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Sciome Update 1/10/2024 #44

Merged
merged 45 commits into from
Jan 11, 2024
Merged

Sciome Update 1/10/2024 #44

merged 45 commits into from
Jan 11, 2024

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ericbair-sciome
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This release contains a number of improvements and bug fixes. The main enhancements are listed below:

  • Univariate models (both Vecchia and full) are now working correctly.
  • The code base has been simplified, with many redundant functions removed.
  • The testing code is much more extensive with coverage for all critical functions. All tests are passing on all platforms we tested.

ericbair-sciome and others added 30 commits November 7, 2023 15:38
@ericbair-sciome @shail-choksi
Pull request #7: Testing
4e0e1ec 
Merge in STAT/prestogp from testing to master

* commit 'a6d1d1b06e9f640140bad7f03746d14ef0629af4':
  Added new testing files
  Added new testthat tests
@ericbair-sciome
Fixed likelihood function and added additional test
f90ce5e
@ericbair-sciome
Fixed likelihood function and added additional tests
6c17318
@ericbair-sciome
Added a simulation file for testing
2dd74a2
@ericbair-sciome @shail-choksi
Pull request #9: Testing
f52ebbb 
* commit '2dd74a21380be960918b6067abec8ec163721853':
  Added a simulation file for testing
  Fixed likelihood function and added additional tests
  Fixed likelihood function and added additional test
@sciome-bot
Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures…
286ba5d 
…-and-Toxicology/PrestoGP
@sciome-bot
Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures…
ea78ffa 
…-and-Toxicology/PrestoGP
@sciome-bot
Add UBSAN/ASAN sanitizers
4822fbc
@ericbair-sciome
Added more likelihood and maxmin ordering tests
80a9818
@ericbair-sciome
Fixed a bug in SparseNN
1ca9586
@ericbair-sciome
Fixed another sparseNN bug and updated tests
7f3ca3c
@ericbair-sciome
Merge branch 'to-git' of http://192.168.167.103:7990/bitbucket/scm/st…
895100d 
…at/prestogp into testing

Conflicts:
	DESCRIPTION
	man/prestogp_fit-PrestoGPModel-method.Rd
	tests/testthat/test-Log_Likelihood.R

Fixed merge conflicts.
@ericbair-sciome @shail-choksi
Pull request #12: Testing
17f5284 
Merge in STAT/prestogp from testing to master

* commit '895100db78d89c5082ddfcf1411dad69bdf1b6c5':
  Fixed another sparseNN bug and updated tests
  Fixed a bug in SparseNN
  Added more likelihood and maxmin ordering tests
@sciome-bot
Add USAN/ASAN pipeline
e530819
@sciome-bot
Merge branch 'master' of ssh://sciome-bot/stat/prestogp into build-wo…
6af43f4 
…rkflow
@sciome-bot
Merge branch 'to-git' of ssh://sciome-bot/stat/prestogp into build-wo…
2c9c2ed 
…rkflow
@shail-choksi
Pull request #16: Add UBSAN/ASAN sanitizers
85517e7 
Merge in STAT/prestogp from build-workflow to master

* commit '2c9c2ede3d40e6e5af24b38a6acfc2dfb2994975':
  Add USAN/ASAN pipeline
  Pull request #14: Additional Testing
  Additional Testing
  Add UBSAN/ASAN sanitizers
@sciome-bot
Ran auto-formatter/linter for R and C++ in vscode. Added some missing…
7c0bbfe 
… imports
@sciome-bot
Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures…
bea8382 
…-and-Toxicology/PrestoGP
@sciome-bot
Merge branch 'master' of ssh://sciome-bot/stat/prestogp
d2a2e3a
@sciome-bot
Merge branch 'master' of ssh://sciome-bot/stat/prestogp into build-wo…
73aed75 
…rkflow
@sciome-bot
Added missing imports
11771e4
@shail-choksi
Pull request #18: Added missing imports and ran auto-formatter in vsc…
710520c 
…ode for R and C++

Merge in STAT/prestogp from build-workflow to master

* commit '11771e4ccbd6311aa35334c5ab4b7e4299a8db56':
  Added missing imports
  Ran auto-formatter/linter for R and C++ in vscode. Added some missing imports
@sciome-bot
Add new files to Collate section in DESCRIPTION file
f037a0b
@sciome-bot
R CMD check fixes
8dac095
@shail-choksi
Pull request #20: R CMD check fixes
2e94403 
Merge in STAT/prestogp from build-workflow to master

* commit '8dac09511058405d630121ca13c589781c932bf4':
  R CMD check fixes
  Add new files to Collate section in DESCRIPTION file
@sciome-bot
Merge branch 'to-git' of ssh://sciome-bot/stat/prestogp
03c3589
@sciome-bot
Merge branch 'master' of ssh://sciome-bot/stat/prestogp
d7794fd
@ericbair-sciome
More test, univariate code fixed
919cd36
@ericbair-sciome
Added new files for testing/documentation
d6d62cf
ericbair-sciome and others added 10 commits December 28, 2023 21:15
@ericbair-sciome
Merge branch 'master' of http://192.168.167.103:7990/bitbucket/scm/st…
b0534e5 
…at/prestogp into testing

Conflicts:
	NAMESPACE
	R/Log_Likelihood.R
	R/PrestoGP_Full.R
	R/PrestoGP_Full_Spatial.R
	R/PrestoGP_Model.R
	R/PrestoGP_Multivariate_Vecchia.R
	R/PrestoGP_Vecchia_Spatial.R
	R/PrestoGP_Vecchia_Spatiotemporal.R
	tests/testthat/Multivariate-Sims-RandomFields.R
	tests/testthat/helper.R
	tests/testthat/spatial_simulation_simple_example.R
	tests/testthat/test-Log_Likelihood.R
	tests/testthat/test-PrestoGP_Multivariate_Vecchia_Model.R
	tests/testthat/test-PrestoGP_Spatial_Full_Model.R
	tests/testthat/test-PrestoGP_Spatial_Model.R
	tests/testthat/test-PrestoGP_Spatiotemporal_Full_Model.R
	tests/testthat/test-PrestoGP_Spatiotemporal_Model.R
@ericbair-sciome
Updated outdated DESCRIPTION file
04e3f9d
@ericbair-sciome @shail-choksi
Pull request #22: Testing
5e4bfb5 
Merge in STAT/prestogp from testing to master

* commit '04e3f9d681c45f31fd34d00ce7b4fa0bbf50e0f4':
  Updated outdated DESCRIPTION file
  Merge branch 'master' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into testing
  Merge branch 'master' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into testing
  Added new files for testing/documentation
  More test, univariate code fixed
@sciome-bot
Auto-formatting changes
82eab44
@shail-choksi
Pull request #23: Auto-formatting changes
9090112 
* commit '82eab4427a8fe3b65d2d7d212b394c7feac840ce':
  Auto-formatting changes
@ericbair-sciome
Univariate prediction, more testing
b50b49e
@ericbair-sciome
Added a data file for testing
d361f2e
@sciome-bot
Merge branch 'master' of ssh://sciome-bot/stat/prestogp into to-git
e9e7607
@ericbair-sciome @shail-choksi
Pull request #24: PrestoGP Update
af6d756 
Merge in STAT/prestogp from eb-dev to master

* commit 'd361f2e67bcf05e306a14a99ba9b7a57a18a281b':
  Added a data file for testing
  Univariate prediction, more testing
@sciome-bot
Merge branch 'master' of ssh://sciome-bot/stat/prestogp into to-git
723c3eb
This was linked to issues Jan 10, 2024
prestogp_fit fails for non-default values of covparams #43
Closed
Code for univariate models needs to be updated #41
Closed
Input validation is inadequate for multivariate models #27
Closed
Consolidate spatial/spatiotemporal functions #23
Closed
testthat tests #20
Closed
kyle-messier
kyle-messier requested changes Jan 10, 2024
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@ericbair-sciome The tests are failing - test-coverage, R-CMD-build, and others seem related to the installation of "pak", so if that is resolved, it may be help a lot of these.

@kyle-messier
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@ericbair-sciome Let me know if it would be helpful to go ahead and merge into main without the tests passing. We would do that if there are key updates (which clearly there are) and then isolate the test checks/passing in a separate pull request.

@ericbair-sciome
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Go ahead and accept the pull request. I think this is a GitHub issue. All of the testthat tests pass when you run devtools::test() from within R. Maybe @shail-choksi has some idea what is causing his and how to fix it. If not, I'll do some research myself. (The R CMD check tests are going to fail for the time being regardless due to a number of issues that I haven't had time to fix yet, such as incomplete documentation. That is next on my list to fix.)

@kyle-messier kyle-messier merged commit c060815 into main Jan 11, 2024
0 of 5 checks passed
sciome-bot pushed a commit that referenced this pull request 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':
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      Fix all indentation errors
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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
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      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
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      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 pull request 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 pull request Apr 9, 2024
@shail-choksi
Pull request #43: Fix documentation issue blocking R CMD check and re…
6c79863 
…vert execute permission on all files

Squashed commit of the following:

commit 00171d7
Merge: cb9236b e0c9039
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Tue Apr 9 17:17:39 2024 -0400

    Pull request #44: Revert execute permissions on all files

    Merge in STAT/prestogp from shail-dev-2 to master

    * commit 'e0c90391f290dd2f6ebe62f6a69db8ec006c1872':
      chmod changes
      Implement imputation beta

commit e0c9039
Merge: b8f91fd 05e7dfb
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Apr 9 17:16:29 2024 -0400

    Merge branch 'to-git' of ssh://sciome-bot/stat/prestogp into shail-dev-2

commit b8f91fd
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Apr 9 17:10:53 2024 -0400

    chmod changes

commit cb9236b
Merge: cae8439 218a18a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Apr 9 17:03:10 2024 -0400

    Pull request #42: Fixed a documentation issue

    Merge in STAT/prestogp from eb-dev to master

    * commit '218a18a6cd2891c7c4975e408f7308243c11abbf':
      Fixed a documentation issue

commit 218a18a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Mon Apr 8 02:18:24 2024 -0400

    Fixed a documentation issue

commit cae8439
Merge: c15c519 6bafe5c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Apr 5 16:38:34 2024 -0400

    Pull request #40: Imputation beta

    Merge in STAT/prestogp from eb-dev to master

    * commit '6bafe5cf9d5574074bdcb0288e4b48efb87a8840':
      Imputation beta implemented
      Updated version number

commit 6bafe5c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Apr 4 00:17:45 2024 -0400

    Imputation beta implemented

commit 1f4bcc7
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Mar 17 16:36:13 2024 -0400

    Updated version number

commit c15c519
Merge: 350b236 bab8357
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Feb 8 14:25:12 2024 -0500

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

commit 350b236
Merge: 55c0e8e 95fef8c
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Feb 8 14:24:34 2024 -0500

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

commit bab8357
Merge: 55c0e8e 5394772
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:19:24 2024 -0500

    Pull request #38: Removed vignette, fixed lint issues

    Merge in STAT/prestogp from eb-dev to master

    * commit '53947729624b47fa1920ef39bd23d86f6e5cd7b7':
      Removed vignette, fixed lint issues

commit 55c0e8e
Merge: 7e330f3 076c0a1
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Date:   Thu Feb 8 14:18:48 2024 -0500

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commit 5394772
Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

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Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

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

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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

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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

... and 35 more commits
sciome-bot pushed a commit that referenced this pull request Apr 25, 2024
@shail-choksi
Remove dependency on sysreqs to fix sanitizer action
d1dd01b 
Squashed commit of the following:

commit 4aa13ad
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Apr 24 20:16:19 2024 -0400

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Merge: 3f3c9e3 df836b7
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Date:   Wed Apr 24 20:12:09 2024 -0400

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commit 3f3c9e3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Apr 24 17:17:41 2024 -0400

    Observation-level lod, imputation tests, updated README

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    Date:   Tue Apr 23 16:41:15 2024 -0400

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        Observation-level lod, imputation tests, updated README

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Merge: cb9236b e0c9039
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Tue Apr 9 17:17:39 2024 -0400

    Pull request #44: Revert execute permissions on all files

    Merge in STAT/prestogp from shail-dev-2 to master

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      chmod changes
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Merge: b8f91fd 05e7dfb
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Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Apr 9 17:10:53 2024 -0400

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commit cb9236b
Merge: cae8439 218a18a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Apr 9 17:03:10 2024 -0400

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    Merge in STAT/prestogp from eb-dev to master

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commit 218a18a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Mon Apr 8 02:18:24 2024 -0400

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commit cae8439
Merge: c15c519 6bafe5c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Apr 5 16:38:34 2024 -0400

    Pull request #40: Imputation beta

    Merge in STAT/prestogp from eb-dev to master

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Date:   Thu Apr 4 00:17:45 2024 -0400

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Date:   Thu Feb 8 14:24:34 2024 -0500

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commit bab8357
Merge: 55c0e8e 5394772
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:19:24 2024 -0500

    Pull request #38: Removed vignette, fixed lint issues

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Merge: 7e330f3 076c0a1
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Date:   Thu Feb 8 14:18:48 2024 -0500

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commit 5394772
Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

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commit b431df4
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

    Removed vignette, fixed lint issues

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

... and 37 more commits
sciome-bot added a commit that referenced this pull request Apr 26, 2024
@sciome-bot
Removed the spam dependency to fix an R CMD check issue
3f9df3e 
Squashed commit of the following:

commit aa730b5
Merge: 4aa13ad d596c46
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Apr 26 14:26:42 2024 -0400

    Pull request #48: Eb dev

    Merge in STAT/prestogp from eb-dev to master

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      Removed the spam dependency to fix an R CMD check issue
      Observation-level lod, imputation tests, updated README

commit d596c46
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Apr 26 14:05:23 2024 -0400

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commit 6543908
Merge: 86bdd92 4aa13ad
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Apr 25 18:19:08 2024 -0400

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commit 86bdd92
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Apr 25 18:11:04 2024 -0400

    Removed the spam dependency to fix an R CMD check issue

commit 4aa13ad
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Apr 24 20:16:19 2024 -0400

    Remove dependency on sysreqs to fix sanitizer action.

commit 7fad5a6
Merge: 3f3c9e3 df836b7
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Apr 24 20:12:09 2024 -0400

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commit 3f3c9e3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Apr 24 17:17:41 2024 -0400

    Observation-level lod, imputation tests, updated README

    Squashed commit of the following:

    commit 9dfcef3
    Merge: 33b0560 68671e6
    Author: Eric Bair <eric.bair@sciome.com>
    Date:   Tue Apr 23 16:41:15 2024 -0400

        Merge branch 'master' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into eb-dev

        Conflicts:
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    commit 33b0560
    Author: Eric Bair <eric.bair@sciome.com>
    Date:   Tue Apr 23 03:05:12 2024 -0400

        Observation-level lod, imputation tests, updated README

commit 9dfcef3
Merge: 33b0560 68671e6
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Apr 23 16:41:15 2024 -0400

    Merge branch 'master' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into eb-dev

    Conflicts:
    	README.md

commit 33b0560
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Apr 23 03:05:12 2024 -0400

    Observation-level lod, imputation tests, updated README

commit 68671e6
Merge: 00171d7 7fe8997
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Apr 10 09:51:12 2024 -0400

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commit 00171d7
Merge: cb9236b e0c9039
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Tue Apr 9 17:17:39 2024 -0400

    Pull request #44: Revert execute permissions on all files

    Merge in STAT/prestogp from shail-dev-2 to master

    * commit 'e0c90391f290dd2f6ebe62f6a69db8ec006c1872':
      chmod changes
      Implement imputation beta

commit e0c9039
Merge: b8f91fd 05e7dfb
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Apr 9 17:16:29 2024 -0400

    Merge branch 'to-git' of ssh://sciome-bot/stat/prestogp into shail-dev-2

commit b8f91fd
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Apr 9 17:10:53 2024 -0400

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commit cb9236b
Merge: cae8439 218a18a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Apr 9 17:03:10 2024 -0400

    Pull request #42: Fixed a documentation issue

    Merge in STAT/prestogp from eb-dev to master

    * commit '218a18a6cd2891c7c4975e408f7308243c11abbf':
      Fixed a documentation issue

commit 218a18a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Mon Apr 8 02:18:24 2024 -0400

    Fixed a documentation issue

commit cae8439
Merge: c15c519 6bafe5c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Apr 5 16:38:34 2024 -0400

    Pull request #40: Imputation beta

    Merge in STAT/prestogp from eb-dev to master

    * commit '6bafe5cf9d5574074bdcb0288e4b48efb87a8840':
      Imputation beta implemented
      Updated version number

commit 6bafe5c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Apr 4 00:17:45 2024 -0400

    Imputation beta implemented

commit 1f4bcc7
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Mar 17 16:36:13 2024 -0400

    Updated version number

commit c15c519
Merge: 350b236 bab8357
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Feb 8 14:25:12 2024 -0500

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

commit 350b236
Merge: 55c0e8e 95fef8c
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Feb 8 14:24:34 2024 -0500

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

... and 43 more commits
sciome-bot pushed a commit that referenced this pull request Dec 29, 2024
@shail-choksi
Pull request #44: Revert execute permissions on all files
00171d7 
Merge in STAT/prestogp from shail-dev-2 to master

* commit 'e0c90391f290dd2f6ebe62f6a69db8ec006c1872':
  chmod changes
  Implement imputation beta
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