Pull request #21: R CMD check fixes

Squashed commit of the following:

commit d7794fd
Merge: 03c3589 2e94403
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 15:10:33 2023 -0500

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

commit 03c3589
Merge: d2a2e3a 961880a
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 15:08:24 2023 -0500

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

commit 2e94403
Merge: 710520c 8dac095
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Thu Dec 28 15:07:40 2023 -0500

    Pull request #20: R CMD check fixes

    Merge in STAT/prestogp from build-workflow to master

    * commit '8dac09511058405d630121ca13c589781c932bf4':
      R CMD check fixes
      Add new files to Collate section in DESCRIPTION file

commit 8dac095
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 15:06:38 2023 -0500

    R CMD check fixes

commit f037a0b
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 14:22:52 2023 -0500

    Add new files to Collate section in DESCRIPTION file

commit 710520c
Merge: d2a2e3a 11771e4
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Thu Dec 28 14:09:40 2023 -0500

    Pull request #18: Added missing imports and ran auto-formatter in vscode 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

commit 11771e4
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 14:07:28 2023 -0500

    Added missing imports

commit 73aed75
Merge: 7c0bbfe d2a2e3a
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 13:58:37 2023 -0500

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

commit d2a2e3a
Merge: bea8382 85517e7
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 13:57:14 2023 -0500

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

commit bea8382
Merge: 17f5284 1e4361d
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 13:55:26 2023 -0500

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

commit 7c0bbfe
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 13:52:27 2023 -0500

    Ran auto-formatter/linter for R and C++ in vscode. Added some missing imports

commit 85517e7
Merge: 17f5284 2c9c2ed
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Thu Dec 28 13:12:00 2023 -0500

    Pull request #16: Add UBSAN/ASAN sanitizers

    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

commit 2c9c2ed
Merge: 6af43f4 56cdbf2
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 13:11:14 2023 -0500

    Merge branch 'to-git' of ssh://sciome-bot/stat/prestogp into build-workflow

commit 6af43f4
Merge: e530819 17f5284
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 13:07:50 2023 -0500

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

commit e530819
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Dec 28 13:06:21 2023 -0500

    Add USAN/ASAN pipeline

commit 17f5284
Merge: ea78ffa 895100d
Author: Eric Bair <eric.bair@sciome.com>
Date:   Fri Dec 1 10:49:09 2023 -0500

    Pull request #12: Testing

    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

commit 895100d
Merge: 7f3ca3c fb060ff
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Nov 29 17:02:10 2023 -0500

    Merge branch 'to-git' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into testing

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

    Fixed merge conflicts.

commit 7f3ca3c
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Nov 29 16:43:40 2023 -0500

    Fixed another sparseNN bug and updated tests

commit 1ca9586
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Nov 28 18:40:36 2023 -0500

    Fixed a bug in SparseNN

commit 80a9818
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Nov 21 17:49:19 2023 -0500

    Added more likelihood and maxmin ordering tests

... and 8 more commits

.Rbuildignore

@@ -5,3 +5,4 @@
 ^\.Rproj\.user$
 ^doc$
 ^Meta$
+^\.github/

.gitignore

@@ -31,6 +31,7 @@ manuscript/
 
 # Output files from R CMD build
 /*.tar.gz
+*.dll
 
 # Output files from R CMD check
 /*.Rcheck/

DESCRIPTION

@@ -36,22 +36,23 @@ Imports:
     knitr,
     dplyr,
     glmnet,
-    rmarkdown,
-    markdown,
     gtools,
     geoR,
-    doParallel,
     RANN,
-    rlang (>= 0.4.11),
-    foreach,
     stats,
-    methods
+    methods,
+    foreach,
+    rlang,
+    mvtnorm,
+    spam,
+    psych
 License: GPL-3
 Encoding: UTF-8
 VignetteBuilder: knitr 
 RoxygenNote: 7.2.3
 Collate: 
     'Log_Likelihood.R'
+    'PrestoGP-package.R'
     'PrestoGP_CreateU_Multivariate.R'
     'PrestoGP_Model.R'
     'PrestoGP_Vecchia_Spatiotemporal.R'
@@ -63,6 +64,7 @@ Collate:
     'RcppExports.R'
     'Visualization.R'
     'package.R'
+    'utils-tidy-eval.R'
 Suggests: 
     roxygen2,
     testthat (>= 3.0.0)

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export(":=")
+export(.data)
 export(FullSpatialModel)
 export(Kr_pred)
 export(MultivariateVecchiaModel)
@@ -8,7 +10,11 @@ export(ST_Krig_Param_Avg)
 export(SpatialModel)
 export(SpatiotemporalFullModel)
 export(SpatiotemporalModel)
+export(as_label)
+export(as_name)
 export(createUMultivariate)
+export(enquo)
+export(enquos)
 export(negloglik.full)
 export(negloglik_full_ST)
 export(negloglik_vecchia)
@@ -27,6 +33,18 @@ import(readxl)
 import(scoringRules)
 importFrom(aod,wald.test)
 importFrom(dplyr,"%>%")
+importFrom(foreach,"%dopar%")
+importFrom(foreach,foreach)
+importFrom(methods,callNextMethod)
+importFrom(methods,new)
+importFrom(methods,validObject)
+importFrom(rlang,":=")
+importFrom(rlang,.data)
+importFrom(rlang,as_label)
+importFrom(rlang,as_name)
+importFrom(rlang,enquo)
+importFrom(rlang,enquos)
+importFrom(stats,coef)
 importFrom(stats,optim)
 importFrom(stats,predict)
 importFrom(stats,var)

R/PrestoGP_Model.R

@@ -460,7 +460,7 @@ setMethod(
       }
 
       model <- transform_data(model, model@Y_train, model@X_train)
-      model <- estimate_betas(model, parallel, foldid)
+      model <- estimate_betas(model, parallel)
       min.error <- compute_error(model)
       ### Check min-error against the previous error and tolerance
       if (min.error < prev.error * tol) {