Minor bug fixes and usability improvements #85
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…t file. Fix all vector_logic_linter warnings
…res-and-Toxicology/PrestoGP into build-workflow
…xicology/PrestoGP into build-workflow
…res-and-Toxicology/PrestoGP into build-workflow
…ne length to 160 chars
Merge in STAT/prestogp from build-workflow to master * commit '7bcfa1aca78cc6b994cc0227c083357c58d50ca0': (21 commits) Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter WIP: Fix linter warnings for 1:nrow, 1:ncol and 1:length. Increase line length to 160 chars Don't build vignettes during the release action Move release action file to correct directory Add release action Reorder imports in RcppExports file Add missing dependency in Namespace/Description Remove unneeded exports from NAMESPACE Add missing comma in Imports section of DESCRIPTION Add missing comma in imports section of DESCRIPTION Rerun auto-formatter WIP - linting Add ignore rules for .lintr and .github for R build remove linter options from lint action as we have added .lintr project file. Fix all vector_logic_linter warnings Remove line length linter to see the remaining errors/warnings workaround for lintr bug: REditorSupport/languageserver#89 Run auto-lint on vscode enable linting on build-workflow Add missing imports in DESCRIPTION ...
Merge in STAT/prestogp from build-workflow to master * commit '81b675dda9b57f2a362c34876364adf5bcf45560': Fix remaining linting issues Fix all indentation errors Add indentation_linter configuration to lintr config file
Merge in STAT/prestogp from eb-dev to master * commit '7da2588abba4491c1ff490de95e834d00f5df88e': Fixed some bugs caused by the linter
…-and-Toxicology/PrestoGP
Merge in STAT/prestogp from eb-dev to master * commit '53621abee364becbdd7f4bc3f860ce2d048f6f9a': More accurate imputation
…res-and-Toxicology/PrestoGP
Merge in STAT/prestogp from eb-dev to master * commit 'e215b772485d2dfcaa151e9b31b78fff5bf64f2a': Added new .Rd files Improved show/accessor methods
* 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
## 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
## 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
This was
linked to
issues
Dec 24, 2024
|
@ericbair-sciome @sciome-bot The |
|
This is really strange. It is possible that the parameter tests could fail due to bad luck, but the likelihood tests should never fail. And I have run these tests on all of my machines and they passed. The only thing I can think of is that maybe this is an issue with different versions of R. I have had issues in the past with tests failing after I upgraded to a new version of R. I will look into this and see if I can figure out what is going on. |
Merge in STAT/prestogp from eb-dev to master * commit 'c7f9bb5b524d150fd9f6dd3604e76c91833b3d4f': Fixed some issues with tests
|
@sciome-bot @ericbair-sciome @shail-choksi Tests passed 🚀 Merging 🌐 |
sciome-bot
added a commit
that referenced
this pull request
Jan 29, 2025
Merge in STAT/prestogp from master to to-git Squashed commit of the following: commit 5ecff193c23747654e165b87dc855ab2c13f2880 Merge: 4b5f559 d5c2427 Author: Eric Bair <[email protected]> Date: Wed Jan 29 13:46:34 2025 -0500 Pull request #72: Faster imputation # PrestoGP 0.2.0.9043 (2025-1-29) ## BUG FIXES * Imputation code has been rewritten to avoid computing the full covariance matrix, resulting in a huge performance improvement * The nntmvn package dependency has been removed to fix errors caused by a recent update * commit 'd5c24277518f3bc3a71d496f1d9afc968f8e0d8b': Faster imputation Faster imputation commit d5c24277518f3bc3a71d496f1d9afc968f8e0d8b Author: Eric Bair <[email protected]> Date: Wed Jan 29 10:24:57 2025 -0500 Faster imputation commit 1cab9af7692852cb3e8bb6505bc6d9b2251a7dbd Author: Eric Bair <[email protected]> Date: Wed Jan 29 10:19:35 2025 -0500 Faster imputation commit 4b5f559603da98895d218e05d0e83746e3f6e2a3 Merge: 8ddb266 6ee742f Author: Eric Bair <[email protected]> Date: Mon Jan 27 12:53:17 2025 -0500 Pull request #71: Relaxed lasso # PrestoGP 0.2.0.9042 (2025-1-14) ## BREAKING CHANGES * The slot `lambda_1se_idx` has been removed from the `PrestoGPModel` superclass ## NEW FEATURES * Added the option `relax` to `prestogp_fit` to allow fitting a relaxed lasso model ## MINOR IMPROVEMENTS * Eliminated the type checking on the `linear_model` slot in the `PrestoGPModel` superclass, which will allow new types of regression models (e.g., relaxed lasso, SCAD, MCP) * commit '6ee742fb4b6553c4945345f56a2f85f337d2fbd9': Relaxed lasso commit 6ee742fb4b6553c4945345f56a2f85f337d2fbd9 Author: Eric Bair <[email protected]> Date: Tue Jan 14 18:03:25 2025 -0500 Relaxed lasso commit 8ddb266aead77c33acb62f7bff1c29b27d41e19c Merge: 98ce34b c405919 Author: Eric Bair <[email protected]> Date: Thu Jan 9 17:41:50 2025 -0500 Pull request #69: Adaptive lasso Merge in STAT/prestogp from eb-dev to master * commit 'c405919b5a3e050eb89869703cca77fe671b49e9': Adaptive lasso commit c405919b5a3e050eb89869703cca77fe671b49e9 Author: Eric Bair <[email protected]> Date: Tue Jan 7 12:38:43 2025 -0500 Adaptive lasso commit 98ce34b36b7156e4d6ecdde22a50ba749635845a Merge: ff0e307 291bb10 Author: sciome-bot <[email protected]> Date: Tue Jan 7 10:59:08 2025 -0500 Merge branch 'main' commit 291bb10ded0f9d21bf6a67178aed6afaa0443f28 Merge: a611fc5 4f5a781 Author: sciome-bot <[email protected]> Date: Tue Jan 7 10:58:42 2025 -0500 Merge branch 'main-sciome' commit 4f5a781 Merge: bce459f ec91a82 Author: sciome-bot <[email protected]> Date: Mon Jan 6 22:25:04 2025 -0500 Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git commit ff0e3077844d006920198eab5dee639c2dd95ad2 Merge: 6b318ba db6c581 Author: Eric Bair <[email protected]> Date: Mon Jan 6 15:54:40 2025 -0500 Pull request #67: Renamed functions and parameters, documentation fixes PrestoGP 0.2.0.9040 (2025-1-3) BREAKING CHANGES The function create.param.sequence has been renamed to be create_param_sequence for consistency with other function names The parameter apanasovich has been renamed common_scale throughout the package MINOR IMPROVEMENTS Tests were updated to reflect the new common_scale parameter and the create_param_sequence function Fixed some formatting issues in NEWS.md DOCUMENTATION FIXES The documentation for create_param_seqence was updated to clarify how to extract/assign scale parameters when there is more than one scale parameter per outcome The documentation for PrestoGP-Model-class and prestogp_fit has been updated to reflect the new common_scale parameter * commit 'db6c581cbc4eb30a3cf141ec85bd369a9f146184': Renamed functions and parameters, documentation fixes commit db6c581cbc4eb30a3cf141ec85bd369a9f146184 Author: Eric Bair <[email protected]> Date: Fri Jan 3 13:06:56 2025 -0500 Renamed functions and parameters, documentation fixes commit a611fc5 Merge: 39c0ffc ec91a82 Author: {SET}group <[email protected]> Date: Sun Dec 29 17:56:58 2024 -0500 Merge pull request #85 from NIEHS/main-sciome Minor bug fixes and usability improvements commit ec91a82 Merge: c8a7d10 fbaed19 Author: sciome-bot <[email protected]> Date: Sun Dec 29 12:56:08 2024 -0500 Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git commit fbaed19 Merge: 491476e b7e6887 Author: sciome-bot <[email protected]> Date: Tue Dec 24 11:48:32 2024 -0500 Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git
sciome-bot
added a commit
that referenced
this pull request
Jan 29, 2025
Merge in STAT/prestogp from master to to-git Squashed commit of the following: commit 5ecff193c23747654e165b87dc855ab2c13f2880 Merge: 4b5f559 d5c2427 Author: Eric Bair <[email protected]> Date: Wed Jan 29 13:46:34 2025 -0500 Pull request #72: Faster imputation # PrestoGP 0.2.0.9043 (2025-1-29) ## BUG FIXES * Imputation code has been rewritten to avoid computing the full covariance matrix, resulting in a huge performance improvement * The nntmvn package dependency has been removed to fix errors caused by a recent update * commit 'd5c24277518f3bc3a71d496f1d9afc968f8e0d8b': Faster imputation Faster imputation commit d5c24277518f3bc3a71d496f1d9afc968f8e0d8b Author: Eric Bair <[email protected]> Date: Wed Jan 29 10:24:57 2025 -0500 Faster imputation commit 1cab9af7692852cb3e8bb6505bc6d9b2251a7dbd Author: Eric Bair <[email protected]> Date: Wed Jan 29 10:19:35 2025 -0500 Faster imputation commit 4b5f559603da98895d218e05d0e83746e3f6e2a3 Merge: 8ddb266 6ee742f Author: Eric Bair <[email protected]> Date: Mon Jan 27 12:53:17 2025 -0500 Pull request #71: Relaxed lasso # PrestoGP 0.2.0.9042 (2025-1-14) ## BREAKING CHANGES * The slot `lambda_1se_idx` has been removed from the `PrestoGPModel` superclass ## NEW FEATURES * Added the option `relax` to `prestogp_fit` to allow fitting a relaxed lasso model ## MINOR IMPROVEMENTS * Eliminated the type checking on the `linear_model` slot in the `PrestoGPModel` superclass, which will allow new types of regression models (e.g., relaxed lasso, SCAD, MCP) * commit '6ee742fb4b6553c4945345f56a2f85f337d2fbd9': Relaxed lasso commit 6ee742fb4b6553c4945345f56a2f85f337d2fbd9 Author: Eric Bair <[email protected]> Date: Tue Jan 14 18:03:25 2025 -0500 Relaxed lasso commit 8ddb266aead77c33acb62f7bff1c29b27d41e19c Merge: 98ce34b c405919 Author: Eric Bair <[email protected]> Date: Thu Jan 9 17:41:50 2025 -0500 Pull request #69: Adaptive lasso Merge in STAT/prestogp from eb-dev to master * commit 'c405919b5a3e050eb89869703cca77fe671b49e9': Adaptive lasso commit c405919b5a3e050eb89869703cca77fe671b49e9 Author: Eric Bair <[email protected]> Date: Tue Jan 7 12:38:43 2025 -0500 Adaptive lasso commit 98ce34b36b7156e4d6ecdde22a50ba749635845a Merge: ff0e307 291bb10 Author: sciome-bot <[email protected]> Date: Tue Jan 7 10:59:08 2025 -0500 Merge branch 'main' commit 291bb10ded0f9d21bf6a67178aed6afaa0443f28 Merge: a611fc5 4f5a781 Author: sciome-bot <[email protected]> Date: Tue Jan 7 10:58:42 2025 -0500 Merge branch 'main-sciome' commit 4f5a781 Merge: bce459f ec91a82 Author: sciome-bot <[email protected]> Date: Mon Jan 6 22:25:04 2025 -0500 Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git commit ff0e3077844d006920198eab5dee639c2dd95ad2 Merge: 6b318ba db6c581 Author: Eric Bair <[email protected]> Date: Mon Jan 6 15:54:40 2025 -0500 Pull request #67: Renamed functions and parameters, documentation fixes PrestoGP 0.2.0.9040 (2025-1-3) BREAKING CHANGES The function create.param.sequence has been renamed to be create_param_sequence for consistency with other function names The parameter apanasovich has been renamed common_scale throughout the package MINOR IMPROVEMENTS Tests were updated to reflect the new common_scale parameter and the create_param_sequence function Fixed some formatting issues in NEWS.md DOCUMENTATION FIXES The documentation for create_param_seqence was updated to clarify how to extract/assign scale parameters when there is more than one scale parameter per outcome The documentation for PrestoGP-Model-class and prestogp_fit has been updated to reflect the new common_scale parameter * commit 'db6c581cbc4eb30a3cf141ec85bd369a9f146184': Renamed functions and parameters, documentation fixes commit db6c581cbc4eb30a3cf141ec85bd369a9f146184 Author: Eric Bair <[email protected]> Date: Fri Jan 3 13:06:56 2025 -0500 Renamed functions and parameters, documentation fixes commit a611fc5 Merge: 39c0ffc ec91a82 Author: {SET}group <[email protected]> Date: Sun Dec 29 17:56:58 2024 -0500 Merge pull request #85 from NIEHS/main-sciome Minor bug fixes and usability improvements commit ec91a82 Merge: c8a7d10 fbaed19 Author: sciome-bot <[email protected]> Date: Sun Dec 29 12:56:08 2024 -0500 Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git commit fbaed19 Merge: 491476e b7e6887 Author: sciome-bot <[email protected]> Date: Tue Dec 24 11:48:32 2024 -0500 Merge branch 'main-sciome' of github-sciome:NIEHS/PrestoGP into to-git
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NEW FEATURES
Added the method
get_Yto extract the Y values (including the imputedY values) from a PrestoGP model
Added the method
get_linear_modelto extract the fitted cv.glmnet objectfrom a PrestoGP model
Added the method
plot_betato plot the glide path of theregression coefficients
MINOR IMPROVEMENTS
Added a NEWS.md file to track changes in each update
Modified the
showmethod to not print zero betasModified
prestogp_predictto retun predictions in the form of alist for multivariate models
BUG FIXES
Fixed a bug in the intercept calculation in
get_betabeing assigned arbitrary variable names
DOCUMENTATION FIXES
Updated the documention in
PrestoGPModel-classto reflect that theY_train slot is updated to contain imputed values during model
fitting