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Squashed commit of the following: 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 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 commit 30ee16f Merge: bc7485f fe89b1d Author: Eric Bair <[email protected]> Date: Tue Jul 30 08:21:10 2024 -0400 Fixed an R CMD check issue * commit 'fe89b1d98a2c721a591248bbd350def08b1b8a29': Fixed an R CMD check issue commit fe89b1d Author: Eric Bair <[email protected]> Date: Mon Jul 29 16:26:09 2024 -0400 Fixed an R CMD check issue commit bc7485f Merge: aa730b5 ad848a2 Author: Eric Bair <[email protected]> Date: Mon Jul 29 10:50:32 2024 -0400 Improved imputation, bug fixes * commit 'ad848a27747b933f69f4405a33dac346e4a7d51a': Improved imputation, bug fixes Improved imputation, bug fixes commit f661f11 Merge: bcecebd 052209a Author: {SET}group <[email protected]> Date: Thu Jul 25 13:29:24 2024 -0400 Merge pull request #66 from NIEHS/kpm-logo usethis logo for site commit 052209a Author: kyle-messier <[email protected]> Date: Thu Jul 25 12:48:25 2024 -0400 removing link in readme commit 613d6d0 Author: kyle-messier <[email protected]> Date: Thu Jul 25 09:15:00 2024 -0400 usethis logo for site commit ad848a2 Author: Eric Bair <[email protected]> Date: Tue Jul 23 04:31:47 2024 -0400 Improved imputation, bug fixes commit 5a2b45c Author: Eric Bair <[email protected]> Date: Tue Jul 23 04:22:44 2024 -0400 Improved imputation, bug fixes commit bcecebd Merge: 1d3285c 7f5cc9d Author: {SET}group <[email protected]> Date: Sat Jul 20 13:39:54 2024 -0400 Merge pull request #65 from NIEHS/kyle-messier-patch-1 Update README.md commit 7f5cc9d Author: {SET}group <[email protected]> Date: Sat Jul 20 13:39:43 2024 -0400 Update README.md commit 1d3285c Merge: 4402255 c8254d4 Author: {SET}group <[email protected]> Date: Fri Jul 19 21:24:23 2024 -0400 Merge pull request #64 from NIEHS/kyle-messier-patch-3 Update README.md commit c8254d4 Author: {SET}group <[email protected]> Date: Fri Jul 19 21:24:13 2024 -0400 Update README.md commit 4402255 Merge: 0306390 ed0bd09 Author: {SET}group <[email protected]> Date: Fri Jul 19 20:43:58 2024 -0400 Merge pull request #63 from NIEHS/kyle-messier-patch-2 Update _pkgdown.yml commit ed0bd09 Author: {SET}group <[email protected]> Date: Fri Jul 19 20:01:18 2024 -0400 Update _pkgdown.yml commit 0306390 Merge: 96b046f 3dfa637 Author: {SET}group <[email protected]> Date: Fri Jul 19 15:13:54 2024 -0400 Merge pull request #62 from NIEHS/kyle-messier-patch-1 Update README.md commit 3dfa637 Author: {SET}group <[email protected]> Date: Thu Jul 18 22:17:04 2024 -0400 Update README.md Fixing badges and workflows from previous direct commit ... and 65 more commits
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I went ahead and merged this pull request because we will be sending a new version in the next few days. |
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Nov 4, 2024
Added documentation and Improved show/accessor methods Squashed commit of the following: 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 commit 30ee16f Merge: bc7485f fe89b1d Author: Eric Bair <[email protected]> Date: Tue Jul 30 08:21:10 2024 -0400 Fixed an R CMD check issue * commit 'fe89b1d98a2c721a591248bbd350def08b1b8a29': Fixed an R CMD check issue commit fe89b1d Author: Eric Bair <[email protected]> Date: Mon Jul 29 16:26:09 2024 -0400 Fixed an R CMD check issue commit bc7485f Merge: aa730b5 ad848a2 Author: Eric Bair <[email protected]> Date: Mon Jul 29 10:50:32 2024 -0400 Improved imputation, bug fixes * commit 'ad848a27747b933f69f4405a33dac346e4a7d51a': Improved imputation, bug fixes Improved imputation, bug fixes commit f661f11 Merge: bcecebd 052209a Author: {SET}group <[email protected]> Date: Thu Jul 25 13:29:24 2024 -0400 Merge pull request #66 from NIEHS/kpm-logo usethis logo for site commit 052209a Author: kyle-messier <[email protected]> Date: Thu Jul 25 12:48:25 2024 -0400 removing link in readme commit 613d6d0 Author: kyle-messier <[email protected]> Date: Thu Jul 25 09:15:00 2024 -0400 usethis logo for site ... and 75 more commits
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Dec 6, 2024
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
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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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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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