thu Oct 24 17:03:43 2024 -0400 Added new .Rd files commit 89f65ae Author: Eric Bair <[email protected]> Date: Thu Oct 24 17:02:36 2024 -0400 Improved show/accessor methods commit 67c103b Merge: e12a1a9 99e85a4 Author: sciome-bot <[email protected]> Date: Tue Sep 10 16:11:37 2024 -0400 Merge branch 'main-sciome' of github-sciome-bot:Spatiotemporal-Exposures-and-Toxicology/PrestoGP commit 99e85a4 Merge: f9712d6 6bf83a9 Author: {SET}group <[email protected]> Date: Thu Sep 5 09:18:56 2024 -0400 Merge pull request #73 from NIEHS/main-sciome Improving imputation accuracy commit e12a1a9 Merge: 44951f2 53621ab Author: Eric Bair <[email protected]> Date: Fri Aug 30 23:34:45 2024 -0400 Pull request #55: More accurate imputation Merge in STAT/prestogp from eb-dev to master * commit '53621abee364becbdd7f4bc3f860ce2d048f6f9a': More accurate imputation commit 53621ab Author: Eric Bair <[email protected]> Date: Sat Aug 24 14:52:27 2024 -0400 More accurate imputation commit f9712d6 Merge: b814826 2ce73ce Author: ericbair-sciome <[email protected]> Date: Sat Aug 24 14:45:45 2024 -0400 Merge pull request #72 from NIEHS/main-sciome Faster imputation commit 44951f2 Merge: edef68f b814826 Author: sciome-bot <[email protected]> Date: Tue Aug 20 13:52:53 2024 -0400 Merge branch 'main' of sciome-bot-git:NIEHS/PrestoGP commit edef68f Merge: 1144744 ca1db91 Author: Eric Bair <[email protected]> Date: Tue Aug 20 12:19:27 2024 -0400 Pull request #53: Faster imputation Merge in STAT/prestogp from eb-dev to master * commit 'ca1db918136625308410d0ae6a37c5d834292fc2': Faster imputation commit ca1db91 Author: Eric Bair <[email protected]> Date: Mon Aug 19 20:40:28 2024 -0400 Faster imputation commit b814826 Merge: f661f11 a80245d Author: {SET}group <[email protected]> Date: Tue Jul 30 14:45:46 2024 -0400 Merge pull request #67 from NIEHS/main-sciome Improved imputation & bug fixes commit 1144744 Merge: 30ee16f 3d3ff39 Author: sciome-bot <[email protected]> Date: Tue Jul 30 10:09:31 2024 -0400 Merge branch 'main-sciome' commit 3d3ff39 Merge: a80245d f661f11 Author: sciome-bot <[email protected]> Date: Tue Jul 30 09:38:32 2024 -0400 Merge branch 'main' into main-sciome ... and 81 more commits
sciome-bot
added a commit
that referenced
this pull request
Dec 24, 2024
## NEW FEATURES
* Added the method `get_Y` to extract the Y values (including the imputed
Y values) from a PrestoGP model
* Added the method `get_linear_model` to extract the fitted cv.glmnet object
from a PrestoGP model
* Added the method `plot_beta` to plot the glide path of the
regression coefficients
## MINOR IMPROVEMENTS
* Added a NEWS.md file to track changes in each update
* Modified the `show` method to not print zero betas
* Modified `prestogp_predict` to retun predictions in the form of a
list for multivariate models
## BUG FIXES
* Fixed a bug in the intercept calculation in `get_beta`
* Fixed a bug where multivariate models with no variable names for X were
being assigned arbitrary variable names
## DOCUMENTATION FIXES
* Updated the documention in `PrestoGPModel-class` to reflect that the
Y_train slot is updated to contain imputed values during model
fitting
* Added documentation for all new methods
Squashed commit of the following:
commit 426aa08
Merge: 8e5ad67 39c0ffc
Author: sciome-bot <[email protected]>
Date: Tue Dec 24 11:24:53 2024 -0500
Merge branch 'main'
commit 8e5ad67
Merge: 93a0e4f 685b855
Author: Eric Bair <[email protected]>
Date: Tue Dec 24 11:15:21 2024 -0500
Pull request #63: Minor bug fixes and usability improvements
## NEW FEATURES
* Added the method `get_Y` to extract the Y values (including the imputed
Y values) from a PrestoGP model
* Added the method `get_linear_model` to extract the fitted cv.glmnet object
from a PrestoGP model
* Added the method `plot_beta` to plot the glide path of the
regression coefficients
## MINOR IMPROVEMENTS
* Added a NEWS.md file to track changes in each update
* Modified the `show` method to not print zero betas
* Modified `prestogp_predict` to retun predictions in the form of a
list for multivariate models
## BUG FIXES
* Fixed a bug in the intercept calculation in `get_beta`
* Fixed a bug where multivariate models with no variable names for X were
being assigned arbitrary variable names
## DOCUMENTATION FIXES
* Updated the documention in `PrestoGPModel-class` to reflect that the
Y_train slot is updated to contain imputed values during model
fitting
* Added documentation for all new methods
* commit '685b8556b5e69dfd5b691c9c17176becdc90fb2e':
Minor bug fixes and usability improvements
commit 685b855
Author: Eric Bair <[email protected]>
Date: Mon Dec 23 02:42:20 2024 -0500
Minor bug fixes and usability improvements
commit 39c0ffc
Merge: c3937f4 b7e6887
Author: {SET}group <[email protected]>
Date: Fri Dec 6 19:12:53 2024 -0300
Merge pull request #78 from NIEHS/main-sciome
Parallel createUMultivariate and test fixes
commit b7e6887
Merge: 10b8611 7625edf
Author: sciome-bot <[email protected]>
Date: Fri Dec 6 15:04:28 2024 -0500
Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git
commit 93a0e4f
Merge: abf92aa 55d9113
Author: sciome-bot <[email protected]>
Date: Fri Dec 6 13:07:51 2024 -0500
Merge branch 'master' into to-git
commit 55d9113
Merge: 49819ab 1416407
Author: Eric Bair <[email protected]>
Date: Fri Dec 6 12:59:52 2024 -0500
Pull request #61: Optimizations, test fixes and BH dependency
* commit '1416407582bda359d58681890fa5853b8f25b48d':
Fixed some lint issues
New data files for tests
Parallel createUMultivariate, fixed tests, and other minor updates
Removed R lib dependency in matern1
commit 1416407
Author: Eric Bair <[email protected]>
Date: Thu Dec 5 03:38:13 2024 -0500
Fixed some lint issues
commit 0bc1a1e
Author: Eric Bair <[email protected]>
Date: Wed Dec 4 23:44:19 2024 -0500
New data files for tests
commit 58e06c1
Author: Eric Bair <[email protected]>
Date: Wed Dec 4 23:43:42 2024 -0500
Parallel createUMultivariate, fixed tests, and other minor updates
commit c3937f4
Merge: 99e85a4 7625edf
Author: {SET}group <[email protected]>
Date: Thu Nov 21 23:33:06 2024 -0300
Merge pull request #74 from NIEHS/main-sciome
Added documentation and Improved show/accessor methods
commit 6ebe45b
Author: Eric Bair <[email protected]>
Date: Thu Nov 14 17:56:19 2024 -0500
Removed R lib dependency in matern1
commit 7625edf
Merge: abf92aa 99e85a4
Author: sciome-bot <[email protected]>
Date: Mon Nov 4 15:16:34 2024 -0500
Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git
commit 49819ab
Merge: 67c103b e215b77
Author: Eric Bair <[email protected]>
Date: Fri Nov 1 12:33:35 2024 -0400
Pull request #57: Eb dev
Merge in STAT/prestogp from eb-dev to master
* commit 'e215b772485d2dfcaa151e9b31b78fff5bf64f2a':
Added new .Rd files
Improved show/accessor methods
commit e215b77
Author: Eric Bair <[email protected]>
Date: Thu Oct 24 17:03:43 2024 -0400
Added new .Rd files
commit 89f65ae
Author: Eric Bair <[email protected]>
Date: Thu Oct 24 17:02:36 2024 -0400
Improved show/accessor methods
commit 67c103b
Merge: e12a1a9 99e85a4
Author: sciome-bot <[email protected]>
Date: Tue Sep 10 16:11:37 2024 -0400
Merge branch 'main-sciome' of github-sciome-bot:Spatiotemporal-Exposures-and-Toxicology/PrestoGP
commit 99e85a4
Merge: f9712d6 6bf83a9
Author: {SET}group <[email protected]>
Date: Thu Sep 5 09:18:56 2024 -0400
Merge pull request #73 from NIEHS/main-sciome
Improving imputation accuracy
commit e12a1a9
Merge: 44951f2 53621ab
Author: Eric Bair <[email protected]>
Date: Fri Aug 30 23:34:45 2024 -0400
Pull request #55: More accurate imputation
Merge in STAT/prestogp from eb-dev to master
* commit '53621abee364becbdd7f4bc3f860ce2d048f6f9a':
More accurate imputation
commit 53621ab
Author: Eric Bair <[email protected]>
Date: Sat Aug 24 14:52:27 2024 -0400
More accurate imputation
... and 88 more commits
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.