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Input validation is inadequate for multivariate models #27

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ericbair-sciome opened this issue Nov 12, 2023 · 1 comment · Fixed by #44
Closed

Input validation is inadequate for multivariate models #27

ericbair-sciome opened this issue Nov 12, 2023 · 1 comment · Fixed by #44
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@ericbair-sciome
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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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Eric Wimberley coded some input validation checks for univariate data (X should be a matrix, y should be a numeric vector, etc.). Currently the checks for multivariate data are inadequate. This should be fixed.
@ericbair-sciome ericbair-sciome added enhancement New feature or request version 1.0 Features that should be included in the initial PrestoGP release labels Nov 12, 2023
@ericbair-sciome ericbair-sciome self-assigned this Dec 16, 2023
@ericbair-sciome ericbair-sciome linked a pull request Jan 10, 2024 that will close this issue
Sciome Update 1/10/2024 #44
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@ericbair-sciome
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This is fixed in the latest update.

sciome-bot pushed a commit that referenced this issue Jan 13, 2024
@shail-choksi
Pull request #31: Fixed merge issues caused by linting. Fixed tests
9b10201 
Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit db6cd4f
Merge: 55607e2 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 12:11:56 2024 -0500

    Pull request #29: Fixed some bugs caused by the linter

    Merge in STAT/prestogp from eb-dev to master

    * commit '7da2588abba4491c1ff490de95e834d00f5df88e':
      Fixed some bugs caused by the linter

commit 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 01:37:58 2024 -0500

    Fixed some bugs caused by the linter

commit 55607e2
Merge: c7ed481 81b675d
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:37:55 2024 -0500

    Pull request #28: Final linting fixes

    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

commit 81b675d
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:36:05 2024 -0500

    Fix remaining linting issues

commit 06673a4
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:23:11 2024 -0500

    Fix all indentation errors

commit c7ed481
Merge: 723c3eb 7bcfa1a
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:02:59 2024 -0500

    Pull request #27: Lintr fixes. Added release and sanitizer actions

    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
      ...

commit 29d82cd
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:40:17 2024 -0500

    Add indentation_linter configuration to lintr config file

commit 7bcfa1a
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:16:01 2024 -0500

    Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file

commit b6df473
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 17:54:50 2024 -0500

    More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter

commit 6f6f91d
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 17:32:12 2024 -0500

    WIP: Fix linter warnings for 1:nrow, 1:ncol and 1:length. Increase line length to 160 chars

commit 2db2e19
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:48:59 2024 -0500

    Don't build vignettes during the release action

commit c539223
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:39:52 2024 -0500

    Move release action file to correct directory

commit f83df2b
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:36:03 2024 -0500

    Add release action

commit c84e159
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:04:36 2024 -0500

    Reorder imports in RcppExports file

commit 0460202
Merge: 245eaa3 43ae272
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 15:48:30 2024 -0500

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

commit 245eaa3
Merge: 5355e24 c060815
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 15:47:42 2024 -0500

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

commit c060815
Merge: 731da76 6d69b69
Author: {SET}group <127860447+Spatiotemporal-Exposures-and-Toxicology@users.noreply.github.com>
Date:   Thu Jan 11 16:02:52 2024 -0500

    Merge pull request #44 from Spatiotemporal-Exposures-and-Toxicology/main-sciome

    Sciome Update 1/10/2024

commit 6d69b69
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Jan 11 14:39:39 2024 -0500

    Add missing dependency in Namespace/Description

commit bdf52c6
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Jan 11 14:30:38 2024 -0500

    Remove unneeded exports from NAMESPACE

commit 06918b0
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Jan 11 14:15:45 2024 -0500

    Add missing comma in Imports section of DESCRIPTION

... and 13 more commits
sciome-bot pushed a commit that referenced this issue Jan 14, 2024
@shail-choksi
Pull request #34: Fix tolerance and expected values for tests
8ffb20b 
Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit 439790c
Merge: f4af0d1 56f881f
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Jan 14 10:58:49 2024 -0500

    Pull request #32: Fixed some testthat issues

    Merge in STAT/prestogp from eb-dev to master

    * commit '56f881f96a0e55e60bca3c8a840ec31291665594':
      Fixed some testthat issues

commit 56f881f
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 14:05:12 2024 -0500

    Fixed some testthat issues

commit f4af0d1
Merge: db6cd4f ee193de
Author: sciome-bot <software.tools@sciome.com>
Date:   Sat Jan 13 12:37:28 2024 -0500

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

commit db6cd4f
Merge: 55607e2 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 12:11:56 2024 -0500

    Pull request #29: Fixed some bugs caused by the linter

    Merge in STAT/prestogp from eb-dev to master

    * commit '7da2588abba4491c1ff490de95e834d00f5df88e':
      Fixed some bugs caused by the linter

commit 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 01:37:58 2024 -0500

    Fixed some bugs caused by the linter

commit 55607e2
Merge: c7ed481 81b675d
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:37:55 2024 -0500

    Pull request #28: Final linting fixes

    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

commit 81b675d
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:36:05 2024 -0500

    Fix remaining linting issues

commit 06673a4
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:23:11 2024 -0500

    Fix all indentation errors

commit c7ed481
Merge: 723c3eb 7bcfa1a
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:02:59 2024 -0500

    Pull request #27: Lintr fixes. Added release and sanitizer actions

    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
      ...

commit 29d82cd
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:40:17 2024 -0500

    Add indentation_linter configuration to lintr config file

commit 7bcfa1a
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:16:01 2024 -0500

    Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file

commit b6df473
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 17:54:50 2024 -0500

    More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter

commit 6f6f91d
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 17:32:12 2024 -0500

    WIP: Fix linter warnings for 1:nrow, 1:ncol and 1:length. Increase line length to 160 chars

commit 2db2e19
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:48:59 2024 -0500

    Don't build vignettes during the release action

commit c539223
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:39:52 2024 -0500

    Move release action file to correct directory

commit f83df2b
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:36:03 2024 -0500

    Add release action

commit c84e159
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 16:04:36 2024 -0500

    Reorder imports in RcppExports file

commit 0460202
Merge: 245eaa3 43ae272
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 15:48:30 2024 -0500

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

commit 245eaa3
Merge: 5355e24 c060815
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 15:47:42 2024 -0500

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

commit c060815
Merge: 731da76 6d69b69
Author: {SET}group <127860447+Spatiotemporal-Exposures-and-Toxicology@users.noreply.github.com>
Date:   Thu Jan 11 16:02:52 2024 -0500

    Merge pull request #44 from Spatiotemporal-Exposures-and-Toxicology/main-sciome

    Sciome Update 1/10/2024

... and 13 more commits
sciome-bot pushed a commit that referenced this issue Feb 8, 2024
@shail-choksi
Pull request #37: Added documentation. Added RandomFields data sets. …
076c0a1 
…Fixed R CMD issues

Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit 7e330f3
Merge: 13a6f44 f49d076
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Feb 7 23:25:05 2024 -0500

    Merge branch 'master' of ssh://sciome-bot/stat/prestogp

commit f49d076
Merge: 439790c 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Feb 7 23:19:54 2024 -0500

    Pull request #35: Eb dev

    Merge in STAT/prestogp from eb-dev to master

    * commit '59baf720737abe59a04c98705c950ef1c7b63321':
      Fixed some documentation issues
      Removed C++11 compiler flag
      Added RandomFields data sets to PrestoGP
      Added knitr to Suggests in DESCRIPTION
      Documentation, R-cmd-check fixes, binomial regression

commit 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

    Fixed some documentation issues

commit d857d8b
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

    Removed C++11 compiler flag

commit 662907d
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

    Added RandomFields data sets to PrestoGP

commit cf2aadb
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 13:40:24 2024 -0500

    Added knitr to Suggests in DESCRIPTION

commit ef5f2c9
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 01:31:53 2024 -0500

    Documentation, R-cmd-check fixes, binomial regression

commit 13a6f44
Merge: 439790c 8ffb20b
Author: sciome-bot <software.tools@sciome.com>
Date:   Sun Jan 14 11:46:17 2024 -0500

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

commit 439790c
Merge: f4af0d1 56f881f
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Jan 14 10:58:49 2024 -0500

    Pull request #32: Fixed some testthat issues

    Merge in STAT/prestogp from eb-dev to master

    * commit '56f881f96a0e55e60bca3c8a840ec31291665594':
      Fixed some testthat issues

commit 56f881f
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 14:05:12 2024 -0500

    Fixed some testthat issues

commit f4af0d1
Merge: db6cd4f ee193de
Author: sciome-bot <software.tools@sciome.com>
Date:   Sat Jan 13 12:37:28 2024 -0500

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

commit db6cd4f
Merge: 55607e2 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 12:11:56 2024 -0500

    Pull request #29: Fixed some bugs caused by the linter

    Merge in STAT/prestogp from eb-dev to master

    * commit '7da2588abba4491c1ff490de95e834d00f5df88e':
      Fixed some bugs caused by the linter

commit 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 01:37:58 2024 -0500

    Fixed some bugs caused by the linter

commit 55607e2
Merge: c7ed481 81b675d
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:37:55 2024 -0500

    Pull request #28: Final linting fixes

    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

commit 81b675d
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:36:05 2024 -0500

    Fix remaining linting issues

commit 06673a4
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:23:11 2024 -0500

    Fix all indentation errors

commit c7ed481
Merge: 723c3eb 7bcfa1a
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:02:59 2024 -0500

    Pull request #27: Lintr fixes. Added release and sanitizer actions

    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
      ...

commit 29d82cd
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:40:17 2024 -0500

    Add indentation_linter configuration to lintr config file

commit 7bcfa1a
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:16:01 2024 -0500

    Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file

commit b6df473
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 17:54:50 2024 -0500

    More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter

... and 21 more commits
sciome-bot pushed a commit that referenced this issue Dec 29, 2024
@shail-choksi @ericbair-sciome
Pull request #27: Lintr fixes. Added release and sanitizer actions
c7ed481 
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
  ...
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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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Sciome Update 1/10/2024 NIEHS/PrestoGP
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