nimble-dev · paciorek · Dec 13, 2025 · Dec 5, 2025 · Dec 5, 2025 · Dec 12, 2025
diff --git a/install_requirements.R b/install_requirements.R
@@ -4,27 +4,21 @@ requirements <- c(
     'igraph',
     'coda',
     'R6',
-    ##'nimble',      ## add back in later
     'testthat',
     'pracma',     ## for AD
     'numDeriv',    ## for AD
     'mvQuad',
     'RTMB',
-    'polynom'
-    ## 'lme4'     ## for test-ADlaplace.R
+    'polynom',
+    'nimble'
+    ## 'lme4'    
     )
 
 for(package in requirements) {
     install.packages(package)
 }
 
-## Apparently a bug in Matrix (as of early 2024) is causing an issue (https://bioconductor.org/packages/devel/bioc/vignettes/dreamlet/inst/doc/errors.html) that is causing test-ADlaplace.R failures when fitting a model with lmer.
+## Apparently a bug in Matrix (as of early 2024) is causing an issue (https://bioconductor.org/packages/devel/bioc/vignettes/dreamlet/inst/doc/errors.html) that is causing Laplace test failures when fitting a model with lmer.
 install.packages('lme4', type = 'source')
 
 
-## later, remove below:
-install.packages('devtools')
-library(devtools)
-devtools::install_github('nimble-dev/nimble', ref = 'no-laplace', subdir = 'packages/nimble', INSTALL_opts = c("--install-tests"))
-## remove until here
-
diff --git a/nimbleQuad/DESCRIPTION b/nimbleQuad/DESCRIPTION
@@ -22,9 +22,7 @@ RoxygenNote: 7.3.2
 Collate:
     quadratureRules.R
     quadratureGrids.R
-    nodeUtils.R
     Laplace.R
     buildNestedApprox.R
     runNestedApprox.R
     summaryUtils.R
-    normTooling.R
diff --git a/nimbleQuad/R/Laplace.R b/nimbleQuad/R/Laplace.R
@@ -3293,7 +3293,7 @@ runAGHQ <- function(AGHQ, pStart,
 #' @param paramNodes a character vector of names of parameter nodes in the
 #'   model; defaults are provided by \code{\link[nimble]{setupMargNodes}}.
 #'   Alternatively, \code{paramNodes} can be a list in the format returned by
-#'   \code{setupMargNodes}, in which case \code{randomEffectsNodes},
+#'   \code{\link[nimble]{setupMargNodes}}, in which case \code{randomEffectsNodes},
 #'   \code{calcNodes}, and \code{calcNodesOther} are not needed (and will be
 #'   ignored).
 #' @param randomEffectsNodes a character vector of names of continuous
@@ -3394,15 +3394,15 @@ runAGHQ <- function(AGHQ, pStart,
 #'   match those here (except for a few arguments which are taken from control
 #'   list elements here).
 #'
-#' \code{setupMargNodes} tries to give sensible defaults from
+#' \code{\link[nimble]{setupMargNodes}} tries to give sensible defaults from
 #'   any combination of \code{paramNodes}, \code{randomEffectsNodes},
 #'   \code{calcNodes}, and \code{calcNodesOther} that are provided. For example,
 #'   if you provide only \code{randomEffectsNodes} (perhaps you want to
 #'   marginalize over only some of the random effects in your model),
-#'   \code{setupMargNodes} will try to determine appropriate choices for the
+#'   \code{\link[nimble]{setupMargNodes}} will try to determine appropriate choices for the
 #'   others.
 #'
-#' \code{setupMargNodes} also determines which integration dimensions are
+#' \code{\link[nimble]{setupMargNodes}} also determines which integration dimensions are
 #' conditionally independent, i.e., which can be done separately from each
 #' other. For example, when possible, 10 univariate random effects will be split
 #' into 10 univariate integration problems rather than one 10-dimensional
@@ -3420,16 +3420,16 @@ runAGHQ <- function(AGHQ, pStart,
 #'   you must provide a \code{randomEffectsNodes} argument to indicate which
 #'   they are.
 #'
-#' It can be helpful to call \code{setupMargNodes} directly to see exactly how
+#' It can be helpful to call \code{\link[nimble]{setupMargNodes}} directly to see exactly how
 #'   nodes will be arranged for Laplace approximation. For example, you may want
 #'   to verify the choice of \code{randomEffectsNodes} or get the order of
 #'   parameters it has established to use for making sense of the MLE and
 #'   results from the \code{summary} method. One can also call
-#'   \code{setupMargNodes}, customize the returned list, and then provide that
+#'   \code{\link[nimble]{setupMargNodes}}, customize the returned list, and then provide that
 #'   to \code{buildLaplace} as \code{paramNodes}. In that case,
-#'   \code{setupMargNodes} will not be called (again) by \code{buildLaplace}.
+#'   \code{\link[nimble]{setupMargNodes}} will not be called (again) by \code{buildLaplace}.
 #'
-#' If \code{setupMargNodes} is emitting an unnecessary warning, simply use
+#' If \code{\link[nimble]{setupMargNodes}} is emitting an unnecessary warning, simply use
 #'   \code{control=list(check=FALSE)}.
 #'
 #' @section Managing parameter transformations that may be used internally:

diff --git a/nimbleQuad/R/buildNestedApprox.R b/nimbleQuad/R/buildNestedApprox.R
@@ -106,12 +106,12 @@
 #'   Laplace approximation to marginalize over all continuous latent nodes
 #'   (both random and fixed effects) in a model. 
 #'
-#' \code{buildNestedApprox} uses \code{setupMargNodes} (in a multi-step process)
+#' \code{buildNestedApprox} uses \code{\link[nimble]{setupMargNodes}} (in a multi-step process)
 #'   to try to give sensible defaults from
 #'   any combination of \code{paramNodes}, \code{latentNodes},
 #'   \code{calcNodes}, and \code{calcNodesOther} that are provided. 
 #'
-#' \code{setupMargNodes} also determines which integration dimensions are
+#' \code{\link[nimble]{setupMargNodes}} also determines which integration dimensions are
 #' conditionally independent, i.e., which can be done separately from each
 #' other. For example, when possible, 10 univariate random effects will be split
 #' into 10 univariate integration problems rather than one 10-dimensional

diff --git a/nimbleQuad/R/nodeUtils.R b/nimbleQuad/R/nodeUtils.R
diff --git a/nimbleQuad/R/normTooling.R b/nimbleQuad/R/normTooling.R
diff --git a/nimbleQuad/tests/testthat/test-AGHQ.R b/nimbleQuad/tests/testthat/test-AGHQ.R
@@ -1,7 +1,5 @@
 library(nimbleQuad)
 # Tests of AGH Quadrature approximation
-source(system.file(file.path('tests', 'testthat', 'test_utils.R'), package = 'nimble'))
-source(system.file(file.path('tests', 'testthat', 'AD_test_utils.R'), package = 'nimble'))
 EDopt <- nimbleOptions("enableDerivs")
 BMDopt <- nimbleOptions("buildModelDerivs")
 nimbleOptions(enableDerivs = TRUE)

diff --git a/nimbleQuad/tests/testthat/test-laplace.R b/nimbleQuad/tests/testthat/test-laplace.R
@@ -1,7 +1,5 @@
 library(nimbleQuad) # to get nimbleQuad's names first
 # Tests of Laplace approximation
-source(system.file(file.path('tests', 'testthat', 'test_utils.R'), package = 'nimble'))
-source(system.file(file.path('tests', 'testthat', 'AD_test_utils.R'), package = 'nimble'))
 EDopt <- nimbleOptions("enableDerivs")
 BMDopt <- nimbleOptions("buildModelDerivs")
 nimbleOptions(enableDerivs = TRUE)

diff --git a/nimbleQuad/tests/testthat/test-laplace2.R b/nimbleQuad/tests/testthat/test-laplace2.R
@@ -1,7 +1,5 @@
 library(nimbleQuad) # to get nimbleQuad's names first
 # Tests of Laplace approximation
-source(system.file(file.path('tests', 'testthat', 'test_utils.R'), package = 'nimble'))
-source(system.file(file.path('tests', 'testthat', 'AD_test_utils.R'), package = 'nimble'))
 EDopt <- nimbleOptions("enableDerivs")
 BMDopt <- nimbleOptions("buildModelDerivs")
 nimbleOptions(enableDerivs = TRUE)

diff --git a/nimbleQuad/tests/testthat/test-laplace3.R b/nimbleQuad/tests/testthat/test-laplace3.R
@@ -1,7 +1,5 @@
 library(nimbleQuad) # to get nimbleQuad's names first
 # Tests of Laplace approximation
-source(system.file(file.path('tests', 'testthat', 'test_utils.R'), package = 'nimble'))
-source(system.file(file.path('tests', 'testthat', 'AD_test_utils.R'), package = 'nimble'))
 EDopt <- nimbleOptions("enableDerivs")
 BMDopt <- nimbleOptions("buildModelDerivs")
 nimbleOptions(enableDerivs = TRUE)

diff --git a/nimbleQuad/tests/testthat/test-nested-fit.R b/nimbleQuad/tests/testthat/test-nested-fit.R
@@ -1,5 +1,3 @@
-source(system.file(file.path('tests', 'testthat', 'test_utils.R'), package = 'nimble'))
-source(system.file(file.path('tests', 'testthat', 'AD_test_utils.R'), package = 'nimble'))
 EDopt <- nimbleOptions("enableDerivs")
 BMDopt <- nimbleOptions("buildModelDerivs")
 nimbleOptions(enableDerivs = TRUE)

diff --git a/nimbleQuad/tests/testthat/test-nested-interface.R b/nimbleQuad/tests/testthat/test-nested-interface.R
@@ -1,5 +1,3 @@
-source(system.file(file.path('tests', 'testthat', 'test_utils.R'), package = 'nimble'))
-source(system.file(file.path('tests', 'testthat', 'AD_test_utils.R'), package = 'nimble'))
 EDopt <- nimbleOptions("enableDerivs")
 BMDopt <- nimbleOptions("buildModelDerivs")
 nimbleOptions(enableDerivs = TRUE)

diff --git a/nimbleQuad/tests/testthat/test-quadrature.R b/nimbleQuad/tests/testthat/test-quadrature.R
@@ -1,5 +1,3 @@
-library(nimbleQuad)
-library(testthat)
 # Tests of Quadrature Rules and Grids for numerical integration:
 
 test_that("Check Basic Quad Rules work.", {