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Implement imputation beta #56

Merged
merged 2 commits into from
Apr 9, 2024
Merged

Implement imputation beta #56

merged 2 commits into from
Apr 9, 2024

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sciome-bot
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Squashed commit of the following:

commit cae8439517a38f41ff826018ce1d4719365695c1
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 6bafe5cf9d5574074bdcb0288e4b48efb87a8840
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Apr 4 00:17:45 2024 -0400

    Imputation beta implemented

commit 1f4bcc714fbd43bfbe315a61ad03120c8fbc07ae
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Mar 17 16:36:13 2024 -0400

    Updated version number

commit c15c519e6a81e7b899090e500cc278c795548ac2
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 350b236ba0b77dfc5056e9e53b00f05cbb1cc4d0
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 bab8357d1f3cdc45ab38110355cc6d106dba8440
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 55c0e8e5ed2e189876c39d9e2337b51020b6505b
Merge: 7e330f3 076c0a1
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Feb 8 14:18:48 2024 -0500

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

commit 53947729624b47fa1920ef39bd23d86f6e5cd7b7
Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

    Resolved merge conflict

commit b431df45c0f80a54451536033c355b47620f3077
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

    Removed vignette, fixed lint issues

commit 7e330f30a659c579a3f291bc65c7918b9859c619
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 f49d0769a892df5dd711a2f8ebe08a3f9ca7af7b
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 59baf720737abe59a04c98705c950ef1c7b63321
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

    Fixed some documentation issues

commit d857d8b367e3b46581677c4925ba8617f462c4d5
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

    Removed C++11 compiler flag

commit 662907d9e98a20ad06602c0dfe7e81b6390e3485
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

    Added RandomFields data sets to PrestoGP

commit cf2aadb50ecebd9e2f4401493da6901f10ee993a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 13:40:24 2024 -0500

    Added knitr to Suggests in DESCRIPTION

commit ef5f2c9145d481e4e24a98792913830d449cba86
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 01:31:53 2024 -0500

    Documentation, R-cmd-check fixes, binomial regression

commit 13a6f449d324e19f61d7e29797fc23c65ec020b8
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 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

... and 30 more commits
@kyle-messier
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@sciome-bot @ericbair-sciome @shail-choksi

It looks like the documentation of the imputation needs to be updated so that the R-CMD-check, santizer-check-asan and sanitizer-check-usan pass. Running roxygenize() so that the impute.y input variable is updated in the Rd files, etc.

I made some updates to the README and updated _pkgdown and gh-pages, but that should not affect your PR.

If we can get this simple thing resolved, then we'll have all tests passing.

…vert execute permission on all files

Squashed commit of the following:

commit 00171d7caa5c0eb0678401379566a722ba6ca7e7
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 e0c90391f290dd2f6ebe62f6a69db8ec006c1872
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 b8f91fdaa970f2eff4608cd71fdf8d7a6e79588f
Author: sciome-bot <software.tools@sciome.com>
Date:   Tue Apr 9 17:10:53 2024 -0400

    chmod changes

commit cb9236b8adab059b338ef4d06c5fc1f4e262a6d8
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 218a18a6cd2891c7c4975e408f7308243c11abbf
Author: Eric Bair <eric.bair@sciome.com>
Date:   Mon Apr 8 02:18:24 2024 -0400

    Fixed a documentation issue

commit cae8439517a38f41ff826018ce1d4719365695c1
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 6bafe5cf9d5574074bdcb0288e4b48efb87a8840
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Apr 4 00:17:45 2024 -0400

    Imputation beta implemented

commit 1f4bcc714fbd43bfbe315a61ad03120c8fbc07ae
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Mar 17 16:36:13 2024 -0400

    Updated version number

commit c15c519e6a81e7b899090e500cc278c795548ac2
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 350b236ba0b77dfc5056e9e53b00f05cbb1cc4d0
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 bab8357d1f3cdc45ab38110355cc6d106dba8440
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 55c0e8e5ed2e189876c39d9e2337b51020b6505b
Merge: 7e330f3 076c0a1
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Feb 8 14:18:48 2024 -0500

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

commit 53947729624b47fa1920ef39bd23d86f6e5cd7b7
Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

    Resolved merge conflict

commit b431df45c0f80a54451536033c355b47620f3077
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

    Removed vignette, fixed lint issues

commit 7e330f30a659c579a3f291bc65c7918b9859c619
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 f49d0769a892df5dd711a2f8ebe08a3f9ca7af7b
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 59baf720737abe59a04c98705c950ef1c7b63321
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

    Fixed some documentation issues

commit d857d8b367e3b46581677c4925ba8617f462c4d5
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

    Removed C++11 compiler flag

commit 662907d9e98a20ad06602c0dfe7e81b6390e3485
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

    Added RandomFields data sets to PrestoGP

commit cf2aadb50ecebd9e2f4401493da6901f10ee993a
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
@kyle-messier kyle-messier merged commit 7fe8997 into main Apr 9, 2024
6 checks passed
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update README with critical functionality Intercept not calculated when estimating yhat's
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