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Allow users to specify options for LOD imputation #70

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ericbair-sciome opened this issue Jul 30, 2024 · 0 comments
Open

Allow users to specify options for LOD imputation #70

ericbair-sciome opened this issue Jul 30, 2024 · 0 comments
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enhancement New feature or request version 1.0 Features that should be included in the initial PrestoGP release

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@ericbair-sciome
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As we discussed, we want to modify the LOD imputation code so that users can specify the number of iterations and the convergence tolerance. We should also display some intermediate output if users turn on the "verbose" option if only so that users can kill the procedure if it is taking too long.
@ericbair-sciome ericbair-sciome added enhancement New feature or request version 1.0 Features that should be included in the initial PrestoGP release labels Jul 30, 2024
sciome-bot added a commit that referenced this issue Jan 29, 2025
@sciome-bot
Pull request #70: Adaptive Lasso
bbd78f0 
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 issue Jan 29, 2025
@sciome-bot
Pull request #70: Adaptive Lasso
16afc95 
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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