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Pull request #34: Fix tolerance and expected values for tests
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Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit 439790cb0d96d85e80a3782ad533eee78afe41dc
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 56f881f96a0e55e60bca3c8a840ec31291665594
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 14:05:12 2024 -0500

    Fixed some testthat issues

commit f4af0d1be3490dd2edd4f4fd0ae97bf729464748
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 db6cd4f6f86e760ee8393adf224cd0231ccde8cf
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 7da2588abba4491c1ff490de95e834d00f5df88e
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 01:37:58 2024 -0500

    Fixed some bugs caused by the linter

commit 55607e291477d174b8323bf258a8e9aa5c4db84c
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 c7ed481479c2ca5a4fc111f429affd01b6c3ce53
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
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shail-choksi committed Jan 14, 2024
1 parent ee193de commit 8ffb20b
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: PrestoGP
Type: Package
Title: Penalized Regression for Spatio-Temporal Outcomes via Gaussian Processes
Version: 0.2.0.9022
Version: 0.2.0.9023
Authors@R: c(
person(given = "Eric",
family = "Bair",
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1 change: 0 additions & 1 deletion NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,6 @@ import(glmnet)
import(ncvreg)
import(readxl)
import(scoringRules)
import(covr)
importFrom(aod,wald.test)
importFrom(dplyr,"%>%")
importFrom(foreach,"%dopar%")
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4 changes: 2 additions & 2 deletions tests/testthat/test-PrestoGP_Univariate.R
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Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@ test_that("Simulated dataset spatiotemporal", {
)
expect_equal(params.out[1], 1.7, tolerance = 0.55)
expect_equal(params.out[2] - 0.19, 0, tolerance = 0.05)
expect_equal(params.out[3], 0.22, tolerance = 0.05)
expect_equal(params.out[3] - 0.22, 0, tolerance = 0.05)
expect_equal(params.out[4], 1.12, tolerance = 0.3)
expect_equal(params.out[5], 0.62, tolerance = 0.05)

Expand Down Expand Up @@ -169,7 +169,7 @@ test_that("Simulated dataset spatiotemporal", {
expect_equal(beta.out[1], beta.out2[1], tolerance = 0.08)
expect_equal(beta.out[-1], beta.out2[-1], tolerance = 0.03)
expect_equal(params.out[1], params.out2[1], tolerance = 0.6)
expect_equal(params.out[2], params.out2[2], tolerance = 0.06)
expect_equal(params.out[2] - params.out2[2], 0, tolerance = 0.06)
expect_equal(params.out[3] - params.out2[3], 0, tolerance = 0.06)
expect_equal(params.out[4], params.out2[4], tolerance = 0.3)
expect_equal(params.out[5], params.out2[5], tolerance = 0.1)
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